pypi: pybedtools | Projects | Ecosyste.ms: Papers

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: almost 8 years ago

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: almost 4 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 6 years ago

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the Drosophila intestine
Cited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: over 3 years ago

10.1186/s12859-019-2706-8

svist4get: a simple visualization tool for genomic tracks from sequencing experiments
Cited by: 32
Author(s): Artyom A. Egorov, Ekaterina Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
Software Mentions: 11
Published: over 5 years ago

10.12688/f1000research.11997.1

valr: Reproducible genome interval analysis in R
Cited by: 43
Author(s): Kent Riemondy, Ryan M. Sheridan, Austin E. Gillen, Yinni Yu, Christopher Bennett, Jay R. Hesselberth
Software Mentions: 10
Published: about 7 years ago

10.3389/fgene.2018.00461

TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pcbi.1008982

Predicting mean ribosome load for 5’UTR of any length using deep learning
Cited by: 14
Author(s): Alexander Karollus, Žiga Avsec, Julien Gagneur
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.65537

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Cited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 3 years ago

10.15252/embj.2020104983

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-018-1597-8

plyranges: a grammar of genomic data transformation
Cited by: 62
Author(s): Stuart Lee, Dianne Cook, Michael C. Lawrence
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-018-1414-4

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Cited by: 140
Author(s): Kevin C.H. Ha, Benjamin J. Blencowe, Quaid Morris
Software Mentions: 9
Published: over 6 years ago

10.1186/s12864-019-5624-2

ALFA: annotation landscape for aligned reads
Cited by: 9
Author(s): Mathieu Bahin, Benoît Noël, Valentine Murigneux, Charles Bernard, Leïla Bastianelli, Hervé Le Hir, Alice Lebreton, Auguste Genovesio
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: over 3 years ago

10.1128/mBio.03221-19

A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor
Cited by: 24
Author(s): Guy E. Townsend, Weiwei Han, Nathan D. Schwalm, Xinyu Hong, Natasha A. Bencivenga-Barry, Andrew L. Goodman, Eduardo A. Groisman
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1007276

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology
Cited by: 19
Author(s): Ezequiel Názer, Ryan Dale, Madoka Chinen, Behram Radmanesh, Elissa P. Lei
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-017-4351-9

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Cited by: 3
Author(s): David Martín‐Gálvez, Denis Dunoyer de Segonzac, Man Chun John, Anne E. Kwitek, David Thybert, Paul Flicek
Software Mentions: 5
Published: almost 7 years ago

10.26508/lsa.202000864

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories
Cited by: 12
Author(s): Sophie G Kellaway, Peter Keane, Benjamin Edginton-White, Kakkad Regha, Ella Kennett, Constanze Bonifer
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.57492

Alternative polyadenylation mediates genetic regulation of gene expression
Cited by: 33
Author(s): Briana E Mittleman, Sebastian Pott, Shane Warland, Teng Zeng, Zepeng Mu, Mayher Kaur, Yoav Gilad, Yang Li
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12896-019-0535-5

VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9
Cited by: 6
Author(s): Laurence O.W. Wilson, Sara Hetzel, Christopher Pockrandt, Knut Reinert, Denis C. Bauer
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-34115-1

Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster
Cited by: 8
Author(s): Ezequiel Názer, Ryan Dale, Cameron D. Palmer, Elissa P. Lei
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.02200

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms
Cited by: 206
Author(s): Mary A. Allen, Zdeněk Andrysík, Veronica L. Dengler, Hestia Mellert, Anna L. Guarnieri, John H. Freeman, Kelly D. Sullivan, Matthew D. Galbraith, Xin Luo, W. Lee Kraus, Robin D. Dowell, Joaquín M. Espinosa
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-019-2781-x

Computational enhancer prediction: evaluation and improvements
Cited by: 10
Author(s): Hasiba Asma, Marc S. Halfon
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1007891

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
Cited by: 47
Author(s): A. Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.62438

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
Cited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-017-1708-7

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Cited by: 322
Author(s): Aziz Khan, Anthony Mathelier
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.2934

FUCHS—towards full circular RNA characterization using RNAseq
Cited by: 43
Author(s): Franziska Metge, Lisa F. Czaja-Hasse, Richard Reinhardt, Chistoph Dieterich
Software Mentions: 4
Published: over 7 years ago

10.4049/jimmunol.1602033

Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells
Cited by: 45
Author(s): Ruth Brignall, Pierre Cauchy, Sarah L Bevington, Bethany Gorman, Angela Oliveira Pisco, James Bagnall, Christopher Boddington, William Rowe, Hazel England, Kevin Rich, Lorraine Schmidt, Nigel P. Dyer, Mark A. Travis, Sascha Ott, Dean A. Jackson, Peter N. Cockerill, Pawel Paszek
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0130622

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications
Cited by: 54
Author(s): Yiming Lu, Wubin Qu, Guangyu Shan, Chenggang Zhang
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1005748

Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
Cited by: 91
Author(s): Jesse R. Raab, Samuel Resnick, Terry Magnuson
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1006080

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Cited by: 6
Author(s): Soroush Samadian, Jeff Bruce, Trevor J. Pugh
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1004226

The Functional Consequences of Variation in Transcription Factor Binding
Cited by: 187
Author(s): Darren A. Cusanovich, Bryan J. Pavlovic, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0085648

RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors
Cited by: 32
Author(s): Ravi Alla, Bradley R. Cairns
Software Mentions: 3
Published: over 10 years ago

10.3389/fgene.2021.638960

Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases
Cited by: 1
Author(s): Paweł Sztromwasser, Damian Skrzypczak, Arkadiusz Michalak, Wojciech Fendler
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-019-1753-9

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1
Cited by: 63
Author(s): Daniel E. Martin‐Herranz, Erfan Aref‐Eshghi, Marc Jan Bonder, Thomas M. Stubbs, Sanaa Choufani, Rosanna Weksberg, Oliver Stegle, Bekim Sadiković, Wolf Reik, Janet M. Thornton
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-33947-1

Genome wide mapping of ETV6 binding sites in pre-B leukemic cells
Cited by: 9
Author(s): Benjamin Neveu, Maxime Caron, Karine Lagacé, Chantal Richer, Daniel Sinnett
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1003069

Tissue-Specific Regulation of Chromatin Insulator Function
Cited by: 49
Author(s): Leah H. Matzat, Ryan K. Dale, Nellie Moshkovich, Elissa P. Lei
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pcbi.1004888

Identifying Network Perturbation in Cancer
Cited by: 34
Author(s): Maxim Grechkin, Benjamin A. Logsdon, Andrew J. Gentles, Su-In Lee
Software Mentions: 2
Published: over 8 years ago

10.1186/s13148-017-0391-x

The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome
Cited by: 29
Author(s): Daniel A. Newkirk, Yen-Yun Chen, Richard Chien, Weihua Zeng, Jacob Biesinger, Ebony Flowers, Shimako Kawauchi, Rosaysela Santos, Anne L. Calof, Arthur D. Lander, Xiaohui Xie, Kyoko Yokomori
Software Mentions: 2
Published: about 7 years ago

10.1016/j.celrep.2015.08.065

Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis
Cited by: 48
Author(s): Laurent Dupays, Catherine A. Shang, Robert Wilson, Surendra Kotecha, Sophie Wood, Norma Towers, Timothy J. Mohun
Software Mentions: 2
Published: almost 9 years ago

10.1093/bioinformatics/btz041

SVIM: structural variant identification using mapped long reads
Cited by: 148
Author(s): David Heller, Martin Vingron
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-017-0447-8

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases
Cited by: 53
Author(s): Stephanie Greer, Lincoln Nadauld, Billy T. Lau, Jiamin Chen, Christina Wood-Bouwens, James M. Ford, Calvin J. Kuo, Hanlee P. Ji
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1637-z

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects
Cited by: 33
Author(s): Emanuel Gonçalvès, Fiona M. Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio, Mathew J. Garnett
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4196-2

Candidate lethal haplotypes and causal mutations in Angus cattle
Cited by: 40
Author(s): Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel, Jeremy F. Taylor
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0199771

Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization
Cited by: 7
Author(s): Vishaka Gopalan, Rahul Siddharthan, Sandeep Krishna
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1006921

ChIPulate: A comprehensive ChIP-seq simulation pipeline
Cited by: 9
Author(s): Vishaka Gopalan, Sridhar Hannenhalli, Rahul Siddharthan
Software Mentions: 1
Published: over 5 years ago

10.1093/g3journal/jkab001

Comparative genomics of white and opaque cell states supports an epigenetic mechanism of phenotypic switching in Candida albicans
Cited by: 8
Author(s): Chapman Beekman, Christina A. Cuomo, Iuliana V. Ene
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: pybedtools

Papers Mentioning pybedtools 48