Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: bwa

https://packages.ecosyste.ms/registries/pypi.org/packages/bwa

Bwa: Simple Notification Sender(Discord, Slack, Gmail and Telegram)
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Latest release: over 3 years ago
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Papers Mentioning bwa 989

10.1038/s41598-020-70334-1
Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential
Cited by: 20
Author(s): Leah S. VandenBosch, Stefanie G. Wohl, Matthew S. Wilken, Marcus Hooper, Connor Finkbeiner, Kristen E. Cox, Laura B. Chipman, Thomas A. Reh
Software Mentions: 6
Published: almost 4 years ago
10.1099/mgen.0.000320
Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Cited by: 0
Author(s): Amol C. Shetty, John Mattick, Matthew Chung, Carrie McCracken, Anup Mahurkar, Scott G. Filler, Claire M. Fraser, David A. Rasko, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 6
Published: over 4 years ago
10.1038/sdata.2016.25
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Cited by: 535
Author(s): Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich B. Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y. Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Kashif Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Madeleine Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
Software Mentions: 6
Published: almost 8 years ago
10.1371/journal.ppat.1009063
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis
Cited by: 20
Author(s): Nathan D. Hicks, Samantha R. Giffen, Peter H. Culviner, Michael C. Chao, Charles L. Dulberger, Qingyun Liu, Sydney Stanley, J. A. Brown, Jaimie Sixsmith, Ian D. Wolf, Sarah M. Fortune
Software Mentions: 6
Published: over 3 years ago
10.1186/1471-2105-15-S3-A7
Oqtans: a multifunctional workbench for RNA-seq data analysis
Cited by: 0
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 6
Published: over 10 years ago
10.1093/gigascience/gix049
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Cited by: 114
Author(s): Sarah S.T. Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel‐Holger S. Sinding, Lukas F. K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomás Marquès-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert
Software Mentions: 6
Published: almost 7 years ago
10.1080/19490976.2021.1900995
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment
Cited by: 21
Author(s): Kang Kang, Lejla Imamovic, Maria-Anna Misiakou, Maria Bornakke Sørensen, Yoshitaro Heshiki, Yueqiong Ni, Tingting Zheng, Jun Li, Mostafa Mostafa Hashim Ellabaan, Marta Colomer-Lluch, Anne A Rode, Peter Bytzer, Gianni Panagiotou, Morten Otto Alexander Sommer
Software Mentions: 6
Published: over 3 years ago
10.1093/gbe/evaa071
Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat
Cited by: 30
Author(s): Benjamin Schwessinger, Yan Jun Chen, Richard Tien, Josef Korbinian Vogt, Jana Sperschneider, Ramawatar Nagar, Mark McMullan, Thomas Sicheritz-Pontén, Chris K. Sørensen, Mogens S. Hovmøller, John P. Rathjen, Annemarie Fejer Justesen
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pgen.1009645
An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: almost 3 years ago
10.1186/s13059-021-02423-x
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Cited by: 58
Author(s): Daniel Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclán, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley, Anthony T. Papenfuss
Software Mentions: 6
Published: almost 3 years ago
10.1093/gbe/evx067
Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations
Cited by: 37
Author(s): Julia Maria Isis Barth, Malte Damerau, Michael Matschiner, Sissel Jentoft, Reinhold Hanel
Software Mentions: 6
Published: about 7 years ago
10.1186/s13059-020-02160-7
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
Cited by: 33
Author(s): Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-021-85913-z
Analysis of false-negative rapid diagnostic tests for symptomatic malaria in the Democratic Republic of the Congo
Cited by: 18
Author(s): Jonathan B. Parr, Eddy Kieto, Fernandine Phanzu, Paul Mansiangi, Kashamuka Mwandagalirwa, Nono Mvuama, Ange Landela, Joseph Atibu, Solange Umesumbu Efundu, Jean W. Olenga, Kyaw L. Thwai, Camille Morgan, Madeline Denton, Alison Poffley, Jonathan J. Juliano, Pomie Mungala, Joris Losimba Likwela, Eric Mukomena Sompwe, Eric Rogier, Antoinette Tshefu, Adrien N’Siala, Albert Kalonji
Software Mentions: 6
Published: about 3 years ago
10.1038/s42003-021-01908-6
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
Cited by: 8
Author(s): Michaël Abrouk, Naveenkumar Athiyannan, Thomas Müller, Yveline Pailles, Christoph Stritt, Anne Roulin, Chenggen Chu, Shuyu Liu, Takumi Morita, Hirokazu Handa, Jesse Poland, Beat Keller, Simon G. Krattinger
Software Mentions: 6
Published: about 3 years ago
10.3389/fgene.2021.673530
Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach
Cited by: 3
Author(s): Sambhavi Animesh, Ruchi Choudhary, Bertrand Jern Han Wong, Charlotte Tze Jia Koh, Xin Yi Ng, J. S. H. Tay, Wan-Qin Chong, Jian Han, Leilei Chen, Boon Cher Goh, Melissa J. Fullwood
Software Mentions: 6
Published: over 2 years ago
10.1038/s41597-020-0458-y
Epigenomic profiling of neuroblastoma cell lines
Cited by: 23
Author(s): Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Software Mentions: 6
Published: about 4 years ago
10.1038/s41598-021-87982-6
Association among extracellular superoxide dismutase genotype, plasma concentration, and comorbidity in the very old and centenarians
Cited by: 7
Author(s): Takashi Sasaki, Yukiko Abe, M. Takayama, Tetsuo Adachi, Hideyuki Okano, Nobuyoshi Hirose, Yasumichi Arai
Software Mentions: 6
Published: about 3 years ago
10.1186/gm549
A genome scale overexpression screen to reveal drug activity in human cells
Cited by: 30
Author(s): Anthony Arnoldo, Saranya Kittanakom, Lawrence E. Heisler, Anthony B. Mak, Andrey I. Shukalyuk, Dax Torti, Jason Moffat, Guri Giaever, Corey Nislow
Software Mentions: 6
Published: over 10 years ago
10.1038/s41598-021-86287-y
Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts
Cited by: 9
Author(s): Jonathan A. Shortt, Laura E. Timm, Nicole R. Hales, Zachary L. Nikolakis, Drew R. Schield, Blair W. Perry, Yang Liu, Bo Zhong, Elizabeth J. Carlton, David D. Pollock
Software Mentions: 6
Published: about 3 years ago
10.1002/ece3.6978
Implications of genetic heterogeneity for plant translocation during ecological restoration
Cited by: 2
Author(s): Taylor M. Crow, C. Alex Buerkle, Daniel E. Runcie, Kristina M. Hufford
Software Mentions: 6
Published: over 3 years ago
10.1007/s00401-018-1821-3
5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma
Cited by: 10
Author(s): Wioletta K. Glowacka, Harshika Jain, Makiko Okura, Abulizi Maimaitiming, Yasin Mamatjan, Romina Nejad, Hamza Farooq, Michael D. Taylor, Kenneth Aldape, Paul Kongkham
Software Mentions: 6
Published: over 6 years ago
10.1002/1878-0261.12161
Comparative genomics reveals that loss of lunatic fringe (<i>LFNG</i>) promotes melanoma metastasis
Cited by: 19
Author(s): Martín Del Castillo Velasco-Herrera, Louise van der Weyden, Jérémie Nsengimana, Anneliese O. Speak, Marcela Sjöberg, D. Timothy Bishop, Göran Jönsson, Julia Newton-Bishop, David J. Adams
Software Mentions: 6
Published: over 6 years ago
10.3390/genes12010048
Probably Correct: Rescuing Repeats with Short and Long Reads
Cited by: 3
Author(s): Monika Čechová
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-018-2019-3
Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: over 6 years ago
10.1534/genetics.120.303038
Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: about 4 years ago
10.3390/genes1010070
Next Generation Sequencing of miRNAs – Strategies, Resources and Methods
Cited by: 111
Author(s): Susanne Motameny, Stefanie Wolters, Peter Nürnberg, Björn Schumacher
Software Mentions: 5
Published: almost 14 years ago
10.1534/g3.120.401184
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout
Cited by: 7
Author(s): Seth Smith, Stephen J. Amish, Louis Bernatchez, Jérémy Le Luyer, Chris Wilson, Olivia Boeberitz, Gordon Luikart, Kim T. Scribner
Software Mentions: 5
Published: about 4 years ago
10.1111/tpj.14760
High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China
Cited by: 20
Author(s): Xiaoqin Nie, Tianwang Wen, Panxia Shao, Binghui Tang, Nurimanguli Aini, Yu Yu, Xinying Du, Chunyuan You, Zhongxu Lin
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pbio.3000799
5-Formylcytosine landscapes of human preimplantation embryos at single-cell resolution
Cited by: 5
Author(s): Yun Gao, Lin Li, Peng Yuan, Fan Zhai, Yixuan Ren, Liying Yan, Rong Li, Ying Lian, Xiaohui Zhu, Xinglong Wu, Kehkooi Kee, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 5
Published: almost 4 years ago
10.1016/j.cell.2016.09.006
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Cited by: 349
Author(s): Angelo Amabile, Alessandro Migliara, Paola Capasso, Mauro Biffi, Davide Cittaro, Luigi Naldini, Angelo Lombardo
Software Mentions: 5
Published: over 7 years ago
10.1186/1471-2164-13-531
Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei
Cited by: 57
Author(s): Oscar Franzén, Carlos Talavera-López, Stephen Ochaya, Claire E. Butler, Louisa A. Messenger, Michael D. Lewis, Martin S. Llewellyn, C. J. Marinkelle, Kevin M. Tyler, Michael A. Miles, Björn Andersson
Software Mentions: 5
Published: over 12 years ago
10.1186/s12859-019-3219-1
uap: reproducible and robust HTS data analysis
Cited by: 12
Author(s): Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller
Software Mentions: 5
Published: over 4 years ago
10.1186/s12864-020-07111-x
Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks
Cited by: 19
Author(s): Perot Saelao, Michael Simone-Finstrom, Arián Avalos, Lelania Bilodeau, Robert G. Danka, Lilia de Guzman, Frank D. L. Rinkevich, Philip Tokarz
Software Mentions: 5
Published: over 3 years ago
10.3389/fpls.2017.00367
Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding
Cited by: 14
Author(s): Jan Ištvánek, Jana Dluhošová, Petr Dluhoš, Lenka Pátková, J. Nedĕlník, Jana Řepková
Software Mentions: 5
Published: about 7 years ago
10.3389/fpls.2020.01005
Similar Seed Composition Phenotypes Are Observed From CRISPR-Generated In-Frame and Knockout Alleles of a Soybean KASI Ortholog
Cited by: 8
Author(s): Kamaldeep S. Virdi, Madison Spencer, Adrian O. Stec, Yer Xiong, Ryan Merry, Gary J. Muehlbauer, Robert M. Stupar
Software Mentions: 5
Published: almost 4 years ago
10.1186/1471-2105-15-144
MOIRAI: a compact workflow system for CAGE analysis
Cited by: 62
Author(s): Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann
Software Mentions: 5
Published: about 10 years ago
10.7554/eLife.13926
Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
Cited by: 122
Author(s): Claude Philippe, Dulce B Vargas-Landin, Aurélien J. Doucet, Dominic van Essen, Jorge Vera-Otárola, Monika Kuciak, Antoine Corbin, Pilvi Nigumann, Gaël Cristofari
Software Mentions: 5
Published: about 8 years ago
10.1371/journal.pone.0123658
A Powerful Statistical Approach for Large-Scale Differential Transcription Analysis
Cited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: about 9 years ago
10.7554/eLife.03549
Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Cited by: 21
Author(s): Brenda Y. Han, Shuang Wu, Chuan-Sheng Foo, Robert M. Horton, Craig N. Jenne, Susan R. Watson, Belinda Whittle, Christopher C. Goodnow, Jason G. Cyster
Software Mentions: 5
Published: over 9 years ago
10.7554/eLife.03703
Selection of chromosomal DNA libraries using a multiplex CRISPR system
Cited by: 298
Author(s): Owen Ryan, Jeffrey M. Skerker, Matthew J. Maurer, Xin Li, Jordan C. Tsai, Snigdha Poddar, Michael E. Lee, Will DeLoache, John E. Dueber, Adam P. Arkin, Jamie H. D. Cate
Software Mentions: 5
Published: almost 10 years ago
10.3390/ijms21051720
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana
Cited by: 27
Author(s): Stephanie Schaarschmidt, Axel Fischer, Ellen Zuther, Dirk K. Hincha
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0015925
PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
Cited by: 526
Author(s): Robert Kofler, Pablo Orozco‐terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer
Software Mentions: 5
Published: over 13 years ago
10.7554/eLife.25762
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
Cited by: 102
Author(s): Yuh Chwen G Lee, Gary H. Karpen
Software Mentions: 5
Published: almost 7 years ago
10.1371/journal.pone.0134880
Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine
Cited by: 99
Author(s): Katie E. Hyma, Paola Barba, Minghui Wang, Jason P. Londo, Charlotte B. Acharya, Sharon E. Mitchell, Qi Sun, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 5
Published: almost 9 years ago
10.3389/fpls.2019.01434
Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques
Cited by: 12
Author(s): Alessandra M. Sullivan, Andrej A Arsovski, Agnieszka Thompson, Richard Sandstrom, Robert E. Thurman, Shane Neph, Audra Johnson, Shawn Sullivan, Peter J. Sabo, Fidencio Neri, Molly Weaver, Morgan Diegel, Jennifer L. Nemhauser, J Stamatoyannopoulos, Kerry L Bubb, Christine Queitsch
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0207250
Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes
Cited by: 12
Author(s): Maxime Caron, Pascal St-Onge, Simon Drouin, Chantal Richer, Thomas Sontag, Stephan Busche, Guillaume Bourque, Tomi Pastinen, Daniel Sinnett
Software Mentions: 5
Published: over 5 years ago
10.1186/gb-2013-14-6-r66
Separating homeologs by phasing in the tetraploid wheat transcriptome
Cited by: 129
Author(s): Ksenia V. Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristóbal Uauy, Jorge Dubcovsky
Software Mentions: 5
Published: almost 11 years ago
10.15252/msb.202010138
Natural variants suppress mutations in hundreds of essential genes
Cited by: 10
Author(s): Leopold Parts, Amandine Batté, Maykel Lopes, Michael Wai-Keong Yuen, Meredith Laver, Bryan-Joseph San Luis, Jia-Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen
Software Mentions: 5
Published: about 3 years ago
10.1038/s41396-020-00794-w
Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
Cited by: 17
Author(s): Sean Meaden, Loris Capria, Ellinor O. Alseth, Sylvain Gandon, Ambarish Biswas, Luca Lenzi, Stineke van Houte, Edze R. Westra
Software Mentions: 5
Published: over 3 years ago
10.15252/msb.20167058
Mechanism for microbial population collapse in a fluctuating resource environment
Cited by: 21
Author(s): Serdar Turkarslan, Arjun V. Raman, Anne Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, Sergey Stolyar, Adrián López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M. Zane, Jeffrey A. Ranish, Judy D. Wall, David A. Stahl, Nitin S. Baliga
Software Mentions: 5
Published: about 7 years ago
10.1371/journal.pone.0169087
The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Cited by: 74
Author(s): Axel Künstner, Maria Hoffmann, Bonnie A. Fraser, Verena A. Kottler, Eshita Sharma, Detlef Weigel, Christine Dreyer
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pgen.1007830
Global transcriptional regulation of innate immunity by ATF-7 in C. elegans
Cited by: 46
Author(s): Marissa Fletcher, Erik J. Tillman, Vincent Butty, Stuart S. Levine, Dennis H. Kim
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pgen.1009121
A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome
Cited by: 20
Author(s): Benjamin L. S. Furman, Caroline M S Cauret, Martin Knytl, Xuhong Song, Tharindu Premachandra, Caleb Ofori‐Boateng, Danielle C. Jordan, Marko E. Horb, Ben Evans
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1008420
Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
Cited by: 50
Author(s): Rena M. Schweizer, Jonathan P. Velotta, Catherine M. Ivy, Matthew R. Jones, Sarah M. Muir, Gideon S. Bradburd, Jay F. Storz, Graham R. Scott, Zachary A. Cheviron
Software Mentions: 5
Published: over 4 years ago
10.1128/mBio.02500-19
A Conserved Streptococcal Virulence Regulator Controls the Expression of a Distinct Class of M-Like Proteins
Cited by: 7
Author(s): Jonathan D. D’Gama, Zhe Ma, Hailong Zhang, Li Xu, Hongjie Fan, Ellen Ruth A. Morris, Noah D. Cohen, Colette Cywes‐Bentley, Gerald B. Pier, Matthew K. Waldor
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2018.01901
Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
Cited by: 59
Author(s): Lavanya Challagundla, Jinnethe Reyes, Iftekhar Rafiqullah, Daniel O. Sordelli, Gabriela Echániz-Avilés, María Elena Velázquez-Meza, Santiago Castillo-Ramírez, Nahuel Fittipaldi, Michael Feldgarden, Sinéad B. Chapman, Michael S. Calderwood, Lina P Carvajal, Sandra Rincón, Blake Hanson, Paul J. Planet, César A. Arias, Lorena Díaz, D. Ashley Robinson
Software Mentions: 5
Published: over 5 years ago
10.1186/s12864-020-6545-9
Trait differentiation and modular toxin expression in palm-pitvipers
Cited by: 16
Author(s): Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson
Software Mentions: 5
Published: over 4 years ago
10.1128/mBio.01496-21
The Interspecific Fungal Hybrid <i>Verticillium longisporum</i> Displays Subgenome-Specific Gene Expression
Cited by: 6
Author(s): Jasper R L Depotter, Fabian van Beveren, Luis Rodríguez‐Moreno, Holger Kramer, Edgar A. Chavarro Carrero, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Thomas A. Wood, Bart P.H.J. Thomma, Michael Seidl
Software Mentions: 5
Published: over 2 years ago
10.3389/fcell.2021.664178
Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pgen.1005693
Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome
Cited by: 24
Author(s): Luke Isbel, Richa Srivastava, Harald Oey, Alex Spurling, Lucia Daxinger, Hamsa Puthalakath, Emma Whitelaw
Software Mentions: 5
Published: over 8 years ago
10.1002/1878-0261.12491
A 17 gene panel for non‐small‐cell lung cancer prognosis identified through integrative epigenomic‐transcriptomic analyses of hypoxia‐induced epithelial–mesenchymal transition
Cited by: 21
Author(s): Yue‐Lei Chen, Yihe Zhang, Junwen Wang, Na Chen, Weiying Fang, Jianing Zhong, Yi Liu, Rui Qin, Xinxin Yu, Zhen Sun, Fei Gao
Software Mentions: 5
Published: almost 5 years ago
10.1002/2211-5463.12744
Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases
Cited by: 13
Author(s): Manli Zou, Zhuye Jie, Bota Cui, Honggang Wang, Qiang Feng, Yuanqiang Zou, Xiuqing Zhang, Huanming Yang, Jian Wang, Faming Zhang, Huijue Jia
Software Mentions: 5
Published: over 4 years ago
10.1099/mgen.0.000122
Aligner optimization increases accuracy and decreases compute times in multi-species sequence data
Cited by: 9
Author(s): Kelly Robinson, Aziah S. Hawkins, Ivette Santana-Cruz, Ricky S. Adkins, Amol C. Shetty, Sushma Nagaraj, Lisa Sadzewicz, Luke J. Tallon, David A. Rasko, Claire M. Fraser, Anup Mahurkar, Joana C. Silva, Julie C. Dunning Hotopp
Software Mentions: 5
Published: over 6 years ago
10.1371/journal.pgen.1007406
Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen
Cited by: 101
Author(s): Darach Miller, Nathan Brandt, David Gresham
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pgen.1008502
Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay
Cited by: 26
Author(s): Kevin H.-C. Wei, Doris Bachtrog
Software Mentions: 5
Published: over 4 years ago
10.1111/eva.12708
The genetic legacy of 50 years of desert bighorn sheep translocations
Cited by: 27
Author(s): Joshua P. Jahner, Marjorie D. Matocq, Jason L. Malaney, Mike Cox, Peregrine L. Wolff, Mitchell A. Gritts, Thomas L. Parchman
Software Mentions: 5
Published: over 5 years ago
10.1111/eva.13219
Whole genome genotyping reveals discrete genetic diversity in north‐east Atlantic maerl beds
Cited by: 3
Author(s): Tom L. Jenkins, Marie‐Laure Guillemin, Cornelia Simon-Nutbrown, Heidi L. Burdett, Jamie R. Stevens, Viviana Peña
Software Mentions: 5
Published: about 3 years ago
10.1002/ece3.5260
Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization
Cited by: 17
Author(s): Grey T. Gustafson, Alana Alexander, John S. Sproul, James M. Pflug, David R. Maddison, Andrew Edward Z. Short
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12936-020-3137-8
Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
Cited by: 25
Author(s): Andrew P. Morgan, Nicholas F. Brazeau, Billy Ngasala, Lwidiko E. Mhamilawa, Madeline Denton, Mwinyi Msellem, Ulrika Morris, Dayne L. Filer, Özkan Aydemir, Jeffrey A. Bailey, Jonathan B. Parr, Andreas Mårtensson, Anders Björkman, Jonathan J. Juliano
Software Mentions: 5
Published: over 4 years ago
10.1186/s13072-016-0079-z
Epigenetic dynamics of monocyte-to-macrophage differentiation
Cited by: 71
Author(s): Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller, Peter Ebert, Thomas Lengauer, Matthias Barann, Philip Rosenstiel, Gilles Gasparoni, Karl Nordström, Jörn Walter, Benedikt Brors, Gideon Zipprich, Bärbel Felder, Ludger Klein-Hitpaß, Corinna Attenberger, Gerd Schmitz, Bernhard Horsthemke
Software Mentions: 5
Published: almost 8 years ago
10.1111/1755-0998.12939
Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish <i>Amphiprion percula</i>
Cited by: 42
Author(s): Robert Lehmann, Damien J. Lightfoot, Celia Schunter, Craig Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Forêt, Michael L. Berumen, David J. Miller, Manuel Aranda, Takashi Gojobori, Philip L. Munday, Timothy Ravasi
Software Mentions: 5
Published: over 5 years ago
10.1098/rsos.170057
Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees (<i>Poecile gambeli</i>)
Cited by: 20
Author(s): Carrie L. Branch, Joshua P. Jahner, Dovid Y. Kozlovsky, Thomas L. Parchman, Vladimir V. Pravosudov
Software Mentions: 5
Published: about 7 years ago
10.1186/s12864-016-3118-z
Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species
Cited by: 10
Author(s): Weizhong Li, René Richter, Yunsup Jung, Quanyin Zhu, Robert W. Li
Software Mentions: 5
Published: over 7 years ago
10.1093/molbev/msv282
Population Structure Shapes Copy Number Variation in Malaria Parasites
Cited by: 43
Author(s): Ian H. Cheeseman, Becky A. Miller, John C. Tan, Aiping Tan, Shalini Nair, Standwell C. Nkhoma, Marcos De Donato, Hectorina Rodulfo, Arjen M. Dondorp, OraLee H. Branch, Lastenia Ruiz Mesía, Paul N. Newton, Mayfong Mayxay, Alfred Amambua-Ngwa, David J. Conway, François Nosten, Michael T. Ferdig, Tim Anderson
Software Mentions: 5
Published: over 8 years ago
10.1093/gbe/evz150
Evolution of Phototransduction Genes in Lepidoptera
Cited by: 26
Author(s): Aide Macias-Muñoz, Aline G. Rangel Olguin, Adriana D. Briscoe
Software Mentions: 5
Published: almost 5 years ago
10.1093/gbe/evaa187
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Cited by: 29
Author(s): Bonnie A. Fraser, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, Deborah Charlesworth, Roberta Bergero, Felix Bemm, Maria Hoffmann, Verena A. Kottler, Chang Liu, Christine Dreyer, Detlef Weigel
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-021-04317-y
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow
Cited by: 12
Author(s): Jochen Bathke, Gesine Lühken
Software Mentions: 5
Published: almost 3 years ago
10.1186/1756-0500-4-171
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Cited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: almost 13 years ago
10.1186/s12864-017-3936-7
Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Cited by: 35
Author(s): Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matt Clark
Software Mentions: 5
Published: almost 7 years ago
10.1186/s13059-017-1196-0
The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
Cited by: 88
Author(s): Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wei Wang, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sébastien Gagneux, Clifton E. Barry, Qian Gao
Software Mentions: 5
Published: about 7 years ago
10.3390/cells10040876
Stability of Imprinting and Differentiation Capacity in Naïve Human Cells Induced by Chemical Inhibition of CDK8 and CDK19
Cited by: 0
Author(s): Raquel Bernad, Cian J. Lynch, Rocío G. Urdinguio, Camille Stephan‐Otto Attolini, Mario F. Fraga, Manuel Serrano
Software Mentions: 5
Published: about 3 years ago
10.1038/s42003-020-01382-6
Adaptation by copy number variation increases insecticide resistance in the fall armyworm
Cited by: 40
Author(s): Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos A. Blanco, Sabine Hänniger, Anthony Bretaudeau, Fabrice Legeai, Nicolas Nègre, Juan Luís Jurat-Fuentes, Emmanuelle d’Alençon, Kiwoong Nam
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1005385
MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: almost 9 years ago
10.1371/journal.pgen.1006335
Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease
Cited by: 54
Author(s): Christoph Preuß, M. Capredon, Florian Wünnemann, Philippe Chétaille, Andrea Prince, Béatrice Godard, Séverine Leclerc, Nara Sobreira, Hua Ling, Philip Awadalla, Maryse Thibeault, Paul Khairy, Mark E. Samuels, Grégor Andelfinger
Software Mentions: 5
Published: over 7 years ago
10.1186/s12859-016-0902-3
NEAT: a framework for building fully automated NGS pipelines and analyses
Cited by: 7
Author(s): Patrick Schorderet
Software Mentions: 5
Published: over 8 years ago
10.1186/1755-8794-6-S2-S6
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
Cited by: 33
Author(s): Carrie Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie
Software Mentions: 5
Published: about 11 years ago
10.3389/fonc.2020.01195
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model
Cited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: almost 4 years ago
10.1111/mec.15539
No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets
Cited by: 16
Author(s): Ján Kočí, Jan Röslein, Jan Pačes, Jan Kotusz, Karel Halačka, Ján Koščo, Jakub Fedorčák, Nataliia Iakovenko, Karel Janko
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41396-020-00773-1
Benchmarking microbial growth rate predictions from metagenomes
Cited by: 45
Author(s): Andrew M. Long, Songjun Hou, J. Cesar Ignacio‐Espinoza, Jed A. Fuhrman
Software Mentions: 5
Published: over 3 years ago
10.1186/1471-2164-12-285
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
Cited by: 56
Author(s): José Blanca, Laura Pascual, Peio Ziarsolo, F. Nuez
Software Mentions: 4
Published: almost 13 years ago
10.1128/AEM.02177-20
Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens
Cited by: 5
Author(s): Rafał Kolenda, Michał Burdukiewicz, Marcjanna Wimonć, Adrianna Aleksandrowicz, Aamir Ali, István Szabó, Karsten Tedin, Josefin Bartholdson Scott, Derek Pickard, Peter Schierack
Software Mentions: 4
Published: over 3 years ago
10.1186/s12862-020-01689-2
Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity
Cited by: 2
Author(s): Britta Bueker, Marco Alexandre Guerreiro, Michael E. Hood, Andreas Brachmann, Sven Rahmann, Dominik Begerow
Software Mentions: 4
Published: over 3 years ago
10.3390/plants9101355
Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review
Cited by: 36
Author(s): Parmeshwar K. Sahu, Richa Sao, Suvendu Mondal, Gautam Vishwakarma, Sudhir Kumar Gupta, Vinay Kumar, Sudhir Singh, Deepak Sharma, Bikram Das
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0019350
Deep Sequencing of Organ- and Stage-Specific microRNAs in the Evolutionarily Basal Insect Blattella germanica (L.) (Dictyoptera, Blattellidae)
Cited by: 82
Author(s): Alexandre S. Cristino, Erica D. Tanaka, Mercedes Rubio, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 4
Published: about 13 years ago
10.1371/journal.pone.0121701
A Next Generation Semiconductor Based Sequencing Approach for the Identification of Meat Species in DNA Mixtures
Cited by: 58
Author(s): Francesca Bertolini, Marco Ciro Ghionda, Enrico D’Alessandro, Calogero Geraci, Vincenzo Chiofalo, Luca Fontanesi
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pone.0249254
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
Cited by: 32
Author(s): Barbara Schrörs, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Thomas Bukur, Thomas W. Rösler, Martin Löwer, Uğur Şahin
Software Mentions: 4
Published: over 2 years ago
10.1534/g3.119.400617
Population Selection and Sequencing of<i>Caenorhabditis elegans</i>Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance
Cited by: 21
Author(s): Amy K. Webster, Anthony Hung, Brad T. Moore, Ryan Guzman, James M. Jordan, Rebecca E. W. Kaplan, Jonathan D. Hibshman, Robyn E. Tanny, Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh
Software Mentions: 4
Published: over 4 years ago
10.1534/genetics.120.303460
Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in <i>Drosophila pseudoobscura</i>
Cited by: 16
Author(s): Zachary L. Fuller, Spencer Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 4
Published: over 3 years ago
10.1186/s12862-020-01739-9
Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Cited by: 4
Author(s): Kelly B. Klingler, Joshua P. Jahner, Thomas L. Parchman, Chris Ray, Mary M. Peacock
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2164-15-S6-S18
Comparative exomics of Phalariscultivars under salt stress
Cited by: 12
Author(s): Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian S. Jensen, Christopher E. Mason, Susanne Barth, Laxmi Parida
Software Mentions: 4
Published: over 9 years ago