MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization

JOURNAL ARTICLE published 1 September 2017 in Bioinformatics

Research funded by NIAID (R01-AI110724,R21-AI117247,U01-AI124302)

Authors: Katherine Maia McCoy | Margaret L Antonio | Tim van Opijnen

Editors: Jonathan Wren

Simulating Epstein-Barr virus infection with C-ImmSim

JOURNAL ARTICLE published 1 June 2007 in Bioinformatics

Authors: Filippo Castiglione | Karen Duca | Abdul Jarrah | Reinhard Laubenbacher | Donna Hochberg | David Thorley-Lawson

CNVVdb: a database of copy number variations across vertebrate genomes

JOURNAL ARTICLE published 1 June 2009 in Bioinformatics

Authors: Feng-Chi Chen | Yen-Zho Chen | Trees-Juen Chuang

A simple statistical method for discriminating outer membrane proteins with better accuracy

JOURNAL ARTICLE published 1 April 2005 in Bioinformatics

Authors: M. Michael Gromiha | Makiko Suwa

Cluster Locator, online analysis and visualization of gene clustering

JOURNAL ARTICLE published 1 October 2018 in Bioinformatics

Research funded by Innovation Technology Department of Bizkaia County (BFU2014-52282-P,BFU2017-84653-P) | Severo Ochoa Excellence Accreditation (SEV-2016-0644)

Authors: Flavio Pazos Obregón | Pablo Soto | José Luis Lavín | Ana Rosa Cortázar | Rosa Barrio | Ana María Aransay | Rafael Cantera

Editors: John Hancock

PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning

JOURNAL ARTICLE published 1 May 2020 in Bioinformatics

Research funded by National Key Research and Development Programme of China (2017YFC1200205) | National Natural Science Foundation of China (31671366)

Authors: Zhencheng Fang | Jie Tan | Shufang Wu | Mo Li | Chunhui Wang | Yongchu Liu | Huaiqiu Zhu

Editors: Inanc Birol

Peptide length-based prediction of peptide–MHC class II binding

JOURNAL ARTICLE published 15 November 2006 in Bioinformatics

Authors: Stewart T. Chang | Debashis Ghosh | Denise E. Kirschner | Jennifer J. Linderman

tRanslatome: an R/Bioconductor package to portray translational control

JOURNAL ARTICLE published 15 January 2014 in Bioinformatics

Authors: Toma Tebaldi | Erik Dassi | Galena Kostoska | Gabriella Viero | Alessandro Quattrone

Fast characterization of segmental duplications in genome assemblies

JOURNAL ARTICLE published 1 September 2018 in Bioinformatics

Research funded by EMBO Installation (IG-2521) | National Institutes of Health (GM108348)

Authors: Ibrahim Numanagić | Alim S Gökkaya | Lillian Zhang | Bonnie Berger | Can Alkan | Faraz Hach

A simple model predicts UGT-mediated metabolism

JOURNAL ARTICLE published 15 October 2016 in Bioinformatics

Research funded by National Institutes of Health (1S10RR022984-01A1,1S10OD018091-01)

Authors: Na Le Dang | Tyler B. Hughes | Varun Krishnamurthy | S. Joshua Swamidass

Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

JOURNAL ARTICLE published 1 September 2019 in Bioinformatics

Research funded by BBSRC Doctoral Training Partnership (BB/M009513/1) | Wellcome Trust (109854/Z/15/Z) | Medical Research Council (MC_PC_15031)

Authors: Andy M C Lau | Zainab Ahdash | Chloe Martens | Argyris Politis

Editors: Alfonso Valencia

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

JOURNAL ARTICLE published 15 October 2015 in Bioinformatics

Authors: Shiwei Lan | Julia A. Palacios | Michael Karcher | Vladimir N. Minin | Babak Shahbaba

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution

JOURNAL ARTICLE published 1 September 2016 in Bioinformatics

Authors: Gelio Alves | Yi-Kuo Yu

Microindel detection in short-read sequence data

JOURNAL ARTICLE published 15 March 2010 in Bioinformatics

Authors: Peter Krawitz | Christian Rödelsperger | Marten Jäger | Luke Jostins | Sebastian Bauer | Peter N. Robinson

Cross-validation under separate sampling: strong bias and how to correct it

JOURNAL ARTICLE published 1 December 2014 in Bioinformatics

Authors: Ulisses M. Braga-Neto | Amin Zollanvari | Edward R. Dougherty

Application of the Bayesian MMSE estimator for classification error to gene expression microarray data

JOURNAL ARTICLE published 1 July 2011 in Bioinformatics

Authors: Lori A. Dalton | Edward R. Dougherty

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl

JOURNAL ARTICLE published 15 October 2009 in Bioinformatics

Authors: Olivier Sand | Morgane Thomas-Chollier | Jacques van Helden

The NEW ESID online database network

JOURNAL ARTICLE published 15 December 2019 in Bioinformatics

Research funded by EURO-POLICY-PID (SP23-CT-2005-006411) | BMBF (01GM0896,01GM1111B,01GM1517C,01EO1303)

Authors: Raphael Scheible | Stephan Rusch | David Guzman | Nizar Mahlaoui | Stephan Ehl | Gerhard Kindle

Editors: Jonathan Wren

Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps

JOURNAL ARTICLE published 1 March 2000 in Bioinformatics

Authors: Osamu Gotoh

All-atom knowledge-based potential for RNA structure prediction and assessment

JOURNAL ARTICLE published 15 April 2011 in Bioinformatics

Authors: Emidio Capriotti | Tomas Norambuena | Marc A. Marti-Renom | Francisco Melo