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BMC Bioinformatics, Volume 21
Volume 21, Number 1, December 2020
- Melanie Fachet, Carina Witte, Robert J. Flassig
, Liisa K. Rihko-Struckmann, Zaid McKie-Krisberg
, Jürgen E. W. Polle, Kai Sundmacher:
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina. 1 - Mehran Aflakparast
, Geert Geeven, Mathisca C. M. de Gunst:
Bayesian mixture regression analysis for regulation of Pluripotency in ES cells. 3 - Robert Esch, Rainer Merkl
:
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. 5 - Rita Torres Sousa
, Sara Silva
, Catia Pesquita
:
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. 6 - Xihui Lin
, Paul C. Boutros:
Optimization and expansion of non-negative matrix factorization. 7 - Feixiao Long
:
Microscopy cell nuclei segmentation with enhanced U-Net. 8 - Attila Csala
, Aeilko H. Zwinderman, Michel H. Hof:
Multiset sparse partial least squares path modeling for high dimensional omics data analysis. 9 - Hiroyuki Fukuda, Kentaro Tomii
:
DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. 10 - Takoua Jendoubi
, Timothy M. D. Ebbels
:
Integrative analysis of time course metabolic data and biomarker discovery. 11 - Yan Li
, Dayou Liu, Tengfei Li, Yungang Zhu:
Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations. 12 - Sarah M. Kim, Matthew I. Peña, Mark Moll
, George N. Bennett, Lydia E. Kavraki
:
Improving the organization and interactivity of metabolic pathfinding with precomputed pathways. 13 - Theresa A. Alexander
, Mitchell J. Machiela
:
LDpop: an interactive online tool to calculate and visualize geographic LD patterns. 14 - Martin Raden
, Teresa Müller
, Stefan Mautner
, Rick Gelhausen, Rolf Backofen:
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. 15 - Clémentine Decamps
, Florian Privé, Raphael Bacher, Daniel Jost
, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik
, Aleksandar Milosavljevic, Michael Scherer
, Michael G. B. Blum, Magali Richard
:
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software. 16 - Xueming Zheng, Xingli Fu, Kaicheng Wang, Meng Wang
:
Deep neural networks for human microRNA precursor detection. 17 - Maxime Folschette
, Vincent Legagneux
, Arnaud Poret, Lokmane Chebouba
, Carito Guziolowski, Nathalie Théret
:
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. 18 - Pavlos Stephanos Bekiaris
, Steffen Klamt
:
Automatic construction of metabolic models with enzyme constraints. 19 - Yichen He
, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi:
PRAP: Pan Resistome analysis pipeline. 20 - Thevaa Chandereng
, Anthony Gitter
:
Lag penalized weighted correlation for time series clustering. 21 - Defne Surujon
, Tim van Opijnen
:
ShinyOmics: collaborative exploration of omics-data. 22 - Antoine Buetti-Dinh
, Malte Herold
, Stephan Christel
, Mohamed El Hajjami, Francesco Delogu
, Olga Ilie, Sören Bellenberg, Paul Wilmes
, Ansgar Poetsch
, Wolfgang Sand, Mario Vera
, Igor V. Pivkin
, Ran Friedman
, Mark Dopson
:
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. 23 - Louis Ranjard, Thomas K. F. Wong, Allen G. Rodrigo:
Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage. 24 - Rudolf Jagdhuber
, Michel Lang
, Arnulf Stenzl, Jochen Neuhaus, Jörg Rahnenführer
:
Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms. 26 - Simon Memmel, Dmitri Sisario, Heiko Zimmermann
, Markus Sauer, Vladimir L. Sukhorukov
, Cholpon S. Djuzenova, Michael Flentje:
FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy. 27 - Bin Liu
, Patrick Lindner, Adan Chari Jirmo
, Ulrich Maus, Thomas Illig, David S. DeLuca
:
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. 28 - Jin-Woo Chung, Wonsuk Yang, Jong-Chan Park
:
Unsupervised inference of implicit biomedical events using context triggers. 29 - Arran K. Turnbull, Cigdem Selli
, Carlos Martinez-Perez
, Anu Fernando, Lorna Renshaw, Jane Keys, Jonine Figueroa
, Xiaping He, Maki Tanioka, Alison F. Munro
, Lee Murphy
, Angie Fawkes
, Richard Clark
, Audrey Coutts, Charles M. Perou
, Lisa A. Carey, Michael J. Dixon, Andrew H. Sims
:
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches. 30 - Jianwei Li, Yan Huang, Qinghua Cui, Yuan Zhou
:
m6Acorr: an online tool for the correction and comparison of m6A methylation profiles. 31 - Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Minh Thanh Truong, Jiuyong Li
, Nini Rao, Thuc Duy Le:
Correction to: Identifying miRNA synergism using multiple-intervention causal inference. 32 - Satya Nanda Vel Arjunan
, Atsushi Miyauchi, Kazunari Iwamoto
, Koichi Takahashi:
pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems. 33 - Mikolaj Rybinski
, Simon Möller, Mikael Sunnåker
, Claude Lormeau
, Jörg Stelling
:
TopoFilter: a MATLAB package for mechanistic model identification in systems biology. 34 - Huiwei Zhou
, Shixian Ning, Zhe Liu, Chengkun Lang, Zhuang Liu, Bizun Lei:
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes. 35 - Miriam Sieg
, Gesa Richter
, Arne S. Schaefer
, Jochen Kruppa
:
Detection of suspicious interactions of spiking covariates in methylation data. 36 - Samuel E. Barnett
, Daniel H. Buckley
:
Simulating metagenomic stable isotope probing datasets with MetaSIPSim. 37 - Junhua Zhou, Minqiong Zhao, Zefang Sun, Feilong Wu, Yucong Liu, Xianghua Liu, Zuping He, Quan-Ze He
, Quan-Yuan He
:
BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS. 38 - Samuel T. Westreich
, Maria Nattestad
, Christopher Meyer
:
BigTop: a three-dimensional virtual reality tool for GWAS visualization. 39 - Tomasz Zok
, Mariusz Popenda
, Marta Szachniuk
:
ElTetrado: a tool for identification and classification of tetrads and quadruplexes. 40 - Zhiqiang Yan, Xiaohui Zhu, Yuqian Wang, Yanli Nie, Shuo Guan, Ying Kuo, Di Chang, Rong Li, Jie Qiao, Liying Yan
:
scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data. 41 - Lachlan Coff
, Jeffrey Chan
, Paul A. Ramsland, Andrew J. Guy
:
Identifying glycan motifs using a novel subtree mining approach. 42 - Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang, Guohua Wang:
ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles. 43 - Laurent S. V. Thomas
, Jochen Gehrig
:
Multi-template matching: a versatile tool for object-localization in microscopy images. 44 - Izaak Coleman
, Giacomo Corleone
, James Arram, Ho-Cheung Ng, Luca Magnani, Wayne Luk:
GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes. 45 - Valentino Palombo
, Marco Milanesi
, Gabriella Sferra
, Stefano Capomaccio, Sandy Sgorlon, Mariasilvia D'Andrea
:
PANEV: an R package for a pathway-based network visualization. 46 - Lvxing Zhu
, Haoran Zheng:
Biomedical event extraction with a novel combination strategy based on hybrid deep neural networks. 47 - Kun Gao
, Jonathan Miller:
Primary orthologs from local sequence context. 48 - Konstantinos Pliakos
, Celine Vens:
Drug-target interaction prediction with tree-ensemble learning and output space reconstruction. 49 - Junwei Luo, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo, Chaokun Yan:
Correction to: SLR: a scaffolding algorithm based on long reads and contig classification. 50 - Qiaoyue Liu, Xiang Cheng, Gan Liu, Bohao Li, Xiuqin Liu
:
Deep learning improves the ability of sgRNA off-target propensity prediction. 51 - Sinead E. Morris
, Luise Dziobek-Garrett, Andrew J. Yates:
ushr: Understanding suppression of HIV in R. 52 - S. K. Hong
, Jae-Gil Lee
:
DTranNER: biomedical named entity recognition with deep learning-based label-label transition model. 53 - Mattia Chiesa
, Giada Maioli, Gualtiero I. Colombo
, Luca Piacentini
:
GARS: Genetic Algorithm for the identification of a Robust Subset of features in high-dimensional datasets. 54 - Jia Li, Yue Yin, Mutian Zhang, Jie Cui
, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
:
GsmPlot: a web server to visualize epigenome data in NCBI. 55 - Gaurav Kumar, Adam Ertel, George Feldman, Joan Kupper, Paolo Fortina
:
iSeqQC: a tool for expression-based quality control in RNA sequencing. 56 - Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong, Chunhua Li:
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification. 57 - Celine Everaert
, Pieter-Jan Volders, Annelien Morlion
, Olivier Thas, Pieter Mestdagh
:
SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups. 58 - Marta B. Lopes
, Susana Vinga:
Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data. 59 - Hai-Cheng Yi
, Zhu-Hong You
, Mei-Neng Wang, Zhen-Hao Guo, Yan-Bin Wang, Ji-Ren Zhou:
RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. 60 - Zhen Gao, Yu-Tian Wang, Qing-Wen Wu, Jian-Cheng Ni, Chun-Hou Zheng:
Graph regularized L2, 1-nonnegative matrix factorization for miRNA-disease association prediction. 61 - Mrinmoy Das, Tarini Shankar Ghosh, Ian B. Jeffery
:
IPCO: Inference of Pathways from Co-variance analysis. 62 - Eugene Lin, Sudipto Mukherjee, Sreeram Kannan:
A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis. 64 - Vasudha Sharma, Sharmistha Majumdar
:
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes. 65 - Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes
:
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. 66 - Gong-Hua Li
, Shaoxing Dai, Feifei Han
, Wenxin Li
, Jingfei Huang, Wenzhong Xiao
:
FastMM: an efficient toolbox for personalized constraint-based metabolic modeling. 67 - Yu-Chuan Chang, June-Tai Wu, Ming-Yi Hong, Yi-An Tung, Ping-Han Hsieh, Sook Wah Yee, Kathleen M. Giacomini, Yen-Jen Oyang, Chien-Yu Chen
:
GenEpi: gene-based epistasis discovery using machine learning. 68 - Ricardo Andrade, Mahdi Doostmohammadi
, João L. Santos, Marie-France Sagot, Nuno P. Mira
, Susana Vinga
:
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering. 69 - Emanuele Pio Barracchia
, Gianvito Pio
, Domenica D'Elia
, Michelangelo Ceci
:
Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. 70 - Ying Xin, Bree Cummins
, Tomás Gedeon
:
Multistability in the epithelial-mesenchymal transition network. 71 - Anna Jaeschke
, Hagen Eckert
, Laura J. Bray
:
proMAD: semiquantitative densitometric measurement of protein microarrays. 72 - Mark R. Segal, Kipper Fletez-Brant:
Assessing stationary distributions derived from chromatin contact maps. 73 - Michelle L. Treiber, Diana H. Taft
, Ian Korf, David A. Mills, Danielle G. Lemay
:
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. 74 - Lucile Mégret
, Satish Sasidharan Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski, Christian Néri
:
Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington's disease mice. 75 - Xingyu Zheng, Christopher I. Amos, H. Robert Frost
:
Comparison of pathway and gene-level models for cancer prognosis prediction. 76 - Robert A. Dromms, Justin Y. Lee
, Mark P. Styczynski
:
LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. 93 - Lotte B. Romijn
, Axel A. Almet, Chin Wee Tan, James M. Osborne
:
Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt. 95 - Nicholas Stoler, Barbara Arbeithuber
, Gundula Povysil, Monika Heinzl, Renato Salazar
, Kateryna D. Makova, Irene Tiemann-Boege, Anton Nekrutenko
:
Family reunion via error correction: an efficient analysis of duplex sequencing data. 96 - Lanling Zhao, Han Liu, Xiguo Yuan, Kun Gao, Junbo Duan
:
Comparative study of whole exome sequencing-based copy number variation detection tools. 97 - David Soong
, Jeran Stratford
, Herve Avet-Loiseau, Nizar Bahlis, Faith Davies, Angela Dispenzieri, A. Kate Sasser, Jordan M. Schecter, Ming Qi, Chad Brown, Wendell D. Jones
, Jonathan J. Keats, Daniel Auclair, Christopher Chiu, Jason Powers, Michael Schaffer:
CNV Radar: an improved method for somatic copy number alteration characterization in oncology. 98 - Jianbo Zhang
, Dilip R. Panthee
:
PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data. 99 - Daniel Jordan de Abreu Santos
, John B. Cole, George E. Liu
, Paul M. Vanraden, Li Ma
:
Gamevar.f90: a software package for calculating individual gametic diversity. 100 - Hung-Ching Chang, Chiao-Pei Chu, Shu-Ju Lin, Chuhsing Kate Hsiao
:
Network hub-node prioritization of gene regulation with intra-network association. 101 - Robin Kobus, José Manuel Abuín
, André Müller
, Sören Lukas Hellmann
, Juan Carlos Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
:
A big data approach to metagenomics for all-food-sequencing. 102 - Yiqian Zhang, Michiaki Hamada
:
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. 103 - Zoltán Dezsö
, Michele Ceccarelli:
Machine learning prediction of oncology drug targets based on protein and network properties. 104 - Tsunglin Liu
, Chen-Yu Chen, An Chen-Deng, Yi-Lin Chen, Jiu-Yao Wang
, Yung-I Hou, Min-Ching Lin:
Joining Illumina paired-end reads for classifying phylogenetic marker sequences. 105 - Du Zhang
, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao
:
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. 106 - Jonas Reeb
, Theresa Wirth
, Burkhard Rost
:
Variant effect predictions capture some aspects of deep mutational scanning experiments. 107 - Joshua J. Levy
, Alexander J. Titus
, Curtis L. Petersen, Youdinghuan Chen
, Lucas A. Salas
, Brock C. Christensen:
MethylNet: an automated and modular deep learning approach for DNA methylation analysis. 108 - Jiabing Fu, Bixin Ke, Shoubin Dong:
LCQS: an efficient lossless compression tool of quality scores with random access functionality. 109 - Xiaokang Zhang
, Inge Jonassen
:
RASflow: an RNA-Seq analysis workflow with Snakemake. 110 - Cheng Yan, Fang-Xiang Wu
, Jianxin Wang, Guihua Duan:
PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences. 111 - Lei Cui, Hansheng Li, Wenli Hui, Sitong Chen, Lin Yang, Yuxin Kang, Qirong Bo, Jun Feng
:
A deep learning-based framework for lung cancer survival analysis with biomarker interpretation. 112 - Martin Lewinski
, Yannik Bramkamp, Tino Köster
, Dorothee Staiger:
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework. 113 - Gianluca Ascolani, Timothy M. Skerry, Damien Lacroix
, Enrico Dall'Ara
, Aban Shuaib
:
Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events. 114 - Konrad Grosser, Dirk Metzler
:
Modeling methylation dynamics with simultaneous changes in CpG islands. 115 - Monica J. Quinzo
, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower, Pedro A. Reche
:
Correction to: Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. 116 - Qiaofeng Ou, Jiabing Xiao, Lei Yu, Kaizhi Wu, Bangshu Xiong:
2D electrophoresis image brightness correction based on gradient interval histogram. 117 - Anna M. Nia
, Tianlong Chen, Brooke L. Barnette
, Kamil Khanipov
, Robert L. Ullrich, Suresh K. Bhavnani, Mark R. Emmett:
Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice. 118 - Aaron M. Smith
, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek, Charles K. Fisher:
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. 119 - Audrey Hulot
, Julien Chiquet
, Florence Jaffrézic, Guillem Rigaill
:
Fast tree aggregation for consensus hierarchical clustering. 120 - Guang-Hui Fu
, Yuan-Jiao Wu, Min-Jie Zong, Jianxin Pan:
Hellinger distance-based stable sparse feature selection for high-dimensional class-imbalanced data. 121 - Yahya Bokhari
, Areej Alhareeri, Tomasz Arodz
:
QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency. 122 - Ajay Abisheck Paul George, Mauricio Lacerda, Benjamin Franz Syllwasschy
, Marie-Thérèse Hopp
, Amelie Wißbrock, Diana Imhof
:
HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs. 124 - Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo
, Yuanyuan Sun, Hongfei Lin:
Exploiting sequence labeling framework to extract document-level relations from biomedical texts. 125 - Dengju Yao
, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li, Jinke Wang:
A random forest based computational model for predicting novel lncRNA-disease associations. 126 - Leilei Wu, Qinfang Deng, Ze Xu, Songwen Zhou, Chao Li, Yi-Xue Li:
A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA. 127 - Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham, Daniel Nilsson
:
pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing. 128 - Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov
:
OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images. 129 - Lea Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King
, Laurence Yang
, Freyr Jóhannsson
, Ólafur E. Sigurjónsson, Ottar Rolfsson
, Julian Heinrich
, Andreas Dräger
:
Visualizing metabolic network dynamics through time-series metabolomic data. 130 - Siqi Chen, Sudhir Ghandikota, Yadu Gautam
, Tesfaye B. Mersha
:
MI-MAAP: marker informativeness for multi-ancestry admixed populations. 131 - Sergey Shityakov
, Elena Bencurova
, Carola Förster, Thomas Dandekar:
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. 132 - Di Shao, Wenzhi Mao, Yaoguang Xing, Haipeng Gong
:
RDb2C2: an improved method to identify the residue-residue pairing in β strands. 133 - Rezvan Ehsani, Finn Drabløs
:
Enhanced identification of significant regulators of gene expression. 134 - José María Martínez-Otzeta
, Itziar Irigoien
, Basilio Sierra
, Concepción Arenas
:
ORdensity: user-friendly R package to identify differentially expressed genes. 135