default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBioinformatics, Volume 39
Volume 39, Number 1, January 2023
- Hong Zhang
, Devan V. Mehrotra, Judong Shen:
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS. - Xuezhi Xie, Pedro A. Valiente, Philip M. Kim:
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. - Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen:
PTMint database of experimentally verified PTM regulation on protein-protein interaction. - Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi, Francesco Iorio:
A heuristic algorithm solving the mutual-exclusivity-sorting problem. - Nelle Varoquaux, William S. Noble, Jean-Philippe Vert:
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. - Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin M. Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes:
JBrowse Jupyter: a Python interface to JBrowse 2. - Neda Shokraneh, Mariam Arab, Maxwell W. Libbrecht:
Integrative chromatin domain annotation through graph embedding of Hi-C data. - Shivam Kumar, Dipanka Sarmah, Shailendra Asthana, Samrat Chatterjee:
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network. - Ngoc-Quang Nguyen, Gwanghoon Jang, Hajung Kim, Jaewoo Kang:
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction. - Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh:
Hierarchical modelling of microbial communities. - José Camacho, Raffaele Vitale, David Morales-Jiménez, Carolina Gómez-Llorente:
Variable-selection ANOVA Simultaneous Component Analysis (VASCA). - Filippo Grazioli, Pierre Machart, Anja Mösch, Kai Li, Leonardo V. Castorina, Nico Pfeifer, Martin Renqiang Min:
Attentive Variational Information Bottleneck for TCR-peptide interaction prediction. - Marcus T. Moen, Iain G. Johnston:
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. - Xingqi Wu, Yi Shi, Minghui Wang, Ao Li:
CAMR: cross-aligned multimodal representation learning for cancer survival prediction. - Jinding Liu, Yaru Zhang, Yapin Shi, Yiqing Zheng, Yali Zhu, Zhuoran Guan, Danyu Shen, Daolong Dou:
FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing. - Marija Stanojevic, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar, Zoran Obradovic:
Discovering research articles containing evolutionary timetrees by machine learning. - Correction to: FASTRAL: improving scalability of phylogenomic analysis.
- Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters, Jeroen F. J. Laros:
A Boolean algebra for genetic variants. - Vamsi Nallapareddy, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. - Chenxi Zhou, Shane A. McCarthy, Richard Durbin:
YaHS: yet another Hi-C scaffolding tool. - Correction to: Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.
- Marek S. Wiewiórka, Agnieszka Szmurlo, Pawel Stankiewicz, Tomasz Gambin:
Cloud-native distributed genomic pileup operations. - Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf:
mOWL: Python library for machine learning with biomedical ontologies. - Dailin Gan, Jun Li:
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. - Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg:
GOThresher: a program to remove annotation biases from protein function annotation datasets. - Yufeng Liu, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding, Hanchuan Peng:
Tracing weak neuron fibers. - Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu:
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. - Abin Abraham, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas, John A. Capra:
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. - Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha:
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes. - Jialun Wu, Yuxin Dong, Zeyu Gao, Tieliang Gong, Chen Li:
Dual Attention and Patient Similarity Network for drug recommendation. - Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei:
A benchmark for automatic medical consultation system: frameworks, tasks and datasets. - Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. - Oluwadamilare Falola, Yagoub Adam, Olabode Ajayi, Judit Kumuthini, Suraju Adewale, Abayomi Mosaku, Chaimae Samtal, Glory O. Adebayo, Jerry Emmanuel, Milaine S. S. Tchamga, Udochukwu Erondu, Adebayo Nehemiah, Suraj Rasaq, Mary Ajayi, Bola Akanle, Olaleye Oladipo, Itunuoluwa Isewon, Marion O. Adebiyi, Jelili Oyelade, Ezekiel F. Adebiyi:
SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets. - Till Hartmann, Christopher Schröder, Elias Kuthe, David Laehnemann, Johannes Köster:
Insane in the vembrane: filtering and transforming VCF/BCF files. - Michael F. Adamer, Eljas Roellin, Lucie Bourguignon, Karsten M. Borgwardt:
SIMBSIG: similarity search and clustering for biobank-scale data. - Sergey Vilov, Matthias Heinig:
DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal. - Correction to: Targeted metabolomics analyses for brain tumor margin assessment during surgery.
- Fabricio Almeida-Silva, Tao Zhao, Kristian K. Ullrich, M. Eric Schranz, Yves Van de Peer:
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. - Hannah Schriever, Dennis Kostka:
Vaeda computationally annotates doublets in single-cell RNA sequencing data. - Expression of Concern: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking.
- Jin Xu, Jessie Jiang, Herbert M. Sauro:
SBMLDiagrams: a python package to process and visualize SBML layout and render. - Antonios Klonizakis, Christoforos Nikolaou, Thomas Graf:
SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data. - Yeonil Kim, Yueh-Yun Chi, Judong Shen, Fei Zou:
Robust genetic model-based SNP-set association test using CauchyGM. - Yohsuke T. Fukai, Kyogo Kawaguchi:
LapTrack: linear assignment particle tracking with tunable metrics. - Wei Shen, Hongyan Xiang, Tianquan Huang, Hui Tang, Mingli Peng, Dachuan Cai, Peng Hu, Hong Ren:
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping. - Sudeep Sahadevan, Thileepan Sekaran, Nadia Ashaf, Marko Fritz, Matthias W. Hentze, Wolfgang Huber, Thomas Schwarzl:
htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets. - Renming Liu, Matthew J. Hirn, Arjun Krishnan:
Accurately modeling biased random walks on weighted networks using node2vec+. - Afshan Nabi, Berke Dilekoglu, Ogun Adebali, Öznur Tastan:
Discovering misannotated lncRNAs using deep learning training dynamics. - Yonghyun Nam, Sang-Hyuk Jung, Jae-Seung Yun, Vivek Sriram, Pankhuri Singhal, Marta Byrska-Bishop, Anurag Verma, Hyunjung Shin, Woong-Yang Park, Hong-Hee Won, Dokyoon Kim:
Discovering comorbid diseases using an inter-disease interactivity network based on biobank-scale PheWAS data. - Lewis Chinery, Newton Wahome, Iain Moal, Charlotte M. Deane:
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors. - Robert Hanes, Pilar Ayuda-Durán, Leiv Rønneberg, Sigve Nakken, Eivind Hovig, Manuela Zucknick, Jorrit M. Enserink:
screenwerk: a modular tool for the design and analysis of drug combination screens. - John C. Braisted, Andrew Patt, Cole Tindall, Timothy Sheils, Jorge Neyra, Kyle Spencer, Tara Eicher, Ewy A Mathé:
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. - Yanyan Diao, Feng Hu, Zihao Shen, Honglin Li:
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities. - Leonardo V. Castorina, Rokas Petrenas, Kartic Subr, Christopher W. Wood:
PDBench: evaluating computational methods for protein-sequence design. - Neng Huang, Minghua Xu, Fan Nie, Peng Ni, Chuan-Le Xiao, Feng Luo, Jianxin Wang:
NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data. - Nicola Apollonio, Daniel Blankenberg, Fabio Cumbo, Paolo Giulio Franciosa, Daniele Santoni:
Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks. - Thao Vu, Elizabeth Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell Bowler, Farnoush Banaei Kashani, Katerina J. Kechris:
NetSHy: network summarization via a hybrid approach leveraging topological properties. - Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijevic, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki:
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. - Qing Mo, Zexin Xu, Hui Yan, Pin Chen, Yutong Lu:
VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2. - Sandra Díaz-Seoane, Xabier Rey-Barreiro, Alejandro F. Villaverde:
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability. - Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam:
Insights from incorporating quantum computing into drug design workflows. - Heng Li:
Protein-to-genome alignment with miniprot. - Ke Yan, Hongwu Lv, Yichen Guo, Wei Peng, Bin Liu:
sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure. - Laura Luebbert, Lior Pachter:
Efficient querying of genomic reference databases with gget. - Caleb A. Class, Caiden J. Lukan, Christopher A. Bristow, Kim-Anh Do:
Easy NanoString nCounter data analysis with the NanoTube. - Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca:
Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease. - Benoit Morel, Tom A. Williams, Alexandros Stamatakis:
Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. - Ha Vu, Zane Koch, Petko Fiziev, Jason Ernst:
A framework for group-wise summarization and comparison of chromatin state annotations. - Wanying Zhu, Hung-Hsin Chen, Alexander S. Petty, Lauren E. Petty, Hannah G. Polikowsky, Eric R. Gamazon, Jennifer E. Below, Heather M. Highland:
IMMerge: merging imputation data at scale. - Ege Ülgen, Ozan Ozisik, Osman Ugur Sezerman:
PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology. - Jiansi Gao, Michael R. May, Bruce Rannala, Brian R. Moore:
PrioriTree: a utility for improving phylodynamic analyses in BEAST. - Correction to: Biomedical evidence engineering for data-driven discovery.
- Diksha Bhalla, Marvin N. Steijaert, Eefje S. Poppelaars, Marc Teunis, Monique van der Voet, Marie Corradi, Elisabeth Dévière, Luke Noothout, Wilco Tomassen, Martijn Rooseboom, Richard A. Currie, Cyrille Krul, Raymond H. H. Pieters, Vera van Noort, Marjolein Wildwater:
DARTpaths, an in silico platform to investigate molecular mechanisms of compounds. - Heng Li, Mijuan Shi, Keyi Ren, Lei Zhang, Weidong Ye, Wanting Zhang, Yingyin Cheng, Xiaoqin Xia:
Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. - Runzhou Yu, Dehan Cai, Yanni Sun:
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data. - Andrea Vandelli, Magdalena Arnal Segura, Michele Monti, Jonathan Fiorentino, Laura Broglia, Alessio Colantoni, Natalia Sanchez de Groot, Marc Torrent Burgas, Alexandros Armaos, Gian Gaetano Tartaglia:
The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates. - Rasmus Amund Henriksen, Lei Zhao, Thorfinn Sand Korneliussen:
NGSNGS: next-generation simulator for next-generation sequencing data. - Alexander Kramer, Theo Sanderson, Russell Corbett-Detig:
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes. - Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu:
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. - Yu K. Mo, Robert Lanfear, Matthew W. Hahn, Bui Quang Minh:
Updated site concordance factors minimize effects of homoplasy and taxon sampling. - Qinhu Zhang, Pengrui Teng, Siguo Wang, Ying He, Zhen Cui, Zhenghao Guo, Yixin Liu, Changan Yuan, Qi Liu, De-Shuang Huang:
Computational prediction and characterization of cell-type-specific and shared binding sites. - Kaibin Huang, Shengyun Huang, Guojing Chen, Xue Li, Shawn Li, Ying Liang, Yi Gao:
An end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning. - Iván Martín Hernández, Yves Dehouck, Ugo Bastolla, José Ramón López-Blanco, Pablo Chacón:
Predicting protein stability changes upon mutation using a simple orientational potential. - Tao Wang, Jinjin Yang, Yifu Xiao, Jingru Wang, Yuxian Wang, Xi Zeng, Yongtian Wang, Jiajie Peng:
DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. - Micha Sam Brickman Raredon, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason, Yuval Kluger:
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. - Junhang Pan, Xiangchen Li, Mingwu Zhang, Yewei Lu, Yelei Zhu, Kunyang Wu, Yiwen Wu, Weixin Wang, Bin Chen, Zhengwei Liu, Xiaomeng Wang, Junshun Gao:
TransFlow: a Snakemake workflow for transmission analysis ofMycobacterium tuberculosiswhole-genome sequencing data. - Gavin M. Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro:
Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. - Ajay Anand Kumar, Bart Loeys, Gerarda Van De Beek, Nils Peeters, Wim Wuyts, Lut Van Laer, Geert Vandeweyer, Maaike Alaerts:
varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data. - Irbaz I Badshah, Pedro R. Cutillas:
Systematic identification of biochemical networks in cancer cells by functional pathway inference analysis. - Jaime Martínez de Villarreal, Mark Kalisz, Gabriel Piedrafita, Osvaldo Graña-Castro, Dafni Chondronasiou, Manuel Serrano, Francisco X. Real:
Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data. - Musu Yuan, Liang Chen, Minghua Deng:
Clustering single-cell multi-omics data with MoClust. - Samuel Martin, Martin Ayling, Livia Patrono, Mario Cáccamo, Pablo Murcia, Richard M. Leggett:
Capturing variation in metagenomic assembly graphs with MetaCortex. - Roshan Kulkarni, Yudi Zhang, Steven B. Cannon, Karin S. Dorman:
CAPG: comprehensive allopolyploid genotyper. - Marine Jeanmougin, Hans Petter Brodal, Heidi Dietrichson Pharo, Hege Marie Vedeld, Guro Elisabeth Lind:
PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data. - Kiran Javkar, Hugh Rand, Errol Strain, Mihai Pop:
PRAWNS: compact pan-genomic features for whole-genome population genomics. - Masaki Asada, Makoto Miwa, Yutaka Sasaki:
Integrating heterogeneous knowledge graphs into drug-drug interaction extraction from the literature. - Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi:
Metadata retrieval from sequence databases with ffq. - Trevor Manz, Sehi L'Yi, Nils Gehlenborg:
Gos: a declarative library for interactive genomics visualization in Python. - Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker:
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. - Jaesub Park, Sangyeon Lee, Kwansoo Kim, Jaegyun Jung, Doheon Lee:
Large-scale prediction of adverse drug reactions-related proteins with network embedding. - Erik Garrison, Andrea Guarracino:
Unbiased pangenome graphs. - Philip C. Dishuck, Allison N. Rozanski, Glennis Logsdon, David Porubsky, Evan E. Eichler:
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads. - Henry Cousins, Taryn Hall, Yinglong Guo, Luke Tso, Kathy T. H. Tzeng, Le Cong, Russ B. Altman:
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. - Adam Platt, E. Josiah Lutton, Edward Offord, Till Bretschneider:
MiCellAnnGELo: annotate microscopy time series of complex cell surfaces with 3D virtual reality. - Chunyu Zhao, Boris Dimitrov, Miriam Goldman, Stephen Nayfach, Katherine S. Pollard:
MIDAS2: Metagenomic Intra-species Diversity Analysis System. - Philip T. L. C. Clausen:
Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining. - Xiaoyu Guan, Zhongnian Li, Yueying Zhou, Wei Shao, Daoqiang Zhang:
Active learning for efficient analysis of high-throughput nanopore data. - Lulu Yan, Xiaoqiang Sun:
Benchmarking and integration of methods for deconvoluting spatial transcriptomic data.