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Improved rat genome gene prediction by integration of ESTs with RNA-Seq information

JOURNAL ARTICLE published 1 January 2015 in Bioinformatics

Authors: Liping Li | Enguo Chen | Chun Yang | Jun Zhu | Pushkala Jayaraman | Jeffrey De Pons | Catherine C. Kaczorowski | Howard J. Jacob | Andrew S. Greene | Matthew R. Hodges | Allen W. Cowley | Mingyu Liang | Haiming Xu | Pengyuan Liu | Yan Lu

https://doi.org/10.1093/bioinformatics/btu608 Actions

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems

JOURNAL ARTICLE published 1 December 2017 in Bioinformatics

Research funded by National Science Centre (2012/07/B/ST6/01537)

Authors: Marcin Radom | Agnieszka Rybarczyk | Bartłomiej Szawulak | Hubert Andrzejewski | Piotr Chabelski | Adam Kozak | Piotr Formanowicz

Editors: Jonathan Wren

https://doi.org/10.1093/bioinformatics/btx492 Actions

Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes

JOURNAL ARTICLE published 1 November 2007 in Bioinformatics

Authors: Sangeeta B. English | Atul J. Butte

https://doi.org/10.1093/bioinformatics/btm483 Actions

CMF-Impute: an accurate imputation tool for single-cell RNA-seq data

JOURNAL ARTICLE published 1 May 2020 in Bioinformatics

Research funded by National Nature Science Foundation of China (11926412,61873076,61863010,61572178,61672214)

Authors: Junlin Xu | Lijun Cai | Bo Liao | Wen Zhu | JiaLiang Yang

Editors: Anthony Mathelier

https://doi.org/10.1093/bioinformatics/btaa109 Actions

Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data

JOURNAL ARTICLE published 9 September 2021 in Bioinformatics

Research funded by National Institute of Health (R01GM126558) | University of Rochester (UL1 TR002001)

Authors: Zihan Cui | Yuhang Liu | Jinfeng Zhang | Xing Qiu

Editors: Peter Robinson

https://doi.org/10.1093/bioinformatics/btab155 Actions

A method for subtype analysis with somatic mutations

JOURNAL ARTICLE published 9 April 2021 in Bioinformatics

Research funded by U.S. National Institutes of Health (R01CA223498,R01CA189532) | ORIP (S10OD028685)

Authors: Meiling Liu | Yang Liu | Michael C Wu | Li Hsu | Qianchuan He

Editors: Russell Schwartz

https://doi.org/10.1093/bioinformatics/btaa1090 Actions

gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles

JOURNAL ARTICLE published 1 March 2020 in Bioinformatics

Authors: Farancesco Napolitano | Diego Carrella | Xin Gao | Diego di Bernardo

Editors: Janet Kelso

https://doi.org/10.1093/bioinformatics/btz803 Actions

Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

JOURNAL ARTICLE published 30 December 2020 in Bioinformatics

Research funded by NSF (DBI 1356548) | National Institutes of Health (R01GM126567-03) | NASA (NNX16AJ30G)

Authors: Jose Barba-Montoya | Qiqing Tao | Sudhir Kumar

https://doi.org/10.1093/bioinformatics/btaa820 Actions

Generative probabilistic models for protein–protein interaction networks—the biclique perspective

JOURNAL ARTICLE published 1 July 2011 in Bioinformatics

Authors: Regev Schweiger | Michal Linial | Nathan Linial

https://doi.org/10.1093/bioinformatics/btr201 Actions

IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets

JOURNAL ARTICLE published 27 July 2021 in Bioinformatics

Research funded by National Institutes of Health (R01 HL141424)

Authors: Phillipe Loher | Nestoras Karathanasis | Eric Londin | Paul F. Bray | Venetia Pliatsika | Aristeidis G. Telonis | Isidore Rigoutsos

Editors: Jan Gorodkin

https://doi.org/10.1093/bioinformatics/btab016 Actions

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

JOURNAL ARTICLE published 15 January 2020 in Bioinformatics

Authors: Antoine Limasset | Jean-François Flot | Pierre Peterlongo

https://doi.org/10.1093/bioinformatics/btz548 Actions

RNA-eXpress annotates novel transcript features in RNA-seq data

JOURNAL ARTICLE published 15 March 2013 in Bioinformatics

Authors: Samuel C. Forster | Alexander M. Finkel | Jodee A. Gould | Paul J. Hertzog

https://doi.org/10.1093/bioinformatics/btt034 Actions

ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR

JOURNAL ARTICLE published 12 January 2022 in Bioinformatics

Research funded by Research Council of Norway through its Centres of Excellence funding scheme (262652)

Authors: Ankush Sharma | Akshay Akshay | Marie Rogne | Ragnhild Eskeland

Editors: Can Alkan

https://doi.org/10.1093/bioinformatics/btab680 Actions

PaGeFinder: quantitative identification of spatiotemporal pattern genes

JOURNAL ARTICLE published 1 June 2012 in Bioinformatics

Authors: Jian-Bo Pan | Shi-Chang Hu | Hao Wang | Quan Zou | Zhi-Liang Ji

https://doi.org/10.1093/bioinformatics/bts169 Actions

Novel algorithms and the benefits of comparative validation

JOURNAL ARTICLE published 15 June 2013 in Bioinformatics

Authors: Robert Smith | Dan Ventura | John T. Prince

https://doi.org/10.1093/bioinformatics/btt176 Actions

MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network

JOURNAL ARTICLE published 15 January 2020 in Bioinformatics

Research funded by Horizon 2020 Program of the European Commission (643063) | Netherlands Organisation for Scientific Research (024.002.003) | Agence Nationale de la Recherche (ANR-17-CE20-0031) | São Paulo Research Foundation (2015/13430-9,2017/05986-2)

Authors: Taneli Pusa | Mariana Galvão Ferrarini | Ricardo Andrade | Arnaud Mary | Alberto Marchetti-Spaccamela | Leen Stougie | Marie-France Sagot

Editors: Lenore Cowen

https://doi.org/10.1093/bioinformatics/btz584 Actions

Thermometer: a webserver to predict protein thermal stability

JOURNAL ARTICLE published 28 March 2022 in Bioinformatics

Research funded by European Research Council (RIBOMYLOME 309545,ASTRA 855923,IASIS 727658,INFORE 25080)

Authors: Mattia Miotto | Alexandros Armaos | Lorenzo Di Rienzo | Giancarlo Ruocco | Edoardo Milanetti | Gian Gaetano Tartaglia

Editors: Alfonso Valencia

https://doi.org/10.1093/bioinformatics/btab868 Actions

DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design

JOURNAL ARTICLE published 13 December 2022 in Bioinformatics

Research funded by State Scholarships Foundation (MIS-5000432) | Hellenic Foundation for Research and Innovation (1780) | Europe – NI4OS Europe” (857645)

Authors: Alexios Chatzigoulas | Zoe Cournia

Editors: Lenore Cowen

https://doi.org/10.1093/bioinformatics/btac680 Actions

MutHTP: mutations in human transmembrane proteins

JOURNAL ARTICLE published 1 July 2018 in Bioinformatics

Research funded by Department of Science and Technology, Government of India (INT/RUS/RSF/P-09) | Russian Science Foundation (16-44-02002)

Authors: A Kulandaisamy | S Binny Priya | R Sakthivel | Svetlana Tarnovskaya | Ilya Bizin | Peter Hönigschmid | Dmitrij Frishman | M Michael Gromiha

Editors: Jonathan Wren

https://doi.org/10.1093/bioinformatics/bty054 Actions

Detection of significant protein coevolution

JOURNAL ARTICLE published 1 July 2015 in Bioinformatics

Authors: David Ochoa | David Juan | Alfonso Valencia | Florencio Pazos

https://doi.org/10.1093/bioinformatics/btv102 Actions
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