pypi: snakemake | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009065

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: about 4 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.7554/eLife.53392

ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair
Cited by: 23
Author(s): Daniel Wells, Emmanuelle Bitoun, Daniela Moralli, Gang Zhang, Anjali Gupta Hinch, Julia Jankowska, Peter Donnelly, Catherine Green, Simon Myers
Software Mentions: 14
Published: over 4 years ago

10.1186/s12859-020-03774-1

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Cited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: about 4 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.1016/j.cell.2021.07.017

Whole-body integration of gene expression and single-cell morphology
Cited by: 59
Author(s): Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-018-2296-x

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Cited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 years ago

10.1186/s13059-021-02473-1

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Cited by: 20
Author(s): Rachel Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Software Mentions: 10
Published: over 3 years ago

10.1534/g3.119.400185

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1007358

Seven quick tips for analysis scripts in neuroimaging
Cited by: 11
Author(s): Marijn van Vliet
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.68312

A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma
Cited by: 12
Author(s): Dayana C Farhat, Matthew W. Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed‐Ali Hakimi, Christopher Swale
Software Mentions: 8
Published: over 3 years ago

10.1111/mec.15287

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus
Cited by: 29
Author(s): Kevin Murray, Jasmine K. Janes, Ashley Jones, Helen M. Bothwell, Rose L. Andrew, Justin O. Borevitz
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.14334

TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
Cited by: 104
Author(s): Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
Software Mentions: 7
Published: over 8 years ago

10.1002/jcsm.12665

Myogenesis modelled by human pluripotent stem cells: a multi‐omic study of Duchenne myopathy early onset
Cited by: 28
Author(s): Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Étienne Kornobis, Hélène Polveche, Margot Jarrige, Alan R L Dorval, Maxime R. F. Gosselin, Antigoni Manousopoulou, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset
Software Mentions: 7
Published: almost 4 years ago

10.1093/gigascience/giaa153

Significantly improving the quality of genome assemblies through curation
Cited by: 540
Author(s): Kerstin Howe, William Chow, Joanna Collins, Sarah Pelan, Damon-Lee Pointon, Ying Sims, James Torrance, Alan S. Tracey, Jonathan Wood
Software Mentions: 7
Published: almost 4 years ago

10.1186/s40168-020-00993-9

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
Cited by: 61
Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz‐Buschart, Cédric Christian Laczny, Patrick May, Paul Wilmes
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-021-02265-7

ReSeq simulates realistic Illumina high-throughput sequencing data
Cited by: 7
Author(s): Stephan Schmeing, Mark D. Robinson
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-018-1415-3

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
Cited by: 49
Author(s): Andreas J. Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martín, Erik van Nimwegen, Mihaela Zavolan
Software Mentions: 6
Published: over 6 years ago

10.12688/f1000research.29032.2

Sustainable data analysis with Snakemake
Cited by: 502
Author(s): Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Förster, Soohyun Lee, Sven Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Software Mentions: 6
Published: over 3 years ago

10.1007/s00429-020-02046-1

CBPtools: a Python package for regional connectivity-based parcellation
Cited by: 9
Author(s): Niels Reuter, Sarah Genon, Shahrzad Kharabian Masouleh, Felix Hoffstaedter, Xiaojin Liu, Tobias Kalenscher, Simon B. Eickhoff, Kaustubh R. Patil
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.7717/peerj.12198

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Cited by: 16
Author(s): Nicholas D. Youngblut, Ruth E. Ley
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2021.670309

Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target
Cited by: 7
Author(s): Alicia A. Gingrich, Taylor Reiter, Sean J Judge, Daniel York, Mio Yanagisawa, Aryana Razmara, Ian R. Sturgill, Ugur Nur Basmaci, Rachel Brady, Kevin Stoffel, William J. Murphy, Robert B. Rebhun, C. Titus Brown, Robert J. Canter
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02296-0

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Cited by: 12
Author(s): Matthew T Parker, Katarzyna Knop, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-017-11807-8

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda
Cited by: 36
Author(s): Barbara Blasi, Hakim Tafer, Christina Kustor, Caroline Poyntner, Ksenija Lopandić, Katja Sterflinger
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection
Cited by: 42
Author(s): Ran Zhou, Yong‐Guan Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Jia Yin, Chu Zhang, Dongfang Ma
Software Mentions: 5
Published: almost 7 years ago

10.12688/f1000research.24751.2

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity
Cited by: 9
Author(s): Evan Bolyen, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, Jason W. Sahl, Andrew Sanchez, Chris Holdgraf, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew R. McKay, Anthony Simard, David M. Engelthaler, Michael Worobey, Paul Keim, J. Gregory Caporaso
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0220728

Advances in gene ontology utilization improve statistical power of annotation enrichment
Cited by: 10
Author(s): Eugene W. Hinderer, Robert M. Flight, Raju Kumar Dubey, James N. MacLeod, Hunter N. B. Moseley
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008222

Genome Complexity Browser: Visualization and quantification of genome variability
Cited by: 1
Author(s): Alexander I. Manolov, Dmitry N. Konanov, Dmitry E. Fedorov, Ivan Osmolovsky, Rinat Vereshchagin, Elena N. Ilina
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-017-4168-6

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms
Cited by: 7
Author(s): Daniela Beißer, Nadine Graupner, Lars Großmann, Henning Timm, Jens Boenigk, Sven Rahmann
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-88516-w

Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
Cited by: 11
Author(s): Roza Berhanu Lemma, Marit Ledsaak, Bettina M. Fuglerud, Geir Kjetil Sandve, Ragnhild Eskeland, Odd S. Gabrielsen
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07747-3

Downregulated luteolytic pathways in the transcriptome of early pregnancy bovine corpus luteum are mimicked by interferon-tau in vitro
Cited by: 6
Author(s): Raghavendra Basavaraja, J. N. Drum, Jackson Sapuleni, Lonice Bibi, Gilgi Friedlander, Sai Kumar, Roberto Sartori, Rina Meidan
Software Mentions: 4
Published: over 3 years ago

10.3389/fpsyt.2021.625247

Predicting Symptoms of Depression and Anxiety Using Smartphone and Wearable Data
Cited by: 88
Author(s): Isaac Moshe, Yannik Terhorst, Kennedy Opoku Asare, Lasse Sander, Denzil Ferreira, Harald Baumeister, David C. Mohr, Laura Pulkki-Råbäck
Software Mentions: 4
Published: almost 4 years ago

10.1093/bioinformatics/btz436

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Cited by: 92
Author(s): Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, Thomas Manke
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-73867-7

Repeated sampling facilitates within- and between-subject modeling of the human sperm transcriptome to identify dynamic and stress-responsive sncRNAs
Cited by: 14
Author(s): Christopher P. Morgan, Amol Shetty, Jackie Chan, David Berger, Seth A. Ament, C. Neill Epperson, Tracy L. Bale
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.56890

Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution
Cited by: 27
Author(s): Racquel Domingo-Gonzalez, Fabio Zanini, Xibing Che, Min Liu, Robert C. Jones, Michael Swift, Stephen R. Quake, David N. Cornfield, Cristina M. Alvira
Software Mentions: 3
Published: over 4 years ago

10.3389/fninf.2018.00046

Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models
Cited by: 32
Author(s): Roman Pauli, Philipp Weidel, Susanne Kunkel, Abigail Morrison
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-020-03887-7

Inferring time-dependent population growth rates in cell cultures undergoing adaptation
Cited by: 9
Author(s): H. Jonathan G. Lindström, Ran Friedman
Software Mentions: 3
Published: about 4 years ago

10.1186/s12284-019-0356-0

Rice Stress-Resistant SNP Database
Cited by: 8
Author(s): Samuel Tareke Woldegiorgis, Shaobo Wang, Yiruo He, Zhenhua Xu, Lijuan Chen, Tao Huan, Yu Zhang, Yang Zou, Andrew Harrison, Lína Zhang, Yufang Ai, Wei Liu, Hongwen He
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1005128

Ten Simple Rules for Developing Public Biological Databases
Cited by: 25
Author(s): Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader
Software Mentions: 2
Published: about 8 years ago

10.1128/AEM.02091-17

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T
Cited by: 64
Author(s): Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti‐Dinh, Igor V. Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-017-16403-4

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide
Cited by: 24
Author(s): Ian T. Cadby, Matthew Faulkner, Jeanne Chèneby, Justine Long, Jacques van Helden, Alain Dolla, Jeffrey A. Cole
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-22414-6

Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study
Cited by: 8
Author(s): Virginie Chesnais, Alban Ott, Emmanuel Chaplais, Samuel Gabillard, Diego Pallares, Christelle Vauloup‐Fellous, Alexandra Benachi, Jean‐Marc Costa, Eric Ginoux
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcimb.2018.00188

Galleria mellonella Reveals Niche Differences Between Highly Pathogenic and Closely Related Strains of Francisella spp.
Cited by: 14
Author(s): Johanna Thelaus, Eva Lundmark, Petter Lindgren, Andreas Sjödin, Mats Forsman
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8214

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
Cited by: 16
Author(s): Arnold Kuzniar, Jason Maassen, Stefan Verhoeven, Luca Santuari, Carl Shneider, Wigard P. Kloosterman, Jeroen de Ridder
Software Mentions: 1
Published: almost 5 years ago

Projects: pypi: snakemake

Papers Mentioning snakemake 45