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@article{DBLP:journals/bmcbi/AhmedBKR24,
author = {Sheikh Hasib Ahmed and
Dibyendu Brinto Bose and
Rafi Khandoker and
M. Saifur Rahman},
title = {StackDPP: a stacking ensemble based DNA-binding protein prediction
model},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {111},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05714-9},
doi = {10.1186/S12859-024-05714-9},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AhmedBKR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AhnD24,
author = {Seungjun Ahn and
Somnath Datta},
title = {Differential network connectivity analysis for microbiome data adjusted
for clinical covariates using jackknife pseudo-values},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {117},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05689-7},
doi = {10.1186/S12859-024-05689-7},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AhnD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AkbarRZ24,
author = {Shahid Akbar and
Ali Raza and
Quan Zou},
title = {Deepstacked-AVPs: predicting antiviral peptides using tri-segment
evolutionary profile and word embedding based multi-perspective features
with deep stacking model},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {102},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05726-5},
doi = {10.1186/S12859-024-05726-5},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AkbarRZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlessandriRRPCPBCA24,
author = {Simone Alessandri and
Maria L. Ratto and
Sergio Rabellino and
Gabriele Piacenti and
Sandro Gepiro Contaldo and
Simone Pernice and
Marco Beccuti and
Raffaele A. Calogero and
Luca Alessandr{\`{\i}}},
title = {{CREDO:} a friendly Customizable, REproducible, DOcker file generator
for bioinformatics applications},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {110},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05695-9},
doi = {10.1186/S12859-024-05695-9},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AlessandriRRPCPBCA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlsaeediAAAAIA24,
author = {Ali Hakem Alsaeedi and
Haider Hameed R. Al{-}Mahmood and
Zainab Fahad Alnaseri and
Mohammad R. Aziz and
Dhiah Al{-}Shammary and
Ayman Ibaida and
Khandakar Ahmed},
title = {Fractal feature selection model for enhancing high-dimensional biological
problems},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {12},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05619-z},
doi = {10.1186/S12859-023-05619-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlsaeediAAAAIA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlvarezMamaniDCI24,
author = {Edwin Alvarez{-}Mamani and
Reinhard Dechant and
C{\'{e}}sar Armando Beltr{\'{a}}n Casta{\~{n}}{\'{o}}n and
Alfredo J. Ib{\'{a}}{\~{n}}ez},
title = {Graph embedding on mass spectrometry- and sequencing-based biomedical
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {1},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05612-6},
doi = {10.1186/S12859-023-05612-6},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AlvarezMamaniDCI24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ArifFGMA24,
author = {Muhammad Arif and
Ge Fang and
Ali Ghulam and
Saleh Musleh and
Tanvir Alam},
title = {DPI{\_}CDF: druggable protein identifier using cascade deep forest},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {145},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05744-3},
doi = {10.1186/S12859-024-05744-3},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ArifFGMA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ArmahSekumSR24,
author = {Robert Ebo Armah{-}Sekum and
S{\'{a}}ndor Szedm{\'{a}}k and
Juho Rousu},
title = {Protein function prediction through multi-view multi-label latent
tensor reconstruction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {174},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05789-4},
doi = {10.1186/S12859-024-05789-4},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ArmahSekumSR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AshyaniWHN24,
author = {Akram Ashyani and
Yu{-}Heng Wu and
Huan{-}Wei Hsu and
Torbj{\"{o}}rn E. M. Nordling},
title = {Ideal adaptive control in biological systems: an analysis of {\textdollar}{\textbackslash}mathbb
\{P\}{\textdollar}-invariance and dynamical compensation properties},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {95},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05718-5},
doi = {10.1186/S12859-024-05718-5},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AshyaniWHN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AslettC24,
author = {Louis J. M. Aslett and
Ryan R. Christ},
title = {kalis: a modern implementation of the Li {\&} Stephens model for
local ancestry inference in {R}},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {86},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05688-8},
doi = {10.1186/S12859-024-05688-8},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AslettC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BaptistaBB24,
author = {Anthony Baptista and
Galadriel Bri{\`{e}}re and
Ana{\"{\i}}s Baudot},
title = {Random walk with restart on multilayer networks: from node prioritisation
to supervised link prediction and beyond},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {70},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05683-z},
doi = {10.1186/S12859-024-05683-Z},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BaptistaBB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BartzisPLE24,
author = {Georgios Bartzis and
Carel F. W. Peeters and
Wilco Ligterink and
Fred A. van Eeuwijk},
title = {A guided network estimation approach using multi-omic information},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {202},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05778-7},
doi = {10.1186/S12859-024-05778-7},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BartzisPLE24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BaumeisterALK24,
author = {Tim U. H. Baumeister and
Eivind Aadland and
Roger G. Linington and
Olav M. Kvalheim},
title = {Multivariate pattern analysis: a method and software to reveal, quantify,
and visualize predictive association patterns in multicollinear data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {51},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05660-6},
doi = {10.1186/S12859-024-05660-6},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BaumeisterALK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BeltranBCFMS24,
author = {Jorge Beltr{\'{a}}n and
Lisandra Herrera Bel{\'{e}}n and
Fernanda Parraguez Contreras and
Jorge G. Farias and
Jorge Machuca{-}Sep{\'{u}}lveda and
Stefania Short},
title = {MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes
of protein toxins using an ensemble machine learning approach},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {148},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05748-z},
doi = {10.1186/S12859-024-05748-Z},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BeltranBCFMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BemmelenSB24,
author = {Jasper van Bemmelen and
Davida S. Smyth and
Jasmijn A. Baaijens},
title = {Amplidiff: an optimized amplicon sequencing approach to estimating
lineage abundances in viral metagenomes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {126},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05735-4},
doi = {10.1186/S12859-024-05735-4},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BemmelenSB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BessaSilva24,
author = {Adam Bessa{-}Silva},
title = {Fasta2Structure: a user-friendly tool for converting multiple aligned
{FASTA} files to {STRUCTURE} format},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {73},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05697-7},
doi = {10.1186/S12859-024-05697-7},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BessaSilva24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BezieuxSFBCRGNPD24,
author = {Hector Roux de B{\'{e}}zieux and
Kelly Street and
Stephan Fischer and
Koen Van den Berge and
Rebecca Chance and
Davide Risso and
Jesse A. Gillis and
John Ngai and
Elizabeth Purdom and
Sandrine Dudoit},
title = {Improving replicability in single-cell RNA-Seq cell type discovery
with Dune},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {198},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05814-6},
doi = {10.1186/S12859-024-05814-6},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BezieuxSFBCRGNPD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BhuvaTLWPLKMD24,
author = {Dharmesh D. Bhuva and
Chin Wee Tan and
Ning Liu and
Holly J. Whitfield and
Nicholas Papachristos and
Samuel C. Lee and
Malvika Kharbanda and
Ahmed Mohamed and
Melissa J. Davis},
title = {vissE: a versatile tool to identify and visualise higher-order molecular
phenotypes from functional enrichment analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {64},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05676-y},
doi = {10.1186/S12859-024-05676-Y},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BhuvaTLWPLKMD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BlumenkampPDBJG24,
author = {Patrick Blumenkamp and
Max Pfister and
Sonja Diedrich and
Karina Brinkrolf and
Sebastian Jaenicke and
Alexander Goesmann},
title = {Curare and GenExVis: a versatile toolkit for analyzing and visualizing
RNA-Seq data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {138},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05761-2},
doi = {10.1186/S12859-024-05761-2},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BlumenkampPDBJG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BofaZ24,
author = {Adusei Bofa and
Temesgen Zewotir},
title = {Optimizing spatio-temporal correlation structures for modeling food
security in Africa: a simulation-based investigation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {168},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05791-w},
doi = {10.1186/S12859-024-05791-W},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BofaZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BollasRCGMW24,
author = {Audrey E. Bollas and
Andrei Rajkovic and
Defne Ceyhan and
Jeffrey B. Gaither and
Elaine R. Mardis and
Peter White},
title = {SNVstory: inferring genetic ancestry from genome sequencing data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {76},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05703-y},
doi = {10.1186/S12859-024-05703-Y},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BollasRCGMW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BonomoR24,
author = {Mariella Bonomo and
Simona E. Rombo},
title = {Neighborhood based computational approaches for the prediction of
lncRNA-disease associations},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {187},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05777-8},
doi = {10.1186/S12859-024-05777-8},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BonomoR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BoussinaLOSMLAPCF24,
author = {Aaron Boussina and
Lennart Langouche and
Augustine C. Obirieze and
Mridu Sinha and
Hannah Mack and
William Leineweber and
April Joy C. Aralar and
David T. Pride and
Todd P. Coleman and
Stephanie I Fraley},
title = {Machine learning based {DNA} melt curve profiling enables automated
novel genotype detection},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {185},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05747-0},
doi = {10.1186/S12859-024-05747-0},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BoussinaLOSMLAPCF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CarterSD24,
author = {Clayton Carter and
Aaron Saporito and
Stephen M. Douglass},
title = {MetageneCluster: a Python package for filtering conflicting signal
trends in metagene plots},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {21},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05647-3},
doi = {10.1186/S12859-024-05647-3},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CarterSD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CastanhoLHM24,
author = {Eduardo N. Castanho and
Jo{\~{a}}o Lobo and
Rui Henriques and
Sara C. Madeira},
title = {Correction: G-bic: generating synthetic benchmarks for biclustering},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {16},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05628-y},
doi = {10.1186/S12859-023-05628-Y},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CastanhoLHM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CebeciEEB24,
author = {Yunus Emre Cebeci and
Rumeysa Aslihan Erturk and
Mehmet Arif Ergun and
Mehmet Baysan},
title = {Improving somatic exome sequencing performance by biological replicates},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {124},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05742-5},
doi = {10.1186/S12859-024-05742-5},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CebeciEEB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChaiLLHYOZ24,
author = {Hua Chai and
Siyin Lin and
Junqi Lin and
Minfan He and
Yuedong Yang and
Yongzhong OuYang and
Huiying Zhao},
title = {An uncertainty-based interpretable deep learning framework for predicting
breast cancer outcome},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {88},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05716-7},
doi = {10.1186/S12859-024-05716-7},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChaiLLHYOZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChanCTP24,
author = {Donny Chan and
Graham L. Cromar and
Billy Taj and
John Parkinson},
title = {Cell4D: a general purpose spatial stochastic simulator for cellular
pathways},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {121},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05739-0},
doi = {10.1186/S12859-024-05739-0},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChanCTP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChangAGK24,
author = {Haiyang Chang and
Daniel A. Ashlock and
Steffen P. Graether and
Stefan M. Keller},
title = {Anchor Clustering for million-scale immune repertoire sequencing data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {42},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05659-z},
doi = {10.1186/S12859-024-05659-Z},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChangAGK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenMXX24,
author = {Xue{-}Qin Chen and
Jie Ma and
Di Xu and
Zuo{-}Lin Xiang},
title = {Correction: Comprehensive analysis of {KLF2} as a prognostic biomarker
associated with fibrosis and immune infiltration in advanced hepatocellular
carcinoma},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {7},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05623-3},
doi = {10.1186/S12859-023-05623-3},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenMXX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenWW24,
author = {Jing Chen and
Haoyu Wu and
Ning Wang},
title = {{KEGG} orthology prediction of bacterial proteins using natural language
processing},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {146},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05766-x},
doi = {10.1186/S12859-024-05766-X},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenWW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenZX24,
author = {Lei Chen and
Chenyu Zhang and
Jing Xu},
title = {PredictEFC: a fast and efficient multi-label classifier for predicting
enzyme family classes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {50},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05665-1},
doi = {10.1186/S12859-024-05665-1},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenZX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChinIST24,
author = {Ka Yin Chin and
Shoichi Ishida and
Yukio Sasaki and
Kei Terayama},
title = {Predicting condensate formation of protein and {RNA} under various
environmental conditions},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {143},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05764-z},
doi = {10.1186/S12859-024-05764-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChinIST24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChoiCC24,
author = {Yongjun Choi and
Junho Cha and
Sungkyoung Choi},
title = {Evaluation of penalized and machine learning methods for asthma disease
prediction in the Korean Genome and Epidemiology Study (KoGES)},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {56},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05677-x},
doi = {10.1186/S12859-024-05677-X},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChoiCC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChowdhuryBO24,
author = {H. M. A. Mohit Chowdhury and
Terrance E. Boult and
Oluwatosin Oluwadare},
title = {Comparative study on chromatin loop callers using Hi-C data reveals
their effectiveness},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {123},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05713-w},
doi = {10.1186/S12859-024-05713-W},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChowdhuryBO24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ClementsGHKOOSR24,
author = {Jody Clements and
Cristian Goina and
Philip M. Hubbard and
Takashi Kawase and
Donald J. Olbris and
Hideo Otsuna and
Robert Svirskas and
Konrad Rokicki},
title = {NeuronBridge: an intuitive web application for neuronal morphology
search across large data sets},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {114},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05732-7},
doi = {10.1186/S12859-024-05732-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ClementsGHKOOSR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CostaGDRRSSP24,
author = {Raquel Lopes Costa and
Luiz M. R. Gadelha Jr. and
Mirela D'arc and
Marcelo Ribeiro{-}Alves and
David L. Robertson and
Jean{-}Marc Schwartz and
Marcelo A. Soares and
F{\'{a}}bio Porto},
title = {{HIHISIV:} a database of gene expression in {HIV} and {SIV} host immune
response},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {125},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05740-7},
doi = {10.1186/S12859-024-05740-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CostaGDRRSSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CrippaFRP24,
author = {Valentina Crippa and
Emanuela Fina and
Daniele Ramazzotti and
Rocco Piazza},
title = {Control-FREEC viewer: a tool for the visualization and exploration
of copy number variation data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {72},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05694-w},
doi = {10.1186/S12859-024-05694-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CrippaFRP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DangV24,
author = {Thanh Hai Dang and
Tien Anh Vu},
title = {xCAPT5: protein-protein interaction prediction using deep and wide
multi-kernel pooling convolutional neural networks with protein language
model},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {106},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05725-6},
doi = {10.1186/S12859-024-05725-6},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DangV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DehghanARBG24,
author = {Alireza Dehghan and
Karim Abbasi and
Parvin Razzaghi and
Hossein Banadkuki and
Sajjad Gharaghani},
title = {{CCL-DTI:} contributing the contrastive loss in drug-target interaction
prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {48},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05671-3},
doi = {10.1186/S12859-024-05671-3},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DehghanARBG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DolezalKDRSSHLMP24,
author = {James M. Dolezal and
Sara Kochanny and
Emma C. Dyer and
Siddhi Ramesh and
Andrew Srisuwananukorn and
Matteo Sacco and
Frederick M. Howard and
Anran Li and
Prajval Mohan and
Alexander T. Pearson},
title = {Slideflow: deep learning for digital histopathology with real-time
whole-slide visualization},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {134},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05758-x},
doi = {10.1186/S12859-024-05758-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DolezalKDRSSHLMP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DongCWHWYZQWFR24,
author = {Yunyun Dong and
Yunqing Chang and
Yuxiang Wang and
Qixuan Han and
Xiaoyuan Wen and
Ziting Yang and
Yan Zhang and
Yan Qiang and
Kun Wu and
Xiaole Fan and
Xiaoqiang Ren},
title = {MFSynDCP: multi-source feature collaborative interactive learning
for drug combination synergy prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {140},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05765-y},
doi = {10.1186/S12859-024-05765-Y},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DongCWHWYZQWFR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DraizenRMB24,
author = {Eli J. Draizen and
John Readey and
Cameron Mura and
Philip E. Bourne},
title = {Prop3D: {A} flexible, Python-based platform for machine learning with
protein structural properties and biophysical data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {11},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05586-5},
doi = {10.1186/S12859-023-05586-5},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DraizenRMB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EidiAMGZ24,
author = {Milad Eidi and
Samaneh Abdolalizadeh and
Soheila Moeini and
Masoud Garshasbi and
Javad Zahiri},
title = {123VCF: an intuitive and efficient tool for filtering {VCF} files},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {68},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05661-5},
doi = {10.1186/S12859-024-05661-5},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/EidiAMGZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ElsherbiniEFGEEM24,
author = {Ahmed M. A. Elsherbini and
Amr Hassan Elkholy and
Youssef M. Fadel and
Gleb Goussarov and
Ahmed Mohamed Elshal and
Mohamed El{-}Hadidi and
Mohamed Mysara},
title = {Utilizing genomic signatures to gain insights into the dynamics of
SARS-CoV-2 through Machine and Deep Learning techniques},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {131},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05648-2},
doi = {10.1186/S12859-024-05648-2},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ElsherbiniEFGEEM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EmamiF24,
author = {Neda Emami and
Reza Ferdousi},
title = {HormoNet: a deep learning approach for hormone-drug interaction prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {87},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05708-7},
doi = {10.1186/S12859-024-05708-7},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/EmamiF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ErgunCBEB24,
author = {Mehmet Arif Ergun and
Omer Cinal and
Berkant Bakisli and
Abdullah Asim Em{\"{u}}l and
Mehmet Baysan},
title = {{COSAP:} Comparative Sequencing Analysis Platform},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {130},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05756-z},
doi = {10.1186/S12859-024-05756-Z},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ErgunCBEB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ErnstBNDMBDLCE24,
author = {Terrence R. Ernst and
John D. Blischak and
Paul Nordlund and
Joe Dalen and
Justin Moore and
Akshay Bhamidipati and
Pankaj Dwivedi and
Joe LoGrasso and
Marco Rocha Curado and
Brett Warren Engelmann},
title = {OmicNavigator: open-source software for the exploration, visualization,
and archival of omic studies},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {162},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05743-4},
doi = {10.1186/S12859-024-05743-4},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ErnstBNDMBDLCE24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FolksNBD24,
author = {Ryan D. Folks and
Bhiken I. Naik and
Donald E. Brown and
Marcel Durieux},
title = {Computer vision digitization of smartphone images of anesthesia paper
health records from low-middle income countries},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {178},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05785-8},
doi = {10.1186/S12859-024-05785-8},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FolksNBD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FrabouletAACGB24,
author = {Rose{-}Marie Fraboulet and
Yanis Si Ahmed and
Marc Aubry and
Sebastien Corre and
Marie{-}Dominique Galibert and
Yuna Blum},
title = {Cirscan: a shiny application to identify differentially active sponge
mechanisms and visualize circRNA-miRNA-mRNA networks},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {53},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05668-y},
doi = {10.1186/S12859-024-05668-Y},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FrabouletAACGB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GamalI24,
author = {Mahmoud Gamal and
Marwa A. Ibrahim},
title = {Introducing the f\({}_{\mbox{0}}\){\%} method: a reliable and accurate
approach for qPCR analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {17},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05630-y},
doi = {10.1186/S12859-024-05630-Y},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GamalI24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GarbeliniSP24,
author = {Jader M. Caldonazzo Garbelini and
Danilo Sipoli Sanches and
Aurora T. R. Pozo},
title = {biomapp::chip: large-scale motif analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {128},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05752-3},
doi = {10.1186/S12859-024-05752-3},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GarbeliniSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GelbachCF24,
author = {Patrick E. Gelbach and
Handan Cetin and
Stacey D. Finley},
title = {Flux sampling in genome-scale metabolic modeling of microbial communities},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {45},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05655-3},
doi = {10.1186/S12859-024-05655-3},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GelbachCF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GiannantoniBSC24,
author = {Leonardo Giannantoni and
Roberta Bardini and
Alessandro Savino and
Stefano Di Carlo},
title = {Biology System Description Language (BiSDL): a modeling language for
the design of multicellular synthetic biological systems},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {166},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05782-x},
doi = {10.1186/S12859-024-05782-X},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GiannantoniBSC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GlascockWDWA24,
author = {Abigail Glascock and
Eric Waltari and
Gytis Dudas and
Joan Wong and
Vida Ahyong},
title = {PoMeLo: a systematic computational approach to predicting metabolic
loss in pathogen genomes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {49},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05640-w},
doi = {10.1186/S12859-024-05640-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GlascockWDWA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GoreMSGZA24,
author = {Steven Gore and
Bailey Meche and
Danyang Shao and
Benjamin Ginnett and
Kelly Zhou and
Rajeev K. Azad},
title = {DiseaseNet: a transfer learning approach to noncommunicable disease
classification},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {107},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05734-5},
doi = {10.1186/S12859-024-05734-5},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GoreMSGZA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuYWJF24,
author = {Lin{-}Lin Gu and
Run{-}Qing Yang and
Zhi{-}Yong Wang and
Dan Jiang and
Ming Fang},
title = {Ensemble learning for integrative prediction of genetic values with
genomic variants},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {120},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05720-x},
doi = {10.1186/S12859-024-05720-X},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GuYWJF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuanYLYMWYG24,
author = {Yongjian Guan and
Chang{-}Qing Yu and
Li{-}Ping Li and
Zhu{-}Hong You and
Weixiao Meng and
Xin{-}Fei Wang and
Chen Yang and
Lu{-}Xiang Guo},
title = {{MHESMMR:} a multilevel model for predicting the regulation of miRNAs
expression by small molecules},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {6},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05629-x},
doi = {10.1186/S12859-023-05629-X},
timestamp = {Fri, 12 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GuanYLYMWYG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuanYWZH24,
author = {Qi Guan and
Xianzhong Yan and
Yida Wu and
Da Zhou and
Jie Hu},
title = {Biclustering analysis on tree-shaped time-series single cell gene
expression data of Caenorhabditis elegans},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {183},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05800-y},
doi = {10.1186/S12859-024-05800-Y},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GuanYWZH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GurusingheS24,
author = {Sagara N. S. Gurusinghe and
Julia M. Shifman},
title = {Cold Spot {SCANNER:} Colab Notebook for predicting cold spots in protein-protein
interfaces},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {172},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05796-5},
doi = {10.1186/S12859-024-05796-5},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GurusingheS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HahnLHPCSWL24,
author = {Georg Hahn and
Sharon Marie Lutz and
Julian Hecker and
Dmitry Prokopenko and
Michael H. Cho and
Edwin K. Silverman and
Scott T. Weiss and
Christoph Lange},
title = {Fast computation of the eigensystem of genomic similarity matrices},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {43},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05650-8},
doi = {10.1186/S12859-024-05650-8},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HahnLHPCSWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HanZGB24,
author = {Wei Han and
Sanguo Zhang and
Hailong Gao and
Deliang Bu},
title = {Clustering on hierarchical heterogeneous data with prior pairwise
relationships},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {40},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05652-6},
doi = {10.1186/S12859-024-05652-6},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HanZGB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HanZLLZ24,
author = {Yu Han and
Qiong Zhou and
Leibo Liu and
Jianwei Li and
Yuan Zhou},
title = {{DNI-MDCAP:} improvement of causal MiRNA-disease association prediction
based on deep network imputation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {22},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05644-6},
doi = {10.1186/S12859-024-05644-6},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HanZLLZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HarriganFWPSB24,
author = {William L. Harrigan and
Barbra D. Ferrell and
K. Eric Wommack and
Shawn W. Polson and
Zachary D. Schreiber and
Mahdi Belcaid},
title = {Improvements in viral gene annotation using large language models
and soft alignments},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {165},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05779-6},
doi = {10.1186/S12859-024-05779-6},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HarriganFWPSB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HauchampsBDHTTLG24,
author = {Philippe Hauchamps and
Babak Bayat and
Simon Delandre and
Mehdi Hamrouni and
Marie Toussaint and
Stephane Temmerman and
Dan Lin and
Laurent Gatto},
title = {CytoPipeline and CytoPipelineGUI: a Bioconductor {R} package suite
for building and visualizing automated pre-processing pipelines for
flow cytometry data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {80},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05691-z},
doi = {10.1186/S12859-024-05691-Z},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HauchampsBDHTTLG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HeXWYJTYF24,
author = {Weiming He and
Lian Xu and
JingXian Wang and
Zhen Yue and
Yi Jing and
Shuaishuai Tai and
Jian Yang and
Xiaodong Fang},
title = {VCF2PCACluster: a simple, fast and memory-efficient tool for principal
component analysis of tens of millions of SNPs},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {173},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05770-1},
doi = {10.1186/S12859-024-05770-1},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HeXWYJTYF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HeY24,
author = {Xiao He and
Ming Yan},
title = {GraphKM: machine and deep learning for K\({}_{\mbox{M}}\) prediction
of wildtype and mutant enzymes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {135},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05746-1},
doi = {10.1186/S12859-024-05746-1},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HeY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HeYY24,
author = {Shihui He and
Lijun Yun and
Haicheng Yi},
title = {Fusing graph transformer with multi-aggregate {GCN} for enhanced drug-disease
associations prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {79},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05705-w},
doi = {10.1186/S12859-024-05705-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HeYY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HolscherGKDCBB24,
author = {David L. H{\"{o}}lscher and
Michael Goedertier and
Barbara Mara Klinkhammer and
Patrick Droste and
Ivan G. Costa and
Peter Boor and
Roman David B{\"{u}}low},
title = {tRigon: an {R} package and Shiny App for integrative (path-)omics
data analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {98},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05721-w},
doi = {10.1186/S12859-024-05721-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HolscherGKDCBB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuLTY24,
author = {Jianqiao Hu and
Sai Luo and
Ming Tian and
Adam Yongxin Ye},
title = {TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous
bases in high-throughput sequencing},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {154},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05775-w},
doi = {10.1186/S12859-024-05775-W},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuLTY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuOOR24,
author = {Anjun Hu and
Awino M. E. Ojwang' and
Kayode D. Olumoyin and
Katarzyna A. Rejniak},
title = {LinG3D: visualizing the spatio-temporal dynamics of clonal evolution},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {201},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05813-7},
doi = {10.1186/S12859-024-05813-7},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuOOR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuangCSZ24,
author = {Yiran Huang and
Fuhao Chen and
Hongtao Sun and
Cheng Zhong},
title = {Exploring gene-patient association to identify personalized cancer
driver genes by linear neighborhood propagation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {34},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05662-4},
doi = {10.1186/S12859-024-05662-4},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuangCSZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuangLCWCT24,
author = {Jiajian Huang and
Jinpeng Li and
Qinchang Chen and
Xia Wang and
Guangyong Chen and
Jin Tang},
title = {Freeprotmap: waiting-free prediction method for protein distance map},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {176},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05771-0},
doi = {10.1186/S12859-024-05771-0},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuangLCWCT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuangZZ24,
author = {Yiran Huang and
Pingfan Zeng and
Cheng Zhong},
title = {Classifying breast cancer subtypes on multi-omics data via sparse
canonical correlation analysis and deep learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {132},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05749-y},
doi = {10.1186/S12859-024-05749-Y},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuangZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuiKAFHSHMS24,
author = {Tay Xin Hui and
Shahreen Kasim and
Izzatdin Abdul Aziz and
Mohd Farhan Md Fudzee and
Nazleeni Samiha Haron and
Tole Sutikno and
Rohayanti Hassan and
Hairulnizam Mahdin and
Seah Choon Sen},
title = {Robustness evaluations of pathway activity inference methods on gene
expression data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {23},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05632-w},
doi = {10.1186/S12859-024-05632-W},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuiKAFHSHMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/IliadisBPW24,
author = {Dimitrios Iliadis and
Bernard De Baets and
Tapio Pahikkala and
Willem Waegeman},
title = {A comparison of embedding aggregation strategies in drug-target interaction
prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {59},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05684-y},
doi = {10.1186/S12859-024-05684-Y},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/IliadisBPW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/IovinoY24,
author = {Benjamin Giovanni Iovino and
Yuzhen Ye},
title = {Protein embedding based alignment},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {85},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05699-5},
doi = {10.1186/S12859-024-05699-5},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/IovinoY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/IrreraMS24,
author = {Ornella Irrera and
Stefano Marchesin and
Gianmaria Silvello},
title = {MetaTron: advancing biomedical annotation empowering relation annotation
and collaboration},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {112},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05730-9},
doi = {10.1186/S12859-024-05730-9},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/IrreraMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JoeK24,
author = {Hyunwhan Joe and
Hong{-}Gee Kim},
title = {Multi-label classification with XGBoost for metabolic pathway prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {52},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05666-0},
doi = {10.1186/S12859-024-05666-0},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JoeK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JosephZBF24,
author = {Cl{\'{e}}mence Joseph and
Haris Zafeiropoulos and
Kristel Bernaerts and
Karoline Faust},
title = {Predicting microbial interactions with approaches based on flux balance
analysis: an evaluation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {36},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05651-7},
doi = {10.1186/S12859-024-05651-7},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JosephZBF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KallenbornS24,
author = {Felix Kallenborn and
Bertil Schmidt},
title = {CAREx: context-aware read extension of paired-end sequencing data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {186},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05802-w},
doi = {10.1186/S12859-024-05802-W},
timestamp = {Fri, 31 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KallenbornS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KibetEJVVWKM24,
author = {Caleb K. Kibet and
Jean{-}Baka Domelevo Entfellner and
Daudi Jjingo and
Etienne Pierre de Villiers and
Santie de Villiers and
Karen Wambui and
Sam Kinyanjui and
Daniel Masiga},
title = {Designing and delivering bioinformatics project-based learning in
East Africa},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {150},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05680-2},
doi = {10.1186/S12859-024-05680-2},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KibetEJVVWKM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimJKH24,
author = {Emma E. Kim and
Chloe Soohyun Jang and
Hakin Kim and
Buhm Han},
title = {{PASTRY:} achieving balanced power for detecting risk and protective
minor alleles in meta-analysis of association studies with overlapping
subjects},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {24},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05627-z},
doi = {10.1186/S12859-023-05627-Z},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KimJKH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KirmaniKMSKMWW24,
author = {Mahira Kirmani and
Gagandeep Kour and
Mudasir Mohd and
Nasrullah Sheikh and
Dawood Ashraf Khan and
Zahid Maqbool and
Mohsin Altaf Wani and
Abid Hussain Wani},
title = {Biomedical semantic text summarizer},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {152},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05712-x},
doi = {10.1186/S12859-024-05712-X},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KirmaniKMSKMWW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KoberBRO24,
author = {Kord M. Kober and
Liam Berger and
Ritu Roy and
Adam B. Olshen},
title = {Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular
phenotypes with graphical processing units},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {71},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05670-4},
doi = {10.1186/S12859-024-05670-4},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KoberBRO24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KoleBPD24,
author = {Arnab Kole and
Arup Kumar Bag and
Anindya Jyoti Pal and
Debashis De},
title = {Generic model to unravel the deeper insights of viral infections:
an empirical application of evolutionary graph coloring in computational
network biology},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {74},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05690-0},
doi = {10.1186/S12859-024-05690-0},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KoleBPD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KongNRPCLYCCBM24,
author = {Garth L. Kong and
Thai T. Nguyen and
Wesley K. Rosales and
Anjali D. Panikar and
John H. W. Cheney and
Theresa A. Lusardi and
William M. Yashar and
Brittany M. Curtiss and
Sarah A. Carratt and
Theodore P. Braun and
Julia E. Maxson},
title = {CITEViz: interactively classify cell populations in CITE-Seq via a
flow cytometry-like gating workflow using R-Shiny},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {142},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05762-1},
doi = {10.1186/S12859-024-05762-1},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KongNRPCLYCCBM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KpanouDRC24,
author = {Rogia Kpanou and
Patrick Dallaire and
Elsa Rousseau and
Jacques Corbeil},
title = {Learning self-supervised molecular representations for drug-drug interaction
prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {47},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05643-7},
doi = {10.1186/S12859-024-05643-7},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KpanouDRC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KravchenkoVSB24,
author = {Anna Kravchenko and
Sjoerd Jacob de Vries and
Malika Sma{\"{\i}}l{-}Tabbone and
Isaure Chauvot de Beauch{\^{e}}ne},
title = {{HIPPO:} HIstogram-based Pseudo-POtential for scoring protein-ssRNA
fragment-based docking poses},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {129},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05733-6},
doi = {10.1186/S12859-024-05733-6},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KravchenkoVSB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KuangZZLZXW24,
author = {Haiyue Kuang and
Zhen Zhang and
Bin Zeng and
Xin Liu and
Hao Zuo and
Xingye Xu and
Lei Wang},
title = {A novel microbe-drug association prediction model based on graph attention
networks and bilayer random forest},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {78},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05687-9},
doi = {10.1186/S12859-024-05687-9},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KuangZZLZXW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KusterS24,
author = {Ryan Kuster and
Margaret Staton},
title = {Readsynth: short-read simulation for consideration of composition-biases
in reduced metagenome sequencing approaches},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {191},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05809-3},
doi = {10.1186/S12859-024-05809-3},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KusterS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KwakKLKGZG24,
author = {Il{-}Youp Kwak and
Byeong{-}Chan Kim and
Juhyun Lee and
Taein Kang and
Daniel J. Garry and
Jianyi Zhang and
Wuming Gong},
title = {Proformer: a hybrid macaron transformer model predicts expression
values from promoter sequences},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {81},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05645-5},
doi = {10.1186/S12859-024-05645-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KwakKLKGZG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LaoZCLAL24,
author = {Chuanqi Lao and
Pengfei Zheng and
Hongyang Chen and
Qiao Liu and
Feng An and
Zhao Li},
title = {DeepAEG: a model for predicting cancer drug response based on data
enhancement and edge-collaborative update strategies},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {105},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05723-8},
doi = {10.1186/S12859-024-05723-8},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LaoZCLAL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LeNNNHVNNC24,
author = {Duc Quang Le and
Son Hoang Nguyen and
Tam Thi Nguyen and
Canh Hao Nguyen and
Tho Huu Ho and
Nam S. Vo and
Trang Nguyen and
Hoang Anh Nguyen and
Minh Duc Cao},
title = {AMRViz enables seamless genomics analysis and visualization of antimicrobial
resistance},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {193},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05792-9},
doi = {10.1186/S12859-024-05792-9},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LeNNNHVNNC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LeeOPDNV24,
author = {Hyun Jung Lee and
Utku Ozbulak and
Homin Park and
Stephen Depuydt and
Wesley De Neve and
Joris Vankerschaver},
title = {Assessing the reliability of point mutation as data augmentation for
deep learning with genomic data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {170},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05787-6},
doi = {10.1186/S12859-024-05787-6},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LeeOPDNV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiLWWSYGLJ24,
author = {Yifan Li and
Qianying Li and
Lvying Wu and
Haiyan Wang and
Hui Shi and
Chenhui Yang and
Yiqun Gu and
Jianyuan Li and
Zhiliang Ji},
title = {SperMD: the expression atlas of sperm maturation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {29},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05631-x},
doi = {10.1186/S12859-024-05631-X},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiLWWSYGLJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiMLHW24,
author = {Shangru Li and
Xiangpeng Meng and
Rui Li and
Bingding Huang and
Xin Wang},
title = {NanoBERTa-ASP: predicting nanobody paratope based on a pretrained
RoBERTa model},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {122},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05750-5},
doi = {10.1186/S12859-024-05750-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiMLHW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiMLHW24a,
author = {Shangru Li and
Xiangpeng Meng and
Rui Li and
Bingding Huang and
Xin Wang},
title = {Correction: NanoBERTa-ASP: predicting nanobody paratope based on a
pretrained RoBERTa model},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {190},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05790-x},
doi = {10.1186/S12859-024-05790-X},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiMLHW24a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiN24,
author = {Bingjun Li and
Sheida Nabavi},
title = {A multimodal graph neural network framework for cancer molecular subtype
classification},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {27},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05622-4},
doi = {10.1186/S12859-023-05622-4},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiYBHCHRSA24,
author = {Lu Li and
Shi Yan and
Barbara M. Bakker and
Huub C. J. Hoefsloot and
Bo Chawes and
David Horner and
Morten A. Rasmussen and
Age K. Smilde and
Evrim Acar},
title = {Analyzing postprandial metabolomics data using multiway models: a
simulation study},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {94},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05686-w},
doi = {10.1186/S12859-024-05686-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiYBHCHRSA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiangYZGW24,
author = {Ying Liang and
XingRui Yin and
YangSen Zhang and
You Guo and
YingLong Wang},
title = {Predicting lncRNA-protein interactions through deep learning framework
employing multiple features and random forest algorithm},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {108},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05727-4},
doi = {10.1186/S12859-024-05727-4},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiangYZGW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LinQR24,
author = {Kevin Z. Lin and
Yixuan Qiu and
Kathryn Roeder},
title = {eSVD-DE: cohort-wide differential expression in single-cell RNA-seq
data using exponential-family embeddings},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {113},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05724-7},
doi = {10.1186/S12859-024-05724-7},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LinQR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuCLZYM24,
author = {Yufang Liu and
Yongkai Chen and
Haoran Lu and
Wenxuan Zhong and
Guo{-}Cheng Yuan and
Ping Ma},
title = {Orthogonal multimodality integration and clustering in single-cell
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {164},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05773-y},
doi = {10.1186/S12859-024-05773-Y},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuCLZYM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuHLHM24,
author = {Qian Liu and
Qiang Hu and
Song Liu and
Alan David Hutson and
Martin Morgan},
title = {ReUseData: an R/Bioconductor tool for reusable and reproducible genomic
data management},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {8},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05626-0},
doi = {10.1186/S12859-023-05626-0},
timestamp = {Fri, 09 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuHLHM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuQHL24,
author = {Renjing Liu and
Kun Qian and
Xinwei He and
Hongwei Li},
title = {Integration of scRNA-seq data by disentangled representation learning
with condition domain adaptation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {116},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05706-9},
doi = {10.1186/S12859-024-05706-9},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuQHL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuZDYLCTZ24,
author = {Yanling Liu and
Ruiyan Zhang and
Xiaojing Dong and
Hong Yang and
Jing Li and
Hongyan Cao and
Jing Tian and
Yanbo Zhang},
title = {{DAE-CFR:} detecting microRNA-disease associations using deep autoencoder
and combined feature representation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {139},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05757-y},
doi = {10.1186/S12859-024-05757-Y},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuZDYLCTZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuZQBDL24,
author = {Wuyong Liu and
Jingyu Zhang and
Guanyu Qiao and
Jilong Bian and
Benzhi Dong and
Yang Li},
title = {{HMMF:} a hybrid multi-modal fusion framework for predicting drug
side effect frequencies},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {196},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05806-6},
doi = {10.1186/S12859-024-05806-6},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuZQBDL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LorenziGCA24,
author = {Jean{-}No{\"{e}}l Lorenzi and
Fran{\c{c}}ois Graner and
Virginie Courtier{-}Orgogozo and
Guillaume Achaz},
title = {{CNCA} aligns small annotated genomes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {89},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05700-1},
doi = {10.1186/S12859-024-05700-1},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LorenziGCA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LudwigM24,
author = {J. Ludwig and
Jan Mr{\'{a}}zek},
title = {OrthoRefine: automated enhancement of prior ortholog identification
via synteny},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {163},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05786-7},
doi = {10.1186/S12859-024-05786-7},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LudwigM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Ma24,
author = {Zhanshan (Sam) Ma},
title = {Towards a unified medical microbiome ecology of the {OMU} for metagenomes
and the {OTU} for microbes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {137},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05591-8},
doi = {10.1186/S12859-023-05591-8},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Ma24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaasD24,
author = {Zachary L. Maas and
Robin D. Dowell},
title = {Internal and external normalization of nascent {RNA} sequencing run-on
experiments},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {19},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05607-3},
doi = {10.1186/S12859-023-05607-3},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaasD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaricKRNS24,
author = {Josip Maric and
Kresimir Krizanovic and
Sylvain Riondet and
Niranjan Nagarajan and
Mile Sikic},
title = {Comparative analysis of metagenomic classifiers for long-read sequencing
datasets},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {15},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05634-8},
doi = {10.1186/S12859-024-05634-8},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaricKRNS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/McCall24,
author = {Andrew D. McCall},
title = {Colocalization by cross-correlation, a new method of colocalization
suited for super-resolution microscopy},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {55},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05675-z},
doi = {10.1186/S12859-024-05675-Z},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/McCall24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/McNairSES24,
author = {Katelyn McNair and
Peter Salamon and
Robert A. Edwards and
Anca M. Segall},
title = {PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic
and viral genomes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {82},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05701-0},
doi = {10.1186/S12859-024-05701-0},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/McNairSES24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MeyerEB24,
author = {Lasse Meyer and
Nils Eling and
Bernd Bodenmiller},
title = {cytoviewer: an R/Bioconductor package for interactive visualization
and exploration of highly multiplexed imaging data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {9},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05546-z},
doi = {10.1186/S12859-023-05546-Z},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MeyerEB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MillerA24,
author = {Jason R. Miller and
Donald A. Adjeroh},
title = {Machine learning on alignment features for parent-of-origin classification
of simulated hybrid RNA-seq},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {109},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05728-3},
doi = {10.1186/S12859-024-05728-3},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MillerA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MinYXHLJWKLGZX24,
author = {Xiaoping Min and
Chongzhou Yang and
Jun Xie and
Yang Huang and
Nan Liu and
Xiaocheng Jin and
Tianshu Wang and
Zhibo Kong and
Xiaoli Lu and
Shengxiang Ge and
Jun Zhang and
Ningshao Xia},
title = {Tpgen: a language model for stable protein design with a specific
topology structure},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {35},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05637-5},
doi = {10.1186/S12859-024-05637-5},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MinYXHLJWKLGZX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MohseniTakallooMMMH24,
author = {Sahar Mohseni{-}Takalloo and
Hadis Mohseni and
Hassan Mozaffari{-}Khosravi and
Masoud Mirzaei and
Mahdieh Hosseinzadeh},
title = {The effect of data balancing approaches on the prediction of metabolic
syndrome using non-invasive parameters based on random forest},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {18},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05633-9},
doi = {10.1186/S12859-024-05633-9},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MohseniTakallooMMMH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MuSAM24,
author = {Lixuan Mu and
Jiangning Song and
Tatsuya Akutsu and
Tomoya Mori},
title = {DiCleave: a deep learning model for predicting human Dicer cleavage
sites},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {13},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05638-4},
doi = {10.1186/S12859-024-05638-4},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MuSAM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MunkIZBM24,
author = {Katharina Munk and
Daria Ilina and
Lisa Ziemba and
G{\"{u}}nter Brader and
Eva M. Molin},
title = {Holomics - a user-friendly {R} shiny application for multi-omics data
integration and analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {93},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05719-4},
doi = {10.1186/S12859-024-05719-4},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MunkIZBM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NambiarPRCRMM24,
author = {Ananthan Nambiar and
Chao Pan and
Vishal Rana and
Mahdi Cheraghchi and
Jo{\~{a}}o Ribeiro and
Sergei Maslov and
Olgica Milenkovic},
title = {Semi-quantitative group testing for efficient and accurate qPCR screening
of pathogens with a wide range of loads},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {195},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05798-3},
doi = {10.1186/S12859-024-05798-3},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NambiarPRCRMM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NazerSMM24,
author = {Naghme Nazer and
Mohammad Hossein Sepehri and
Hoda Mohammadzade and
Mahya Mehrmohamadi},
title = {A novel approach toward optimal workflow selection for {DNA} methylation
biomarker discovery},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {37},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05658-0},
doi = {10.1186/S12859-024-05658-0},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NazerSMM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Nguyen24,
author = {Phuong{-}Nam Nguyen},
title = {Biomarker discovery with quantum neural networks: a case-study in
CTLA4-activation pathways},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {149},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05755-0},
doi = {10.1186/S12859-024-05755-0},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Nguyen24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NguyenNV24,
author = {Thi{-}Hau Nguyen and
Ha{-}Nam Nguyen and
Trung{-}Nghia Vu},
title = {CircNetVis: an interactive web application for visualizing interaction
networks of circular RNAs},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {31},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05646-4},
doi = {10.1186/S12859-024-05646-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NguyenNV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NoseSYU24,
author = {Shota Nose and
Hirotsugu Shiroma and
Takuji Yamada and
Yushi Uno},
title = {QNetDiff: a quantitative measurement of network rewiring},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {118},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05702-z},
doi = {10.1186/S12859-024-05702-Z},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NoseSYU24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NulsenHAYUYA24,
author = {Joel Nulsen and
Nosheen Hussain and
Aws Al{-}Deka and
Jason Yap and
Khalil Uddin and
Christopher Yau and
Ahmed Ashour Ahmed},
title = {Correction: Completing a genomic characterisation of microscopic tumour
samples with copy number},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {20},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05642-8},
doi = {10.1186/S12859-024-05642-8},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NulsenHAYUYA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OhJJ24,
author = {Wonseok Oh and
Junghyun Jung and
Jong Wha J. Joo},
title = {{MR-GGI:} accurate inference of gene-gene interactions using Mendelian
randomization},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {192},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05808-4},
doi = {10.1186/S12859-024-05808-4},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OhJJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OkimotoMNNFS24,
author = {Leandro Y. S. Okimoto and
Rayol Mendonca{-}Neto and
Fab{\'{\i}}ola G. Nakamura and
Eduardo Freire Nakamura and
David Feny{\"{o}} and
Cl{\'{a}}udio Teixeira Silva},
title = {Few-shot genes selection: subset of {PAM50} genes for breast cancer
subtypes classification},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {92},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05715-8},
doi = {10.1186/S12859-024-05715-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OkimotoMNNFS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OliverADAF24,
author = {Matthieu Oliver and
Nicolas Allou and
Marjolaine Devineau and
J{\'{e}}r{\^{o}}me Allyn and
Cyril Ferdynus},
title = {A transformer model for cause-specific hazard prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {175},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05799-2},
doi = {10.1186/S12859-024-05799-2},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OliverADAF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OshternianLBF24,
author = {S. R. Oshternian and
S. Loipfinger and
A. Bhattacharya and
Rudolf S. N. Fehrmann},
title = {Exploring combinations of dimensionality reduction, transfer learning,
and regularization methods for predicting binary phenotypes with transcriptomic
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {167},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05795-6},
doi = {10.1186/S12859-024-05795-6},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OshternianLBF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PanWYL24,
author = {Li Pan and
Haoyue Wang and
Bo Yang and
Wenbin Li},
title = {A protein network refinement method based on module discovery and
biological information},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {157},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05772-z},
doi = {10.1186/S12859-024-05772-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PanWYL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PangCQ24,
author = {Weixiong Pang and
Ming Chen and
Yufang Qin},
title = {Prediction of anticancer drug sensitivity using an interpretable model
guided by deep learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {182},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05669-x},
doi = {10.1186/S12859-024-05669-X},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PangCQ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PappalardoAZBM24,
author = {Vincent Y. Pappalardo and
Leyla Azarang and
Egija Zaura and
Bernd W. Brandt and
Ren{\'{e}}e X. de Menezes},
title = {A new approach to describe the taxonomic structure of microbiome and
its application to assess the relationship between microbial niches},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {58},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05575-8},
doi = {10.1186/S12859-023-05575-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PappalardoAZBM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ParkH24,
author = {Youngjun Park and
Anne{-}Christin Hauschild},
title = {The effect of data transformation on low-dimensional integration of
single-cell RNA-seq},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {171},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05788-5},
doi = {10.1186/S12859-024-05788-5},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ParkH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ParkYSP24,
author = {Yeon{-}Ji Park and
Geun{-}Je Yang and
Chae{-}Bong Sohn and
Soo Jun Park},
title = {GPDminer: a tool for extracting named entities and analyzing relations
in biological literature},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {101},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05710-z},
doi = {10.1186/S12859-024-05710-Z},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ParkYSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PiquerEstebanADM24,
author = {Samuel Piquer{-}Esteban and
Vicente Arnau and
Wladimiro D{\'{\i}}az and
Andr{\'{e}}s Moya},
title = {{OMD} Curation Toolkit: a workflow for in-house curation of public
omics datasets},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {184},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05803-9},
doi = {10.1186/S12859-024-05803-9},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PiquerEstebanADM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PrinceNKEP24,
author = {Rukundo Prince and
Zhendong Niu and
Zahid Younas Khan and
Masabo Emmanuel and
Niyishaka Patrick},
title = {{COVID-19} detection from chest X-ray images using CLAHE-YCrCb, LBP,
and machine learning algorithms},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {28},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05427-5},
doi = {10.1186/S12859-023-05427-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PrinceNKEP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/QiYYL24,
author = {Haiou Qi and
Ting Yu and
Wenwen Yu and
Chenxi Liu},
title = {Drug-target affinity prediction with extended graph learning-convolutional
networks},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {75},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05698-6},
doi = {10.1186/S12859-024-05698-6},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/QiYYL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/QiaoLLHMTG24,
author = {Lei Qiao and
Chang Li and
Wei Lin and
Xiaoqi He and
Jia Mi and
Yigang Tong and
Jingyang Gao},
title = {ViroISDC: a method for calling integration sites of hepatitis {B}
virus based on feature encoding},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {177},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05763-0},
doi = {10.1186/S12859-024-05763-0},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/QiaoLLHMTG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RabeloSSWGSV24,
author = {Luan Pinto Rabelo and
Davidson Sodr{\'{e}} and
Rodrigo Petry Corr{\^{e}}a de Sousa and
Luciana Watanabe and
Grazielle Gomes and
Iracilda Sampaio and
Marcelo Vallinoto},
title = {SynGenes: a Python class for standardizing nomenclatures of mitochondrial
and chloroplast genes and a web form for enhancing searches for evolutionary
analyses},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {160},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05781-y},
doi = {10.1186/S12859-024-05781-Y},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RabeloSSWGSV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RahitACT24,
author = {K. M. Tahsin Hassan Rahit and
Vladimir Avramovic and
Jessica X. Chong and
Maja Tarailo{-}Graovac},
title = {{GPAD:} a natural language processing-based application to extract
the gene-disease association discovery information from {OMIM}},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {84},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05693-x},
doi = {10.1186/S12859-024-05693-X},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RahitACT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RakhshaninejadFSBG24,
author = {Morteza Rakhshaninejad and
Mohammad Fathian and
Reza Shirkoohi and
Farnaz Barzinpour and
Amir H. Gandomi},
title = {Refining breast cancer biomarker discovery and drug targeting through
an advanced data-driven approach},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {33},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05657-1},
doi = {10.1186/S12859-024-05657-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RakhshaninejadFSBG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RastaghiST24,
author = {Sedighe Rastaghi and
Azadeh Saki and
Hamed Tabesh},
title = {Correction: Modifying the false discovery rate procedure based on
the information theory under arbitrary correlation structure and its
performance in high-dimensional genomic data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {83},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05696-8},
doi = {10.1186/S12859-024-05696-8},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RastaghiST24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RastahiST24,
author = {Sedighe Rastahi and
Azadeh Saki and
Hamed Tabesh},
title = {Modifying the false discovery rate procedure based on the information
theory under arbitrary correlation structure and its performance in
high-dimensional genomic data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {57},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05678-w},
doi = {10.1186/S12859-024-05678-W},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RastahiST24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ReboiroJatoPSVVVL24,
author = {Miguel Reboiro{-}Jato and
Daniel P{\'{e}}rez{-}Rodr{\'{\i}}guez and
Miguel Jos{\'{e}} Da Silva and
David Vila{-}Fern{\'{a}}ndez and
Cristina P. Vieira and
Jorge Vieira and
Hugo L{\'{o}}pez{-}Fern{\'{a}}ndez},
title = {{SEDA} 2024 update: enhancing the SEquence DAtaset builder for seamless
integration into automated data analysis pipelines},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {200},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05818-2},
doi = {10.1186/S12859-024-05818-2},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ReboiroJatoPSVVVL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ReiterV24,
author = {Michael A. Reiter and
Julia A. Vorholt},
title = {Dashing Growth Curves: a web application for rapid and interactive
analysis of microbial growth curves},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {67},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05692-y},
doi = {10.1186/S12859-024-05692-Y},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ReiterV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RojasVelazquezKKTOGR24,
author = {David Rojas{-}Velazquez and
Sarah Kidwai and
Aletta D. Kraneveld and
Alberto Tonda and
Daniel L. Oberski and
Johan Garssen and
Alejandro Lopez Rincon},
title = {Methodology for biomarker discovery with reproducibility in microbiome
data using machine learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {26},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05639-3},
doi = {10.1186/S12859-024-05639-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RojasVelazquezKKTOGR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RoseanSORSG24,
author = {Samuel Rosean and
Eric A. Sosa and
Donal F. O'Shea and
Srilakshmi M. Raj and
Cathal Seoighe and
John M. Greally},
title = {Regulatory landscape enrichment analysis {(RLEA):} a computational
toolkit for non-coding variant enrichment and cell type prioritization},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {179},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05794-7},
doi = {10.1186/S12859-024-05794-7},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RoseanSORSG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RudraZNW24,
author = {Pratyaydipta Rudra and
Yi{-}Hui Zhou and
Andrew B. Nobel and
Fred A. Wright},
title = {Control of false discoveries in grouped hypothesis testing for eQTL
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {147},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05736-3},
doi = {10.1186/S12859-024-05736-3},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RudraZNW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SaaZDN24,
author = {Pedro A. Saa and
Sebastian Zapararte and
Christopher C. Drovandi and
Lars K. Nielsen},
title = {LooplessFluxSampler: an efficient toolbox for sampling the loopless
flux solution space of metabolic models},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {3},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05616-2},
doi = {10.1186/S12859-023-05616-2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SaaZDN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SamadiMMS24,
author = {Moein E. Samadi and
Hedieh Mirzaieazar and
Alexander Mitsos and
Andreas Schuppert},
title = {Noisecut: a python package for noise-tolerant classification of binary
data using prior knowledge integration and max-cut solutions},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {155},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05769-8},
doi = {10.1186/S12859-024-05769-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SamadiMMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SamiER24,
author = {Amira Sami and
Sara El{-}Metwally and
M. Z. Rashad},
title = {MAC-ErrorReads: machine learning-assisted classifier for filtering
erroneous {NGS} reads},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {61},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05681-1},
doi = {10.1186/S12859-024-05681-1},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SamiER24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SargsyanL24,
author = {Karen Sargsyan and
Carmay Lim},
title = {Using protein language models for protein interaction hot spot prediction
with limited data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {115},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05737-2},
doi = {10.1186/S12859-024-05737-2},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SargsyanL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ScharlG24,
author = {Theresa Scharl and
Bettina Gr{\"{u}}n},
title = {A clustering procedure for three-way {RNA} sequencing data using data
transformations and matrix-variate Gaussian mixture models},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {90},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05717-6},
doi = {10.1186/S12859-024-05717-6},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ScharlG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SergiBMM24,
author = {Aldo Sergi and
Luca Beltrame and
Sergio Marchini and
Marco Masseroli},
title = {Integrated approach to generate artificial samples with low tumor
fraction for somatic variant calling benchmarking},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {180},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05793-8},
doi = {10.1186/S12859-024-05793-8},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SergiBMM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShabbirM24,
author = {Madiha Shabbir and
Aziz Mithani},
title = {Roast: a tool for reference-free optimization of supertranscriptome
assemblies},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {2},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05614-4},
doi = {10.1186/S12859-023-05614-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShabbirM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShahirSP24,
author = {Jamshaid A. Shahir and
Natalie Stanley and
Jeremy E. Purvis},
title = {Cellograph: a semi-supervised approach to analyzing multi-condition
single-cell RNA-sequencing data using graph neural networks},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {25},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05641-9},
doi = {10.1186/S12859-024-05641-9},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShahirSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShenWDSWT24,
author = {Junjie Shen and
Shuo Wang and
Yongfei Dong and
Hao Sun and
Xichao Wang and
Zaixiang Tang},
title = {A non-negative spike-and-slab lasso generalized linear stacking prediction
modeling method for high-dimensional omics data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {119},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05741-6},
doi = {10.1186/S12859-024-05741-6},
timestamp = {Thu, 11 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShenWDSWT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SherinaMPLLM24,
author = {Valeriia Sherina and
Helene R. McMurray and
Winslow Powers and
Hartmut Land and
Tanzy M. T. Love and
Matthew N. McCall},
title = {Correction: Multiple imputation and direct estimation for qPCR data
with non-detects},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {63},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05653-5},
doi = {10.1186/S12859-024-05653-5},
timestamp = {Thu, 22 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SherinaMPLLM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SilvaSN24,
author = {Rafael Peres da Silva and
Chayaporn Suphavilai and
Niranjan Nagarajan},
title = {MetageNN: a memory-efficient neural network taxonomic classifier robust
to sequencing errors and missing genomes},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {153},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05760-3},
doi = {10.1186/S12859-024-05760-3},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SilvaSN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SimeonRLCBP24,
author = {Andrea Simeon and
Milos Radovanovic and
Tatjana Loncar{-}Turukalo and
Michelangelo Ceci and
Sanja Brdar and
Gianvito Pio},
title = {Multi-class boosting for the analysis of multiple incomplete views
on microbiome data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {188},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05767-w},
doi = {10.1186/S12859-024-05767-W},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SimeonRLCBP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SkublenyGSSR24,
author = {Daniel Skubleny and
Sunita Ghosh and
Jennifer Spratlin and
Daniel E. Schiller and
Gina R. Rayat},
title = {Feature-specific quantile normalization and feature-specific mean-variance
normalization deliver robust bi-directional classification and feature
selection performance between microarray and RNAseq data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {136},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05759-w},
doi = {10.1186/S12859-024-05759-W},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SkublenyGSSR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SmelkoKBN24,
author = {Adam Smelko and
Miroslav Kratochv{\'{\i}}l and
Emmanuel Barillot and
Vincent No{\"{e}}l},
title = {Maboss for {HPC} environments: implementations of the continuous time
Boolean model simulator for large {CPU} clusters and {GPU} accelerators},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {199},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05815-5},
doi = {10.1186/S12859-024-05815-5},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SmelkoKBN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StephensK24,
author = {Zachary Stephens and
Jean{-}Pierre A. Kocher},
title = {Characterization of telomere variant repeats using long reads enables
allele-specific telomere length estimation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {194},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05807-5},
doi = {10.1186/S12859-024-05807-5},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/StephensK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SunJZ24,
author = {Wenyuan Sun and
Kyongson Jon and
Wensheng Zhu},
title = {Multiple phenotype association tests based on sliced inverse regression},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {144},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05731-8},
doi = {10.1186/S12859-024-05731-8},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SunJZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TangWOW24,
author = {Huanrong Tang and
Yaowu Wang and
Jianquan Ouyang and
Jinlin Wang},
title = {Simcryocluster: a semantic similarity clustering method of cryo-EM
images by adopting contrastive learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {77},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05565-w},
doi = {10.1186/S12859-023-05565-W},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TangWOW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ToSRBTMAK24,
author = {Kimberly To and
Judy Strickland and
Emily Reinke and
Alexandre Borrel and
Jim Truax and
Heather Maldonado and
David G. Allen and
Nicole C. Kleinstreuer},
title = {Computational application of internationally harmonized defined approaches
to skin sensitization: {DASS} App},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {4},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05617-1},
doi = {10.1186/S12859-023-05617-1},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ToSRBTMAK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TuWXS24,
author = {Gang Tu and
Xuan Wang and
Rong Xia and
Bowen Song},
title = {m6A-TCPred: a web server to predict tissue-conserved human m\({}^{\mbox{6}}\)A
sites using machine learning approach},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {127},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05738-1},
doi = {10.1186/S12859-024-05738-1},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TuWXS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TutsoyK24,
author = {Onder Tutsoy and
Gizem Gul Ko{\c{c}}},
title = {Deep self-supervised machine learning algorithms with a novel feature
elimination and selection approaches for blood test-based multi-dimensional
health risks classification},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {103},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05729-2},
doi = {10.1186/S12859-024-05729-2},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TutsoyK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VanAMGRNH24,
author = {Richard Van and
Daniel Alvarez and
Travis Mize and
Sravani Gannavarapu and
Lohitha Chintham Reddy and
Fatma Nasoz and
Mira V. Han},
title = {A comparison of RNA-Seq data preprocessing pipelines for transcriptomic
predictions across independent studies},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {181},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05801-x},
doi = {10.1186/S12859-024-05801-X},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VanAMGRNH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VazquezGonzalezRBBTC24,
author = {Lara V{\'{a}}zquez{-}Gonz{\'{a}}lez and
Alba Regueira{-}Iglesias and
Carlos Balsa{-}Castro and
Nicol{\'{a}}s Vila Blanco and
Inmaculada Tom{\'{a}}s and
Mar{\'{\i}}a J. Carreira},
title = {PrimerEvalPy: a tool for in-silico evaluation of primers for targeting
the microbiome},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {189},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05805-7},
doi = {10.1186/S12859-024-05805-7},
timestamp = {Sun, 19 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VazquezGonzalezRBBTC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VennLZM24,
author = {Benedikt Venn and
Thomas Leifeld and
Ping Zhang and
Timo M{\"{u}}hlhaus},
title = {Temporal classification of short time series data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {30},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05636-6},
doi = {10.1186/S12859-024-05636-6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/VennLZM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VermaRM24,
author = {Ghanshyam Verma and
Dietrich Rebholz{-}Schuhmann and
Michael G. Madden},
title = {Enabling personalised disease diagnosis by combining a patient's time-specific
gene expression profile with a biomedical knowledge base},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {62},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05674-0},
doi = {10.1186/S12859-024-05674-0},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/VermaRM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VoglKYKKBMM24,
author = {Claus Vogl and
Mariia Karapetiants and
Bur{\c{c}}in Yildirim and
Hr{\"{o}}nn Kjartansd{\'{o}}ttir and
Carolin Kosiol and
Juraj Bergman and
Michal Majka and
Lynette Caitlin Mikula},
title = {Inference of genomic landscapes using ordered Hidden Markov Models
with emission densities (oHMMed)},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {151},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05751-4},
doi = {10.1186/S12859-024-05751-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VoglKYKKBMM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WalshSBHVJRKKHKJK24,
author = {Jesse R. Walsh and
Guangchao Sun and
Jagadheshwar Balan and
Jayson Hardcastle and
Jason Vollenweider and
Calvin Jerde and
Kandelaria Rumilla and
Christy Koellner and
Alaa Koleilat and
Linda Hasadsri and
Benjamin Kipp and
W. Garrett Jenkinson and
Eric W. Klee},
title = {A supervised learning method for classifying methylation disorders},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {66},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05673-1},
doi = {10.1186/S12859-024-05673-1},
timestamp = {Thu, 22 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WalshSBHVJRKKHKJK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangHWZSZ24,
author = {Honglei Wang and
Tao Huang and
Dong Wang and
Wenliang Zeng and
Yanjing Sun and
Lin Zhang},
title = {{MSCAN:} multi-scale self- and cross-attention network for {RNA} methylation
site prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {32},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05649-1},
doi = {10.1186/S12859-024-05649-1},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangHWZSZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangJLTAWY24,
author = {Ruimin Wang and
Hengxuan Jiang and
Miaoshan Lu and
Junjie Tong and
Shaowei An and
Jinyin Wang and
Changbin Yu},
title = {MRMPro: a web-based tool to improve the speed of manual calibration
for multiple reaction monitoring data analysis by mass spectrometry},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {60},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05685-x},
doi = {10.1186/S12859-024-05685-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangJLTAWY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangLSS24,
author = {Hengkang Wang and
Han Lu and
Ju Sun and
Sandra E. Safo},
title = {Interpretable deep learning methods for multiview learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {69},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05679-9},
doi = {10.1186/S12859-024-05679-9},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangLSS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangLWW24,
author = {Dong Wang and
Jie Li and
Edwin Wang and
Yadong Wang},
title = {{DVA:} predicting the functional impact of single nucleotide missense
variants},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {100},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05709-6},
doi = {10.1186/S12859-024-05709-6},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangLWW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangLZL24,
author = {Shuo Wang and
Yuanning Liu and
Hao Zhang and
Zhen Liu},
title = {SurvConvMixer: robust and interpretable cancer survival prediction
based on ConvMixer using pathway-level gene expression images},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {133},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05745-2},
doi = {10.1186/S12859-024-05745-2},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangLZL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangNMCWZZC24,
author = {Lifei Wang and
Rui Nie and
Xuexia Miao and
Yankai Cai and
Anqi Wang and
Hanwen Zhang and
Jiang Zhang and
Jun Cai},
title = {InClust+: the deep generative framework with mask modules for multimodal
data integration, imputation, and cross-modal generation},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {41},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05656-2},
doi = {10.1186/S12859-024-05656-2},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangNMCWZZC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangS24,
author = {Gao{-}Fei Wang and
Longying Shen},
title = {Cauchy hyper-graph Laplacian nonnegative matrix factorization for
single-cell RNA-sequencing data analysis},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {169},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05797-4},
doi = {10.1186/S12859-024-05797-4},
timestamp = {Sun, 05 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WeiLS24,
author = {Jiahao Wei and
Linzhang Lu and
Tie Shen},
title = {Predicting drug-protein interactions by preserving the graph information
of multi source data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {10},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05620-6},
doi = {10.1186/S12859-023-05620-6},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WeiLS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WeiZZXXWXYF24,
author = {Zhenyu Wei and
Chengkui Zhao and
Min Zhang and
Jiayu Xu and
Nan Xu and
Shiwei Wu and
Xiaohui Xin and
Lei Yu and
Weixing Feng},
title = {PrCRS: a prediction model of severe {CRS} in {CAR-T} therapy based
on transfer learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {197},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05804-8},
doi = {10.1186/S12859-024-05804-8},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WeiZZXXWXYF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WestrinKE24,
author = {Karl Johan Westrin and
Warren Kretzschmar and
Olof Emanuelsson},
title = {ClusTrast: a short read de novo transcript isoform assembler guided
by clustered contigs},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {54},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05663-3},
doi = {10.1186/S12859-024-05663-3},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WestrinKE24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuHZHSYZW24,
author = {Xiaotian Wu and
Wenju Hou and
Ziqi Zhao and
Lan Huang and
Nan Sheng and
Qixing Yang and
Shuangquan Zhang and
Yan Wang},
title = {{MMGAT:} a graph attention network framework for ATAC-seq motifs finding},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {158},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05774-x},
doi = {10.1186/S12859-024-05774-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WuHZHSYZW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuMZ24,
author = {Chengzhou Wu and
Xichen Mou and
Hongmei Zhang},
title = {Gbdmr: identifying differentially methylated CpG regions in the human
genome via generalized beta regressions},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {97},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05711-y},
doi = {10.1186/S12859-024-05711-Y},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WuMZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XiePL24,
author = {Yuke Xie and
Xueqing Peng and
Peiluan Li},
title = {{MIWE:} detecting the critical states of complex biological systems
by the mutual information weighted entropy},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {44},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05667-z},
doi = {10.1186/S12859-024-05667-Z},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XiePL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XingY24,
author = {Hanwen Xing and
Christopher Yau},
title = {Bayesian inference for identifying tumour-specific cancer dependencies
through integration of ex-vivo drug response assays and drug-protein
profiling},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {104},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05682-0},
doi = {10.1186/S12859-024-05682-0},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XingY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XuBLTHRZH24,
author = {Qingru Xu and
Xiaoqiong Bao and
Zhuobin Lin and
Lin Tang and
Li{-}na He and
Jian Ren and
Zhixiang Zuo and
Kunhua Hu},
title = {AStruct: detection of allele-specific {RNA} secondary structure in
structuromic probing data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {91},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05704-x},
doi = {10.1186/S12859-024-05704-X},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XuBLTHRZH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XuQWZGH24,
author = {Xiaolu Xu and
Zitong Qi and
Lei Wang and
Meiwei Zhang and
Zhaohong Geng and
Xiumei Han},
title = {Gsw-fi: a {GLM} model incorporating shrinkage and double-weighted
strategies for identifying cancer driver genes with functional impact},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {99},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05707-8},
doi = {10.1186/S12859-024-05707-8},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XuQWZGH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangWH24,
author = {Tingpeng Yang and
Yu Wang and
Yonghong He},
title = {TEC-miTarget: enhancing microRNA target prediction based on deep learning
of ribonucleic acid sequences},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {159},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05780-z},
doi = {10.1186/S12859-024-05780-Z},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YangWH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YaoCWGCYWYLYW24,
author = {Tianhua Yao and
Xicheng Chen and
Haojia Wang and
Chengcheng Gao and
Jia Chen and
Dali Yi and
Zeliang Wei and
Ning Yao and
Yang Li and
Dong Yi and
Yazhou Wu},
title = {Deep evolutionary fusion neural network: a new prediction standard
for infectious disease incidence rates},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {38},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05621-5},
doi = {10.1186/S12859-023-05621-5},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YaoCWGCYWYLYW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YaoDZZ24,
author = {Dengju Yao and
Yuexiao Deng and
Xiaojuan Zhan and
Xiaorong Zhan},
title = {Predicting lncRNA-disease associations using multiple metapaths in
hierarchical graph attention networks},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {46},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05672-2},
doi = {10.1186/S12859-024-05672-2},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YaoDZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YaoLZZY24,
author = {Dengju Yao and
Bailin Li and
Xiaojuan Zhan and
Xiaorong Zhan and
Liyang Yu},
title = {{GCNFORMER:} graph convolutional network and transformer for predicting
lncRNA-disease associations},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {5},
year = {2024},
url = {https://doi.org/10.1186/s12859-023-05625-1},
doi = {10.1186/S12859-023-05625-1},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YaoLZZY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuditskiyBKKS24,
author = {Konstantin Yuditskiy and
Igor Bezdvornykh and
Anastasiya Kazantseva and
Alexander Kanapin and
Anastasia Samsonova},
title = {BSXplorer: analytical framework for exploratory analysis of BS-seq
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {96},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05722-9},
doi = {10.1186/S12859-024-05722-9},
timestamp = {Mon, 11 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuditskiyBKKS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZengCL24,
author = {Xiaoting Zeng and
Weilin Chen and
Baiying Lei},
title = {{CAT-DTI:} cross-attention and Transformer network with domain adaptation
for drug-target interaction prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {141},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05753-2},
doi = {10.1186/S12859-024-05753-2},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZengCL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZengSLLWL24,
author = {Xin Zeng and
Guang{-}Peng Su and
Shu{-}Juan Li and
Shuang{-}Qing Lv and
Meng{-}Liang Wen and
Yi Li},
title = {Drug-Online: an online platform for drug-target interaction, affinity,
and binding sites identification using deep learning},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {156},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05783-w},
doi = {10.1186/S12859-024-05783-W},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZengSLLWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLLWG24,
author = {Hao Zhang and
Yang Liu and
Xiaoyan Liu and
Cheng Wang and
Maozu Guo},
title = {Equivariant score-based generative diffusion framework for 3D molecules},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {203},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05810-w},
doi = {10.1186/S12859-024-05810-W},
timestamp = {Sun, 02 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLLWG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangSLSFW24,
author = {Xu Zhang and
Ya Su and
Andrew N. Lane and
Arnold J. Stromberg and
Teresa W.{-}M. Fan and
Chi Wang},
title = {Correction: Bayesian kinetic modeling for tracer-based metabolomic
data},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {14},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05635-7},
doi = {10.1186/S12859-024-05635-7},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangSLSFW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhengSY24,
author = {Andrew Zheng and
Jim Shaw and
Yun William Yu},
title = {Mora: abundance aware metagenomic read re-assignment for disentangling
similar strains},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {161},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05768-9},
doi = {10.1186/S12859-024-05768-9},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhengSY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuCJXYZ24,
author = {Jing Zhu and
Chao Che and
Hao Jiang and
Jian Xu and
Jiajun Yin and
Zhaoqian Zhong},
title = {{SSF-DDI:} a deep learning method utilizing drug sequence and substructure
features for drug-drug interaction prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {39},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05654-4},
doi = {10.1186/S12859-024-05654-4},
timestamp = {Thu, 01 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuCJXYZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuangKFML24,
author = {Yongwen Zhuang and
Na Yeon Kim and
Lars G. Fritsche and
Bhramar Mukherjee and
Seunggeun Lee},
title = {Incorporating functional annotation with bilevel continuous shrinkage
for polygenic risk prediction},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {65},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05664-2},
doi = {10.1186/S12859-024-05664-2},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuangKFML24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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