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Volume 22;  2021

Database

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm
Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira, Raquel C. de Melo-Minardi
BMC Bioinformatics. 2021; 22: 1. Published online 2021 Jan 2. doi: 10.1186/s12859-020-03881-z
PMCID:
PMC7776311
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H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection
Nan Zhou, Jinku Bao, Yuping Ning
BMC Bioinformatics. 2021; 22: 18. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03935-2
PMCID:
PMC7789886
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Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines
Marcos José Andrade Viana, Adhemar Zerlotini, Mauricio de Alvarenga Mudadu
BMC Bioinformatics. 2021; 22: 46. Published online 2021 Feb 5. doi: 10.1186/s12859-020-03792-z
PMCID:
PMC7863420
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GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms
Paulien Adamse, Emilie Dagand, Karen Bohmert-Tatarev, Daniela Wahler, Manoela Miranda, Esther J. Kok, Joachim Bendiek
BMC Bioinformatics. 2021; 22: 48. Published online 2021 Feb 5. doi: 10.1186/s12859-020-03880-0
PMCID:
PMC7863250
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Software

recoup: flexible and versatile signal visualization from next generation sequencing
Panagiotis Moulos
BMC Bioinformatics. 2021; 22: 2. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03902-x
PMCID:
PMC7789646
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SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva
BMC Bioinformatics. 2021; 22: 4. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03770-5
PMCID:
PMC7788957
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MiBiOmics: an interactive web application for multi-omics data exploration and integration
Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
BMC Bioinformatics. 2021; 22: 6. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03921-8
PMCID:
PMC7789220
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DISTEVAL: a web server for evaluating predicted protein distances
Badri Adhikari, Bikash Shrestha, Matthew Bernardini, Jie Hou, Jamie Lea
BMC Bioinformatics. 2021; 22: 8. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03938-z
PMCID:
PMC7788990
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PCirc: random forest-based plant circRNA identification software
Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun, Guanglin Li
BMC Bioinformatics. 2021; 22: 10. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03944-1
PMCID:
PMC7789375
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MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes
Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis
BMC Bioinformatics. 2021; 22: 11. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03940-5
PMCID:
PMC7789693
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G-Tric: generating three-way synthetic datasets with triclustering solutions
João Lobo, Rui Henriques, Sara C. Madeira
BMC Bioinformatics. 2021; 22: 16. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03925-4
PMCID:
PMC7789692
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MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning
Eliza Dhungel, Yassin Mreyoud, Ho-Jin Gwak, Ahmad Rajeh, Mina Rho, Tae-Hyuk Ahn
BMC Bioinformatics. 2021; 22: 25. Published online 2021 Jan 18. doi: 10.1186/s12859-020-03933-4
PMCID:
PMC7814621
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GECO: gene expression clustering optimization app for non-linear data visualization of patterns
A. N. Habowski, T. J. Habowski, M. L. Waterman
BMC Bioinformatics. 2021; 22: 29. Published online 2021 Jan 25. doi: 10.1186/s12859-020-03951-2
PMCID:
PMC7831185
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P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps
Takuma Nishimaki, Keiko Sato
BMC Bioinformatics. 2021; 22: 36. Published online 2021 Jan 30. doi: 10.1186/s12859-021-03978-z
PMCID:
PMC7847139
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IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
Ana M. Vasconcelos, Maria Beatriz Carmo, Beatriz Ferreira, Inês Viegas, Margarida Gama-Carvalho, António Ferreira, Andreia J. Amaral
BMC Bioinformatics. 2021; 22: 37. Published online 2021 Feb 1. doi: 10.1186/s12859-021-03955-6
PMCID:
PMC7852101
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DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
BMC Bioinformatics. 2021; 22: 38. Published online 2021 Feb 1. doi: 10.1186/s12859-020-03952-1
PMCID:
PMC7852092
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tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda E. Kroehl
BMC Bioinformatics. 2021; 22: 41. Published online 2021 Feb 1. doi: 10.1186/s12859-021-03967-2
PMCID:
PMC7852128
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IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences
Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts
BMC Bioinformatics. 2021; 22: 51. Published online 2021 Feb 6. doi: 10.1186/s12859-021-03983-2
PMCID:
PMC7866733
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Visual4DTracker: a tool to interact with 3D + t image stacks
Ermanno Cordelli, Paolo Soda, Giulio Iannello
BMC Bioinformatics. 2021; 22: 53. Published online 2021 Feb 8. doi: 10.1186/s12859-020-03820-y
PMCID:
PMC7869512
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NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences
Elma H. Akand, John M. Murray
BMC Bioinformatics. 2021; 22: 54. Published online 2021 Feb 8. doi: 10.1186/s12859-020-03901-y
PMCID:
PMC7869453
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lncEvo: automated identification and conservation study of long noncoding RNAs
Oleksii Bryzghalov, Izabela Makałowska, Michał Wojciech Szcześniak
BMC Bioinformatics. 2021; 22: 59. Published online 2021 Feb 9. doi: 10.1186/s12859-021-03991-2
PMCID:
PMC7871587
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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets
Ryan D. Crawford, Evan S. Snitkin
BMC Bioinformatics. 2021; 22: 70. Published online 2021 Feb 15. doi: 10.1186/s12859-021-03981-4
PMCID:
PMC7885345
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PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
BMC Bioinformatics. 2021; 22: 72. Published online 2021 Feb 17. doi: 10.1186/s12859-021-03984-1
PMCID:
PMC7890960
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CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Xiao Wen, Lin Gao, Tuo Song, Chaoqun Jiang
BMC Bioinformatics. 2021; 22: 75. Published online 2021 Feb 18. doi: 10.1186/s12859-021-04012-y
PMCID:
PMC7890952
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MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gian Vincenzo Zuccotti, Francesco Comandatore
BMC Bioinformatics. 2021; 22: 76. Published online 2021 Feb 18. doi: 10.1186/s12859-021-04020-y
PMCID:
PMC7891011
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FiNGS: high quality somatic mutations using filters for next generation sequencing
Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer
BMC Bioinformatics. 2021; 22: 77. Published online 2021 Feb 18. doi: 10.1186/s12859-021-03995-y
PMCID:
PMC7890800
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CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets
Matthew N. Bernstein, Zijian Ni, Michael Collins, Mark E. Burkard, Christina Kendziorski, Ron Stewart
BMC Bioinformatics. 2021; 22: 83. Published online 2021 Feb 23. doi: 10.1186/s12859-021-04021-x
PMCID:
PMC7903756
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geneRFinder: gene finding in distinct metagenomic data complexities
Raíssa Silva, Kleber Padovani, Fabiana Góes, Ronnie Alves
BMC Bioinformatics. 2021; 22: 87. Published online 2021 Feb 25. doi: 10.1186/s12859-021-03997-w
PMCID:
PMC7905635
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Pattern recognition in lymphoid malignancies using CytoGPS and Mercator
Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo, Kevin R. Coombes
BMC Bioinformatics. 2021; 22: 100. Published online 2021 Mar 1. doi: 10.1186/s12859-021-03992-1
PMCID:
PMC7923511
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PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants
Sebastian M. Siegner, Mehmet E. Karasu, Markus S. Schröder, Zacharias Kontarakis, Jacob E. Corn
BMC Bioinformatics. 2021; 22: 101. Published online 2021 Mar 2. doi: 10.1186/s12859-021-04034-6
PMCID:
PMC7923538
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InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
Dominik Jens Elias Waibel, Sayedali Shetab Boushehri, Carsten Marr
BMC Bioinformatics. 2021; 22: 103. Published online 2021 Mar 2. doi: 10.1186/s12859-021-04037-3
PMCID:
PMC7971147
Article PubReader PDF–1.3MCite
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Robert H. Dolin, Shaileshbhai R. Gothi, Aziz Boxwala, Bret S. E. Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby, Varun Suraj, Ning Xie, Srikar Chamala, Gil Alterovitz
BMC Bioinformatics. 2021; 22: 104. Published online 2021 Mar 2. doi: 10.1186/s12859-021-04039-1
PMCID:
PMC7923512
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OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons
Jakob Willforss, Valentina Siino, Fredrik Levander
BMC Bioinformatics. 2021; 22: 107. Published online 2021 Mar 4. doi: 10.1186/s12859-021-04043-5
PMCID:
PMC7931979
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SomatoSim: precision simulation of somatic single nucleotide variants
Marwan A. Hawari, Celine S. Hong, Leslie G. Biesecker
BMC Bioinformatics. 2021; 22: 109. Published online 2021 Mar 6. doi: 10.1186/s12859-021-04024-8
PMCID:
PMC7936459
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R.ROSETTA: an interpretable machine learning framework
Mateusz Garbulowski, Klev Diamanti, Karolina Smolińska, Nicholas Baltzer, Patricia Stoll, Susanne Bornelöv, Aleksander Øhrn, Lars Feuk, Jan Komorowski
BMC Bioinformatics. 2021; 22: 110. Published online 2021 Mar 6. doi: 10.1186/s12859-021-04049-z
PMCID:
PMC7937228
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Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
BMC Bioinformatics. 2021; 22: 114. Published online 2021 Mar 9. doi: 10.1186/s12859-021-04057-z
PMCID:
PMC7941695
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mtDNAcombine: tools to combine sequences from multiple studies
Eleanor F. Miller, Andrea Manica
BMC Bioinformatics. 2021; 22: 115. Published online 2021 Mar 9. doi: 10.1186/s12859-021-04048-0
PMCID:
PMC7945669
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AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Xiao Liang, Kyle Akers, Ishi Keenum, Lauren Wind, Suraj Gupta, Chaoqi Chen, Reem Aldaihani, Amy Pruden, Liqing Zhang, Katharine F. Knowlton, Kang Xia, Lenwood S. Heath
BMC Bioinformatics. 2021; 22: 117. Published online 2021 Mar 10. doi: 10.1186/s12859-021-04035-5
PMCID:
PMC7944603
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ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
Zachary Deng, Eric Delwart
BMC Bioinformatics. 2021; 22: 119. Published online 2021 Mar 12. doi: 10.1186/s12859-021-04038-2
PMCID:
PMC7953547
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stochprofML: stochastic profiling using maximum likelihood estimation in R
Lisa Amrhein, Christiane Fuchs
BMC Bioinformatics. 2021; 22: 123. Published online 2021 Mar 15. doi: 10.1186/s12859-021-03970-7
PMCID:
PMC7958472
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Alvis: a tool for contig and read ALignment VISualisation and chimera detection
Samuel Martin, Richard M. Leggett
BMC Bioinformatics. 2021; 22: 124. Published online 2021 Mar 16. doi: 10.1186/s12859-021-04056-0
PMCID:
PMC7967992
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Dualmarker: a flexible toolset for exploratory analysis of combinatorial dual biomarkers for clinical efficacy
Xiaopeng Ma, Ruiqi Huang, Xikun Wu, Pei Zhang
BMC Bioinformatics. 2021; 22: 127. Published online 2021 Mar 17. doi: 10.1186/s12859-021-04050-6
PMCID:
PMC7972341
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SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints
Yiqun Zhang, Fengju Chen, Chad J. Creighton
BMC Bioinformatics. 2021; 22: 135. Published online 2021 Mar 21. doi: 10.1186/s12859-021-04072-0
PMCID:
PMC7981925
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SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
Marius A. Wenzel, Berndt Müller, Jonathan Pettitt
BMC Bioinformatics. 2021; 22: 140. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04009-7
PMCID:
PMC7986045
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WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis
Martin Lyčka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jiří Fajkus, Miloslava Fojtová
BMC Bioinformatics. 2021; 22: 145. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04064-0
PMCID:
PMC7986547
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ATAV: a comprehensive platform for population-scale genomic analyses
Zhong Ren, Gundula Povysil, Joseph A. Hostyk, Hongzhu Cui, Nitin Bhardwaj, David B. Goldstein
BMC Bioinformatics. 2021; 22: 149. Published online 2021 Mar 23. doi: 10.1186/s12859-021-04071-1
PMCID:
PMC7988908
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SAveRUNNER: an R-based tool for drug repurposing
Giulia Fiscon, Paola Paci
BMC Bioinformatics. 2021; 22: 150. Published online 2021 Mar 23. doi: 10.1186/s12859-021-04076-w
PMCID:
PMC7987121
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m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network
Jiani Ma, Lin Zhang, Jin Chen, Bowen Song, Chenxuan Zang, Hui Liu
BMC Bioinformatics. 2021; 22: 152. Published online 2021 Mar 24. doi: 10.1186/s12859-021-04007-9
PMCID:
PMC7992861
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RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O’Brien
BMC Bioinformatics. 2021; 22: 156. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04068-w
PMCID:
PMC7992832
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SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
Lidong Guo, Mengyang Xu, Wenchao Wang, Shengqiang Gu, Xia Zhao, Fang Chen, Ou Wang, Xun Xu, Inge Seim, Guangyi Fan, Li Deng, Xin Liu
BMC Bioinformatics. 2021; 22: 158. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04081-z
PMCID:
PMC7993450
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BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
Jeremy Fan, Steven Huang, Samuel D. Chorlton
BMC Bioinformatics. 2021; 22: 160. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04089-5
PMCID:
PMC7993542
Article PubReader PDF–1.6MCite

Research Articles

Examination of hydrogen cross-feeders using a colonic microbiota model
Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy, Warren C. McNabb
BMC Bioinformatics. 2021; 22: 3. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03923-6
PMCID:
PMC7789523
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MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism
Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Youdong Pan, Qi Song, Xing Liu, Ji Wan
BMC Bioinformatics. 2021; 22: 7. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03946-z
PMCID:
PMC7787246
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Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm
Jiaxing Lu, Ming Chen, Yufang Qin
BMC Bioinformatics. 2021; 22: 13. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03949-w
PMCID:
PMC7788947
Article PubReader PDF–3.8MCite
Predicting chemosensitivity using drug perturbed gene dynamics
Joshua D. Mannheimer, Ashok Prasad, Daniel L. Gustafson
BMC Bioinformatics. 2021; 22: 15. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03947-y
PMCID:
PMC7789515
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Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform
Shengqiao Gao, Lu Han, Dan Luo, Gang Liu, Zhiyong Xiao, Guangcun Shan, Yongxiang Zhang, Wenxia Zhou
BMC Bioinformatics. 2021; 22: 17. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03915-6
PMCID:
PMC7788535
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A stack LSTM structure for decoding continuous force from local field potential signal of primary motor cortex (M1)
Mehrdad Kashefi, Mohammad Reza Daliri
BMC Bioinformatics. 2021; 22: 26. Published online 2021 Jan 22. doi: 10.1186/s12859-020-03953-0
PMCID:
PMC7821526
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SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks
Tamer N. Jarada, Jon G. Rokne, Reda Alhajj
BMC Bioinformatics. 2021; 22: 28. Published online 2021 Jan 22. doi: 10.1186/s12859-020-03950-3
PMCID:
PMC7821180
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Distance-based functional criticality in the human brain: intelligence and emotional intelligence
Lili Jiang, Kaini Qiao, Chunlin Li
BMC Bioinformatics. 2021; 22: 32. Published online 2021 Jan 26. doi: 10.1186/s12859-021-03973-4
PMCID:
PMC7836498
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Boolean implication analysis unveils candidate universal relationships in microbiome data
Daniella Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo
BMC Bioinformatics. 2021; 22: 49. Published online 2021 Feb 5. doi: 10.1186/s12859-020-03941-4
PMCID:
PMC7863539
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In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces
Hailin Chen, Zuping Zhang, Jingpu Zhang
BMC Bioinformatics. 2021; 22: 52. Published online 2021 Feb 8. doi: 10.1186/s12859-021-03988-x
PMCID:
PMC7868667
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Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images
Florent Grélard, David Legland, Mathieu Fanuel, Bastien Arnaud, Loïc Foucat, Hélène Rogniaux
BMC Bioinformatics. 2021; 22: 56. Published online 2021 Feb 8. doi: 10.1186/s12859-020-03954-z
PMCID:
PMC7869484
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Impact of concurrency on the performance of a whole exome sequencing pipeline
Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone Castellani, Enrico Giampieri
BMC Bioinformatics. 2021; 22: 60. Published online 2021 Feb 9. doi: 10.1186/s12859-020-03780-3
PMCID:
PMC7874478
Article PubReader PDF–2.2MCite
Multiple-testing correction in metabolome-wide association studies
Alina Peluso, Robert Glen, Timothy M. D. Ebbels
BMC Bioinformatics. 2021; 22: 67. Published online 2021 Feb 12. doi: 10.1186/s12859-021-03975-2
PMCID:
PMC7881646
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WACS: improving ChIP-seq peak calling by optimally weighting controls
Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins
BMC Bioinformatics. 2021; 22: 69. Published online 2021 Feb 15. doi: 10.1186/s12859-020-03927-2
PMCID:
PMC7885521
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Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes
Momoko Imakubo, Jun Takayama, Hatsumi Okada, Shuichi Onami
BMC Bioinformatics. 2021; 22: 73. Published online 2021 Feb 17. doi: 10.1186/s12859-021-03990-3
PMCID:
PMC7890843
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Grouping of genomic markers in populations with family structure
Dörte Wittenburg, Michael Doschoris, Jan Klosa
BMC Bioinformatics. 2021; 22: 79. Published online 2021 Feb 19. doi: 10.1186/s12859-021-04010-0
PMCID:
PMC7893918
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CANTARE: finding and visualizing network-based multi-omic predictive models
Janet C. Siebert, Martine Saint-Cyr, Sarah J. Borengasser, Brandie D. Wagner, Catherine A. Lozupone, Carsten Görg
BMC Bioinformatics. 2021; 22: 80. Published online 2021 Feb 19. doi: 10.1186/s12859-021-04016-8
PMCID:
PMC7896366
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Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel, Eivind Almaas
BMC Bioinformatics. 2021; 22: 81. Published online 2021 Feb 23. doi: 10.1186/s12859-021-03985-0
PMCID:
PMC7901079
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A base measure of precision for protein stability predictors: structural sensitivity
Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
BMC Bioinformatics. 2021; 22: 88. Published online 2021 Feb 25. doi: 10.1186/s12859-021-04030-w
PMCID:
PMC7908712
Article PubReader PDF–2.3MCite
Sparse data embedding and prediction by tropical matrix factorization
Amra Omanović, Hilal Kazan, Polona Oblak, Tomaž Curk
BMC Bioinformatics. 2021; 22: 89. Published online 2021 Feb 25. doi: 10.1186/s12859-021-04023-9
PMCID:
PMC7908717
Article PubReader PDF–4.0MCite
Accurate and fast mitotic detection using an anchor-free method based on full-scale connection with recurrent deep layer aggregation in 4D microscopy images
Titinunt Kitrungrotsakul, Yutaro Iwamoto, Satoko Takemoto, Hideo Yokota, Sari Ipponjima, Tomomi Nemoto, Lanfen Lin, Ruofeng Tong, Jingsong Li, Yen-Wei Chen
BMC Bioinformatics. 2021; 22: 91. Published online 2021 Feb 26. doi: 10.1186/s12859-021-04014-w
PMCID:
PMC7908657
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Biomedical articles share annotations with their citation neighbors
Raul Rodriguez-Esteban
BMC Bioinformatics. 2021; 22: 95. Published online 2021 Feb 26. doi: 10.1186/s12859-021-04044-4
PMCID:
PMC7912518
Article PubReader PDF–1.5MCite
A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications
Umesh Kathad, Aditya Kulkarni, Joseph Ryan McDermott, Jordan Wegner, Peter Carr, Neha Biyani, Rama Modali, Jean-Philippe Richard, Panna Sharma, Kishor Bhatia
BMC Bioinformatics. 2021; 22: 102. Published online 2021 Mar 2. doi: 10.1186/s12859-021-04040-8
PMCID:
PMC7923321
Article PubReader PDF–1.8MCite
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models
Fetulhak Abdurahman, Kinde Anlay Fante, Mohammed Aliy
BMC Bioinformatics. 2021; 22: 112. Published online 2021 Mar 8. doi: 10.1186/s12859-021-04036-4
PMCID:
PMC7938584
Article PubReader PDF–2.3MCite
Deep active learning for classifying cancer pathology reports
Kevin De Angeli, Shang Gao, Mohammed Alawad, Hong-Jun Yoon, Noah Schaefferkoetter, Xiao-Cheng Wu, Eric B. Durbin, Jennifer Doherty, Antoinette Stroup, Linda Coyle, Lynne Penberthy, Georgia Tourassi
BMC Bioinformatics. 2021; 22: 113. Published online 2021 Mar 9. doi: 10.1186/s12859-021-04047-1
PMCID:
PMC7941989
Article PubReader PDF–2.9MCite
Associations of longitudinal D-Dimer and Factor II on early trauma survival risk
Richard M. Jiang, Arya A. Pourzanjani, Mitchell J. Cohen, Linda Petzold
BMC Bioinformatics. 2021; 22: 122. Published online 2021 Mar 13. doi: 10.1186/s12859-021-04065-z
PMCID:
PMC7955634
Article PubReader PDF–1.1MCite
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction
Jingjing Wang, Yanpeng Zhao, Weikang Gong, Yang Liu, Mei Wang, Xiaoqian Huang, Jianjun Tan
BMC Bioinformatics. 2021; 22: 133. Published online 2021 Mar 19. doi: 10.1186/s12859-021-04069-9
PMCID:
PMC7980572
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A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations
Zhuangwei Shi, Han Zhang, Chen Jin, Xiongwen Quan, Yanbin Yin
BMC Bioinformatics. 2021; 22: 136. Published online 2021 Mar 21. doi: 10.1186/s12859-021-04073-z
PMCID:
PMC7983260
Article PubReader PDF–2.6MCite
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments
Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan Holmes
BMC Bioinformatics. 2021; 22: 137. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04067-x
PMCID:
PMC7983283
Article PubReader PDF–1.2MCite
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Weili Zhao, Xiao-Jian Sun, Jinyan Huang
BMC Bioinformatics. 2021; 22: 138. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04054-2
PMCID:
PMC7983272
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Weighted minimum feedback vertex sets and implementation in human cancer genes detection
Ruiming Li, Chun-Yu Lin, Wei-Feng Guo, Tatsuya Akutsu
BMC Bioinformatics. 2021; 22: 143. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04062-2
PMCID:
PMC7986389
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Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species
Silvia Madritsch, Agnes Burg, Eva M. Sehr
BMC Bioinformatics. 2021; 22: 146. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04078-8
PMCID:
PMC7986043
Article PubReader PDF–1.0MCite
Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals
Linjun Zhou, Deling Fan, Wei Yin, Wen Gu, Zhen Wang, Jining Liu, Yanhua Xu, Lili Shi, Mingqing Liu, Guixiang Ji
BMC Bioinformatics. 2021; 22: 151. Published online 2021 Mar 24. doi: 10.1186/s12859-020-03903-w
PMCID:
PMC7992851
Article PubReader PDF–1.6MCite
ModularBoost: an efficient network inference algorithm based on module decomposition
Xinyu Li, Wei Zhang, Jianming Zhang, Guang Li
BMC Bioinformatics. 2021; 22: 153. Published online 2021 Mar 24. doi: 10.1186/s12859-021-04074-y
PMCID:
PMC7992795
Article PubReader PDF–4.3MCite
Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat, Farzam Vaziri
BMC Bioinformatics. 2021; 22: 154. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04100-z
PMCID:
PMC7992940
Article PubReader PDF–1.0MCite
Improved two-stage model averaging for high-dimensional linear regression, with application to Riboflavin data analysis
Juming Pan
BMC Bioinformatics. 2021; 22: 155. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04053-3
PMCID:
PMC7992957
Article PubReader PDF–2.0MCite
Denoising large-scale biological data using network filters
Andrew J. Kavran, Aaron Clauset
BMC Bioinformatics. 2021; 22: 157. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04075-x
PMCID:
PMC7992843
Article PubReader PDF–1.8MCite
Combined embedding model for MiRNA-disease association prediction
Bailong Liu, Xiaoyan Zhu, Lei Zhang, Zhizheng Liang, Zhengwei Li
BMC Bioinformatics. 2021; 22: 161. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04092-w
PMCID:
PMC7995599
Article PubReader PDF–2.4MCite

Methodology Articles

SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model
Yan Zheng, Yuanke Zhong, Jialu Hu, Xuequn Shang
BMC Bioinformatics. 2021; 22: 5. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03878-8
PMCID:
PMC7788948
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HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
Edwin A. Solares, Yuan Tao, Anthony D. Long, Brandon S. Gaut
BMC Bioinformatics. 2021; 22: 9. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03939-y
PMCID:
PMC7788845
Article PubReader PDF–1.1MCite
mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes
Bing Song, August E. Woerner, John Planz
BMC Bioinformatics. 2021; 22: 12. Published online 2021 Jan 6. doi: 10.1186/s12859-020-03945-0
PMCID:
PMC7788837
Article PubReader PDF–1.8MCite
PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation
Changyong Li, Yongxian Fan, Xiaodong Cai
BMC Bioinformatics. 2021; 22: 14. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03943-2
PMCID:
PMC7788933
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Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture
Zhengfeng Wang, Xiujuan Lei
BMC Bioinformatics. 2021; 22: 19. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03942-3
PMCID:
PMC7792089
Article PubReader PDF–2.5MCite
Set-theory based benchmarking of three different variant callers for targeted sequencing
Jose Arturo Molina-Mora, Mariela Solano-Vargas
BMC Bioinformatics. 2021; 22: 20. Published online 2021 Jan 7. doi: 10.1186/s12859-020-03926-3
PMCID:
PMC7791862
Article PubReader PDF–2.1MCite
Impact of explicit area scaling on kinetic models involving multiple compartments
Pascal Holzheu, Ruth Großeholz, Ursula Kummer
BMC Bioinformatics. 2021; 22: 21. Published online 2021 Jan 11. doi: 10.1186/s12859-020-03913-8
PMCID:
PMC7798250
Article PubReader PDF–1.9MCite
Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach
Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes Dazard, Mark J. Cameron
BMC Bioinformatics. 2021; 22: 22. Published online 2021 Jan 12. doi: 10.1186/s12859-020-03929-0
PMCID:
PMC7805197
Article PubReader PDF–1.9MCite
Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data
Xinping Fan, Guanghao Luo, Yu S. Huang
BMC Bioinformatics. 2021; 22: 23. Published online 2021 Jan 15. doi: 10.1186/s12859-020-03924-5
PMCID:
PMC7811225
Article PubReader PDF–3.6MCite
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms
Dipan Shaw, Hao Chen, Minzhu Xie, Tao Jiang
BMC Bioinformatics. 2021; 22: 24. Published online 2021 Jan 18. doi: 10.1186/s12859-020-03914-7
PMCID:
PMC7814738
Article PubReader PDF–1.5MCite
Mining influential genes based on deep learning
Lingpeng Kong, Yuanyuan Chen, Fengjiao Xu, Mingmin Xu, Zutan Li, Jingya Fang, Liangyun Zhang, Cong Pian
BMC Bioinformatics. 2021; 22: 27. Published online 2021 Jan 22. doi: 10.1186/s12859-021-03972-5
PMCID:
PMC7821411
Article PubReader PDF–1.3MCite
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
BMC Bioinformatics. 2021; 22: 30. Published online 2021 Jan 25. doi: 10.1186/s12859-021-03960-9
PMCID:
PMC7831258
Article PubReader PDF–4.5MCite
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model
Akram Emdadi, Changiz Eslahchi
BMC Bioinformatics. 2021; 22: 33. Published online 2021 Jan 28. doi: 10.1186/s12859-021-03974-3
PMCID:
PMC7844991
Article PubReader PDF–2.1MCite
Data-driven biological network alignment that uses topological, sequence, and functional information
Shawn Gu, Tijana Milenković
BMC Bioinformatics. 2021; 22: 34. Published online 2021 Jan 29. doi: 10.1186/s12859-021-03971-6
PMCID:
PMC7847157
Article PubReader PDF–1.8MCite
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements
Tara Eicher, Jany Chan, Han Luu, Raghu Machiraju, Ewy A. Mathé
BMC Bioinformatics. 2021; 22: 35. Published online 2021 Jan 30. doi: 10.1186/s12859-021-03976-1
PMCID:
PMC7847148
Article PubReader PDF–1.8MCite
Selecting single cell clustering parameter values using subsampling-based robustness metrics
Ryan B. Patterson-Cross, Ariel J. Levine, Vilas Menon
BMC Bioinformatics. 2021; 22: 39. Published online 2021 Feb 1. doi: 10.1186/s12859-021-03957-4
PMCID:
PMC7852188
Article PubReader PDF–2.5MCite
Search for SINE repeats in the rice genome using correlation-based position weight matrices
Yulia M. Suvorova, Anastasia M. Kamionskaya, Eugene V. Korotkov
BMC Bioinformatics. 2021; 22: 42. Published online 2021 Feb 2. doi: 10.1186/s12859-021-03977-0
PMCID:
PMC7852121
Article PubReader PDF–1.2MCite
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data
Liangqun Lu, Kevin A. Townsend, Bernie J. Daigle, Jr.
BMC Bioinformatics. 2021; 22: 44. Published online 2021 Feb 3. doi: 10.1186/s12859-020-03932-5
PMCID:
PMC7860207
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ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi, Mariangela Bonizzoni
BMC Bioinformatics. 2021; 22: 45. Published online 2021 Feb 4. doi: 10.1186/s12859-021-03980-5
PMCID:
PMC7863434
Article PubReader PDF–2.1MCite
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model
Jiarui Feng, Heming Zhang, Fuhai Li
BMC Bioinformatics. 2021; 22: 47. Published online 2021 Feb 5. doi: 10.1186/s12859-020-03850-6
PMCID:
PMC7863359
Article PubReader PDF–2.1MCite
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets
Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing
BMC Bioinformatics. 2021; 22: 50. Published online 2021 Feb 5. doi: 10.1186/s12859-021-03959-2
PMCID:
PMC7866684
Article PubReader PDF–2.4MCite
DRPnet: automated particle picking in cryo-electron micrographs using deep regression
Nguyen Phuoc Nguyen, Ilker Ersoy, Jacob Gotberg, Filiz Bunyak, Tommi A. White
BMC Bioinformatics. 2021; 22: 55. Published online 2021 Feb 8. doi: 10.1186/s12859-020-03948-x
PMCID:
PMC7869254
Article PubReader PDF–10MCite
ComHub: Community predictions of hubs in gene regulatory networks
Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson
BMC Bioinformatics. 2021; 22: 58. Published online 2021 Feb 9. doi: 10.1186/s12859-021-03987-y
PMCID:
PMC7871572
Article PubReader PDF–1.1MCite
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis
William R. P. Denault, Astanand Jugessur
BMC Bioinformatics. 2021; 22: 61. Published online 2021 Feb 10. doi: 10.1186/s12859-021-03979-y
PMCID:
PMC7876806
Article PubReader PDF–1.3MCite
Ranking cancer drivers via betweenness-based outlier detection and random walks
Cesim Erten, Aissa Houdjedj, Hilal Kazan
BMC Bioinformatics. 2021; 22: 62. Published online 2021 Feb 10. doi: 10.1186/s12859-021-03989-w
PMCID:
PMC7877041
Article PubReader PDF–2.9MCite
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites
Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu
BMC Bioinformatics. 2021; 22: 63. Published online 2021 Feb 10. doi: 10.1186/s12859-021-03993-0
PMCID:
PMC7877110
Article PubReader PDF–1.8MCite
S-conLSH: alignment-free gapped mapping of noisy long reads
Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay
BMC Bioinformatics. 2021; 22: 64. Published online 2021 Feb 11. doi: 10.1186/s12859-020-03918-3
PMCID:
PMC7879691
Article PubReader PDF–2.2MCite
A graph-based algorithm for detecting rigid domains in protein structures
Truong Khanh Linh Dang, Thach Nguyen, Michael Habeck, Mehmet Gültas, Stephan Waack
BMC Bioinformatics. 2021; 22: 66. Published online 2021 Feb 12. doi: 10.1186/s12859-021-03966-3
PMCID:
PMC7881620
Article PubReader PDF–2.8MCite
CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis
Olga Permiakova, Romain Guibert, Alexandra Kraut, Thomas Fortin, Anne-Marie Hesse, Thomas Burger
BMC Bioinformatics. 2021; 22: 68. Published online 2021 Feb 12. doi: 10.1186/s12859-021-03969-0
PMCID:
PMC7881590
Article PubReader PDF–4.7MCite
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata
Moustafa Shokrof, C. Titus Brown, Tamer A. Mansour
BMC Bioinformatics. 2021; 22: 71. Published online 2021 Feb 16. doi: 10.1186/s12859-021-03996-x
PMCID:
PMC7885209
Article PubReader PDF–1.4MCite
Empowering individual trait prediction using interactions for precision medicine
Damian Gola, Inke R. König
BMC Bioinformatics. 2021; 22: 74. Published online 2021 Feb 18. doi: 10.1186/s12859-021-04011-z
PMCID:
PMC7890638
Article PubReader PDF–1.6MCite
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images
Anna Maria Masci, Scott White, Ben Neely, Maryanne Ardini-Polaske, Carol B. Hill, Ravi S. Misra, Bruce Aronow, Nathan Gaddis, Lina Yang, Susan E. Wert, Scott M. Palmer, Cliburn Chan, LungMAP Consortium
BMC Bioinformatics. 2021; 22: 82. Published online 2021 Feb 23. doi: 10.1186/s12859-021-04008-8
PMCID:
PMC7901098
Article PubReader PDF–2.0MCite
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, Michael P. Snyder, Euan A. Ashley
BMC Bioinformatics. 2021; 22: 85. Published online 2021 Feb 24. doi: 10.1186/s12859-020-03934-3
PMCID:
PMC7903625
Article PubReader PDF–2.7MCite
Penalized partial least squares for pleiotropy
Camilo Broc, Therese Truong, Benoit Liquet
BMC Bioinformatics. 2021; 22: 86. Published online 2021 Feb 24. doi: 10.1186/s12859-021-03968-1
PMCID:
PMC7905667
Article PubReader PDF–3.6MCite
miTAR: a hybrid deep learning-based approach for predicting miRNA targets
Tongjun Gu, Xiwu Zhao, William Bradley Barbazuk, Ji-Hyun Lee
BMC Bioinformatics. 2021; 22: 96. Published online 2021 Feb 27. doi: 10.1186/s12859-021-04026-6
PMCID:
PMC7912887
Article PubReader PDF–852KCite
Multi-dimensional data integration algorithm based on random walk with restart
Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo
BMC Bioinformatics. 2021; 22: 97. Published online 2021 Feb 27. doi: 10.1186/s12859-021-04029-3
PMCID:
PMC7912853
Article PubReader PDF–2.7MCite
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection
Casey B. Bernhards, Matthew W. Lux, Sarah E. Katoski, Tyler D. P. Goralski, Alvin T. Liem, Henry S. Gibbons
BMC Bioinformatics. 2021; 22: 98. Published online 2021 Mar 1. doi: 10.1186/s12859-021-04019-5
PMCID:
PMC7919090
Article PubReader PDF–1.0MCite
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
BMC Bioinformatics. 2021; 22: 108. Published online 2021 Mar 4. doi: 10.1186/s12859-021-04046-2
PMCID:
PMC7934467
Article PubReader PDF–1.6MCite
Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel
David Toubiana, Helena Maruenda
BMC Bioinformatics. 2021; 22: 116. Published online 2021 Mar 10. doi: 10.1186/s12859-021-03994-z
PMCID:
PMC7945624
Article PubReader PDF–1.2MCite
Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers
Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Elodie Bohers, Nicolas Vergne, Caroline Berard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, Fabrice Jardin
BMC Bioinformatics. 2021; 22: 120. Published online 2021 Mar 12. doi: 10.1186/s12859-021-04060-4
PMCID:
PMC7971104
Article PubReader PDF–1.6MCite
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation
Elena Tea Russo, Alessandro Laio, Marco Punta
BMC Bioinformatics. 2021; 22: 121. Published online 2021 Mar 12. doi: 10.1186/s12859-021-04013-x
PMCID:
PMC7955657
Article PubReader PDF–4.7MCite
Juxtapose: a gene-embedding approach for comparing co-expression networks
Katie Ovens, Farhad Maleki, B. Frank Eames, Ian McQuillan
BMC Bioinformatics. 2021; 22: 125. Published online 2021 Mar 16. doi: 10.1186/s12859-021-04055-1
PMCID:
PMC7968242
Article PubReader PDF–1.5MCite
ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries
Liangliang Zhang, Yushu Shi, Kim-Anh Do, Christine B. Peterson, Robert R. Jenq
BMC Bioinformatics. 2021; 22: 126. Published online 2021 Mar 17. doi: 10.1186/s12859-021-04061-3
PMCID:
PMC7972227
Article PubReader PDF–4.6MCite
Statistical integration of two omics datasets using GO2PLS
Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat, Hae-Won Uh
BMC Bioinformatics. 2021; 22: 131. Published online 2021 Mar 18. doi: 10.1186/s12859-021-03958-3
PMCID:
PMC7977326
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Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles
Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu
BMC Bioinformatics. 2021; 22: 132. Published online 2021 Mar 18. doi: 10.1186/s12859-021-04052-4
PMCID:
PMC7977599
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The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli
Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis
BMC Bioinformatics. 2021; 22: 134. Published online 2021 Mar 20. doi: 10.1186/s12859-021-04066-y
PMCID:
PMC7981984
Article PubReader PDF–4.1MCite
Nonlinear ridge regression improves cell-type-specific differential expression analysis
Fumihiko Takeuchi, Norihiro Kato
BMC Bioinformatics. 2021; 22: 141. Published online 2021 Mar 22. doi: 10.1186/s12859-021-03982-3
PMCID:
PMC7986289
Article PubReader PDF–2.0MCite
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo
BMC Bioinformatics. 2021; 22: 144. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04063-1
PMCID:
PMC7986029
Article PubReader PDF–2.1MCite
Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences
Dawit A. Yohannes, Katri Kaukinen, Kalle Kurppa, Päivi Saavalainen, Dario Greco
BMC Bioinformatics. 2021; 22: 159. Published online 2021 Mar 25. doi: 10.1186/s12859-021-04087-7
PMCID:
PMC7993519
Article PubReader PDF–1.8MCite
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