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: about 4 years ago
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Papers Mentioning bwa 989

10.18632/oncotarget.26352
Genomic characterization of metastatic ultra-hypermutated interdigitating dendritic cell sarcoma through rapid research autopsy
Cited by: 6
Author(s): Hui-Zi Chen, Russell Bonneville, Lianbo Yu, Michele R. Wing, Julie W. Reeser, Melanie A. Krook, Jharna Miya, Eric Samorodnitsky, Amy M. Smith, Dorrelyn M. Martin, Thuy Dao, Qishan Guo, David A. Liebner, Aharon G. Freud, Patricia Allenby, Sameek Roychowdhury
Software Mentions: 4
Published: almost 6 years ago
10.3390/ijms22126503
Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake
Cited by: 5
Author(s): Giuseppe Persico, Francesca Casciaro, Alessandra Marinelli, Chiara Tonelli, Katia Petroni, Marco Giorgio
Software Mentions: 4
Published: over 3 years ago
10.7554/eLife.49002
Dynamic turnover of centromeres drives karyotype evolution in Drosophila
Cited by: 57
Author(s): Ryan Bracewell, Kamalakar Chatla, Matthew J. Nalley, Doris Bachtrog
Software Mentions: 4
Published: about 5 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: about 3 years ago
10.3390/ijms20051100
Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes
Cited by: 6
Author(s): Claudia Savini, Ruwen Yang, Larisa Savelyeva, Elke Göckel-Krzikalla, Agnes Hotz‐Wagenblatt, Frank Westermann, Frank Rösl
Software Mentions: 4
Published: over 5 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: almost 4 years ago
10.1371/journal.pone.0216366
Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia
Cited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.04729
The genetic architecture of gene expression levels in wild baboons
Cited by: 99
Author(s): Jenny Tung, Xiang Zhou, Susan C. Alberts, Matthew Stephens, Yoav Gilad
Software Mentions: 4
Published: over 9 years ago
10.7554/eLife.36828
Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor
Cited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.62865
Developmental hourglass and heterochronic shifts in fin and limb development
Cited by: 7
Author(s): Koh Onimaru, Kaori Tatsumi, Chiharu Tanegashima, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13100-021-00235-1
Genomic properties of variably methylated retrotransposons in mouse
Cited by: 13
Author(s): Jessica L. Elmer, Amir D. Hay, Noah J. Kessler, Tessa M. Bertozzi, Eve Ainscough, Anne C. Ferguson-Smith
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0081809
Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: almost 11 years ago
10.1186/s12859-016-0969-x
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data
Cited by: 11
Author(s): Mohammed‐Amin Madoui, Carole Dossat, Léo d'Agata, Jan van Oeveren, Edwin van der Vossen, Jean‐Marc Aury
Software Mentions: 4
Published: over 8 years ago
10.1186/s12983-019-0316-y
Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex
Cited by: 11
Author(s): Jana S. Dömel, Till‐Hendrik Macher, Lars Dietz, sabrina e duncan, Christoph Mayer, Andrey Rozenberg, Katherine Wolcott, Florian Leese, Roland R. Melzer
Software Mentions: 4
Published: about 5 years ago
10.3390/microorganisms8060940
Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum
Cited by: 3
Author(s): Jennifer Yuzon, Renaud Travadon, Mathu Malar C, Sucheta Tripathy, Nathan E. Rank, Heather K. Mehl, David M. Rizzo, Richard C. Cobb, Corinn Small, Tiffany Tang, Haley E. McCown, Matteo Garbelotto, Takao Kasuga
Software Mentions: 4
Published: over 4 years ago
10.3389/fpubh.2020.00455
Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages
Cited by: 1
Author(s): Alexander C. Outhred, Ulziijargal Gurjav, Peter Jelfs, Nadine McCallum, Qinning Wang, Grant A. Hill-Cawthorne, Ben J. Marais, Vitali Sintchenko
Software Mentions: 4
Published: about 4 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: about 10 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: about 5 years ago
10.3389/fpls.2020.01118
Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice
Cited by: 6
Author(s): Sarah J. Whitcomb, Apidet Rakpenthai, Franziska Brückner, Axel Fischer, S. Parmar, Alexander Erban, Joachim Kopka, Malcolm J. Hawkesford, Rainer Hoefgen
Software Mentions: 4
Published: over 4 years ago
10.3389/fpls.2020.00551
Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis
Cited by: 8
Author(s): Seulbee Lee, Myung‐Hee Kim, Jae Ho Lee, Jieun Jeon, June M. Kwak, Yun Ju Kim
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0094447
Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis
Cited by: 69
Author(s): Candice A. Stafford-Banks, Dorith Rotenberg, Brian R. Johnson, Anna E. Whitfield, Diane E. Ullman
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pone.0223680
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Cited by: 51
Author(s): Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
Software Mentions: 4
Published: almost 5 years ago
10.7554/eLife.67577
Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: over 3 years ago
10.1186/s12859-015-0795-6
TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pone.0131504
A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2164-14-494
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Cited by: 6
Author(s): Quang Trinh, Fei-Yang Arthur Jen, Ziru Zhou, Kar Ming Chu, Marc D. Perry, Ellen Kephart, Sergio Contrino, Peter Ruzanov, Lincoln Stein
Software Mentions: 4
Published: over 11 years ago
10.3389/fmicb.2018.00280
Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 6 years ago
10.1007/s00442-020-04797-4
Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment
Cited by: 21
Author(s): Mark Anthony, Kristina A. Stinson, Jessica A. M. Moore, Serita D. Frey
Software Mentions: 4
Published: about 4 years ago
10.3389/fmicb.2019.01400
Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pntd.0007612
An improved genome assembly of the fluke Schistosoma japonicum
Cited by: 44
Author(s): Fang Luo, Mingbo Yin, Xiaojin Mo, Chengsong Sun, Qunfeng Wu, Bingkuan Zhu, Manyu Xiang, Jipeng Wang, Yi Wang, Jian Li, Ting Zhang, Bin Xu, Huajun Zheng, Zijian Feng, Wei Hu
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.69808
Common host variation drives malaria parasite fitness in healthy human red cells
Cited by: 15
Author(s): Emily R. Ebel, Frans A. Kuypers, Carrie Lin, Dmitri A. Petrov, Elizabeth S. Egan
Software Mentions: 4
Published: about 3 years ago
10.7554/eLife.20983
A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: almost 8 years ago
10.3389/fgene.2019.00826
Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing
Cited by: 27
Author(s): Stephen R. Doyle, Geetha Sankaranarayanan, Fiona Allan, Duncan Berger, Pablo David Jimenez Castro, James B. Collins, Thomas Crellen, María A. Duque-Correa, Peter Ellis, Tegegn G. Jaleta, Roz Laing, Kirsty Maitland, Catherine McCarthy, Tchonfienet Moundai, Ben Softley, Elizabeth A. Thiele, Philippe Tchindebet Ouakou, John Vianney Tushabe, Joanne P. Webster, Adam Weiss, James B. Lok, Eileen Devaney, Ray M. Kaplan, James A. Cotton, Matthew Berriman, Nancy Holroyd
Software Mentions: 4
Published: about 5 years ago
10.1099/mgen.0.000059
Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK
Cited by: 23
Author(s): Ali Al‐Shahib, Anthony Underwood, Baharak Afshar, Claire E. Turner, Theresa Lamagni, Shiranee Sriskandan, Androulla Efstratiou
Software Mentions: 4
Published: over 8 years ago
10.1099/mgen.0.000418
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Cited by: 16
Author(s): Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene R. Bowers, David M. Engelthaler, Apurva Narechania, Darrin Lemmer, Júlio Croda, Jason R Andrews
Software Mentions: 4
Published: over 4 years ago
10.1099/mgen.0.000039
Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case
Cited by: 9
Author(s): Steven T. Pullan, Talima Pearson, Jennie Latham, Joanne Mason, Barry Atkinson, Nigel Silman, Chung K. Marston, Jason W. Sahl, Dawn N. Birdsell, Alex R. Hoffmaster, Paul Keim, Richard Vipond
Software Mentions: 4
Published: about 9 years ago
10.1002/humu.23674
Allele balance bias identifies systematic genotyping errors and false disease associations
Cited by: 17
Author(s): Francesc Muyas, Mattia Bosio, Anna Puig, Hana Sušak, Laura Domènech, Geòrgia Escaramís, Luís Zapata, German Demidov, Xavier Estivill, Raquel Rabionet, Stephan Ossowski
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-016-2738-7
Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102
Cited by: 22
Author(s): Nathan Brown, Robert F. Mueller, Jonathan W. Shepardson, Zachary C. Landry, Jeff Morré, Christoph Maier, F. Joan Hardy, Theo W. Dreher
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-021-92993-4
Whole genome sequencing of nearly isogenic WMI and WLI inbred rats identifies genes potentially involved in depression and stress reactivity
Cited by: 5
Author(s): Tristan V de Jong, Panjun Kim, Victor Guryev, Megan K. Mulligan, Robert W. Williams, Eva E. Redei, Hao Chen
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-021-07417-4
Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae
Cited by: 3
Author(s): Klavdija Pačnik, Mojca Ogrizović, Matthias Diepold, Tobias Eisenberg, Mia Žganjar, Gašper Žun, Beti Kužnik, Cene Gostinčar, Tomaž Curk, Uroš Petrovič, Klaus Natter
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41398-018-0342-0
Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia
Cited by: 15
Author(s): John F. Fullard, Alexander Charney, Georgios Voloudakis, Andrew Uzilov, Vahram Haroutunian, Panos Roussos
Software Mentions: 4
Published: almost 6 years ago
10.3389/fgene.2019.00854
New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data
Cited by: 7
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 4
Published: about 5 years ago
10.1128/mBio.02317-16
<i>Plasmodium falciparum Maf1</i> Confers Survival upon Amino Acid Starvation
Cited by: 26
Author(s): Kyle Jarrod McLean, Marcelo Jacobs‐Lorena
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pgen.1004410
Speciation and Introgression between Mimulus nasutus and Mimulus guttatus
Cited by: 227
Author(s): Yaniv Brandvain, Amanda M. Kenney, Lex E. Flagel, Graham Coop, Andrea L. Sweigart
Software Mentions: 4
Published: over 10 years ago
10.1038/s41598-020-76137-8
Evolution from adherent to suspension: systems biology of HEK293 cell line development
Cited by: 41
Author(s): Magdalena Malm, Rasool Saghaleyni, Magnus Lundqvist, Marco Giudici, Véronique Chotteau, Ray Field, Paul Varley, Diane Hatton, Luigi Grassi, Thomas Svensson, Jens Nielsen, Johan Rockberg
Software Mentions: 4
Published: about 4 years ago
10.12688/f1000research.15895.2
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
Cited by: 5
Author(s): Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander Dilthey
Software Mentions: 4
Published: almost 6 years ago
10.1007/s11306-017-1270-3
The dental calculus metabolome in modern and historic samples
Cited by: 43
Author(s): Irina M. Velsko, Katherine A. Overmyer, Camilla Speller, Lauren Klaus, Matthew J. Collins, Louise Loe, Laurent Frantz, Krithivasan Sankaranarayanan, Cecil M. Lewis, Juan Bautista Rodriguez Martinez, Eros Chaves, Joshua J. Coon, Greger Larson, Christina Warinner
Software Mentions: 4
Published: about 7 years ago
10.1002/1878-0261.12651
Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival
Cited by: 66
Author(s): Lisa Quetel, Clément Meiller, Jean-Baptiste Assié, Yuna Blum, Sandrine Imbeaud, François Montagne, Robin Tranchant, Julien De Wolf, Stefano Caruso, Marie‐Christine Copin, Véronique Hofman, Laure Gibault, Cécile Badoual, Ecaterina Pintilie, Paul Hofman, I. Monnet, Arnaud Scherpereel, Françoise Le Pimpec‐Barthes, Jessica Zucman‐Rossi, Marie‐Claude Jaurand, Didier Jean
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1006297
Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution
Cited by: 24
Author(s): Vítor G. Faria, Nelson Martins, Sara Magalhães, Tânia F. Paulo, Viola Nolte, Christian Schlötterer, Élio Sucena, Luı́s Teixeira
Software Mentions: 4
Published: about 8 years ago
10.1002/lno.11361
The global <i>Microcystis</i> interactome
Cited by: 51
Author(s): Katherine V. Cook, Chuang Li, Haiyuan Cai, Lee R. Krumholz, K. David Hambright, Hans W. Paerl, Morgan M. Steffen, Alan E. Wilson, Michele A. Burford, Hans‐Peter Grossart, David P. Hamilton, Helong Jiang, Assaf Sukenik, Delphine Latour, Elisabeth I. Meyer, Judit Padisák, Boqiang Qin, Richard M. Zamor, Guangwei Zhu
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-019-39395-9
Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages
Cited by: 24
Author(s): Cheng Wang, Luca Nanni, Boris Novakovic, Wout Megchelenbrink, Т. Н. Кузнецова, Hendrik G. Stunnenberg, Stefano Ceri, Colin Logie
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pgen.1009745
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution
Cited by: 9
Author(s): Matthew H. Van Dam, Analyn Cabras, James Henderson, Andrew J. Rominger, Cynthia Pérez Estrada, Arina D. Omer, Olga Dudchenko, E Aiden, Athena Lam
Software Mentions: 4
Published: about 3 years ago
10.1038/s41598-019-52832-z
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies
Cited by: 14
Author(s): Weihong Qi, Andrea Colarusso, Miriam Olombrada, Ermenegilda Parrilli, Andrea Patrignani, Maria Luisa Tutino, Macarena Toll‐Riera
Software Mentions: 4
Published: about 5 years ago
10.1093/bib/bbw020
A review of bioinformatic pipeline frameworks
Cited by: 155
Author(s): Jeremy Leipzig
Software Mentions: 4
Published: over 8 years ago
10.1002/ece3.7531
Population differences in Chinook salmon (<i>Oncorhynchus tshawytscha</i>) DNA methylation: Genetic drift and environmental factors
Cited by: 6
Author(s): Clare J. Venney, Ben J. G. Sutherland, Terry D. Beacham, Daniel D. Heath
Software Mentions: 4
Published: over 3 years ago
10.1002/ece3.5463
Impact of demography on linked selection in two outcrossing Brassicaceae species
Cited by: 9
Author(s): Tiina M. Mattila, Benjamin Laenen, Róbert Horváth, Tuomas Hämälä, Outi Savolainen, Tanja Slotte
Software Mentions: 4
Published: over 5 years ago
10.1111/imb.12688
Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13040-017-0149-1
Genetically improved BarraCUDA
Cited by: 7
Author(s): William B. Langdon, Brian Y.H. Lam
Software Mentions: 4
Published: over 7 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: about 4 years ago
10.15252/embj.2019104159
Deciphering the regulatory landscape of fetal and adult γδ T‐cell development at single‐cell resolution
Cited by: 38
Author(s): Sagar, Maria Pokrovskii, Josip Stefan Herman, Shruti Naik, Elisabeth Sock, Patrice Zeis, Ute Lausch, Michael Wegner, Yakup Tanriver, Dan R. Littman, Dominic Grün
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1007376
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Cited by: 59
Author(s): Michael B. Burns, Emmanuel Montassier, Juan E. Abrahante, Sambhawa Priya, David Niccum, Alexander Khoruts, Timothy K. Starr, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: over 6 years ago
10.1016/j.cub.2017.04.057
Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2
Cited by: 76
Author(s): Thomas W. Marchant, Edward J. Johnson, Lynn McTeir, Craig Johnson, Adam Gow, Tiziana Liuti, Dana Kuehn, Karen L. Svenson, Mairead Lesley Bermingham, Michaela Drögemüller, Marc Nussbaumer, Megan Davey, David Argyle, Roger M. Powell, Sérgio Guilherme, Johann Lang, Gert ter Haar, Tosso Leeb, Tobias Schwarz, Richard J. Mellanby, Dylan Clements, Jeffrey J. Schoenebeck
Software Mentions: 4
Published: over 7 years ago
10.1002/ajpa.23763
The efficacy of whole human genome capture on ancient dental calculus and dentin
Cited by: 21
Author(s): Kirsten A. Ziesemer, Jazmín Ramos‐Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno L. P. Hoogland, Courtney A. Hofman, Domingo C. Salazar‐García, Bruno Fröhlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pgen.1007332
Genome-wide detection of conservative site-specific recombination in bacteria
Cited by: 37
Author(s): Ognjen Sekulović, Elizabeth M. Garrett, Jacob Bourgeois, Rita Tamayo, Aimee Shen, Andrew Camilli
Software Mentions: 4
Published: over 6 years ago
10.1093/gigascience/giy081
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
Cited by: 14
Author(s): Xia Li, Dongmei Ai, Hojoon Lee, Noemi Andor, Chao Li, Nancy R. Zhang, Hanlee P. Ji
Software Mentions: 4
Published: over 6 years ago
10.1073/pnas.2001337117
Natural selection maintains species despite frequent hybridization in the desert shrub <i>Encelia</i>
Cited by: 21
Author(s): Christopher Todd DiVittorio, Sonal Singhal, Adam B. Roddy, Felipe Zapata, David D. Ackerly, Bruce G. Baldwin, Craig R. Brodersen, Alberto Búrquez, Paul V. A. Fine, Mayra Padilla Flores, Elizabeth Solis, Jaime Morales-Villavicencio, David Morales-Arce, Donald W. Kyhos
Software Mentions: 4
Published: almost 4 years ago
10.1098/rsos.180903
Bracketing phenogenotypic limits of mammalian hybridization
Cited by: 26
Author(s): Yoland Savriama, Mia Valtonen, Juhana Kammonen, Pasi Rastas, Olli‐Pekka Smolander, Ari Löytynoja, Teemu J. Häkkinen, Ian J. Corfe, Sylvain Gerber, Isaac Salazar‐Ciudad, Lars Paulín, Liisa Holm, Ari Löytynoja, Petri Auvinen, Jukka Jernvall
Software Mentions: 4
Published: about 6 years ago
10.7717/peerj.2477
Whole genome sequencing of<i>Streptococcus pneumoniae</i>: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
Cited by: 103
Author(s): Georgia Kapatai, Carmen Sheppard, Ali Al‐Shahib, David Litt, Anthony Underwood, Timothy G. Harrison, Norman K. Fry
Software Mentions: 4
Published: about 8 years ago
10.1371/journal.pgen.1005848
A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects
Cited by: 47
Author(s): Jinglan Zhang, Véronik Lachance, Adam D. Schaffner, Xianting Li, Anastasia Fedick, Lauren E. Kaye, Jun Liao, Jill A. Rosenfeld, Naomi Yachelevich, Mary Lynn Chu, Wendy G. Mitchell, Richard G. Boles, Ellen Moran, Mari Tokita, Elizabeth Gorman, Kaytee Bagley, Wei Zhang, Fan Xia, Magalie S. Leduc, Yaping Yang, Christine M. Eng, Lee Jun Wong, Raphael Schiffmann, George A. Diaz, Ruth Kornreich, Ryan Thummel, Melissa P. Wasserstein, Zhenyu Yue, Lisa Edelmann
Software Mentions: 4
Published: over 8 years ago
10.1186/s12870-016-0788-2
Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
Cited by: 33
Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: over 8 years ago
10.7717/peerj.10947
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Cited by: 34
Author(s): James A. Fellows Yates, Thiseas Christos Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime Garcia, Judith Neukamm, Alexander Peltzer
Software Mentions: 4
Published: over 3 years ago
10.5808/GI.2020.18.1.e6
Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
Cited by: 2
Author(s): Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, Erin L. Crowgey
Software Mentions: 4
Published: over 4 years ago
10.1016/j.patter.2021.100212
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Cited by: 26
Author(s): Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti‐Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
Software Mentions: 4
Published: over 3 years ago
10.1007/s10577-020-09643-0
CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites
Cited by: 4
Author(s): Michi Miura, Honglin Chen
Software Mentions: 4
Published: about 4 years ago
10.1038/s42003-020-0888-2
Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells
Cited by: 21
Author(s): Soyeong Jun, Hee‐Jung Lim, Honggu Chun, Ji Hyun Lee, Duhee Bang
Software Mentions: 4
Published: over 4 years ago
10.3390/v12111255
Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION
Cited by: 22
Author(s): Crystal M. Gigante, Gowri Yale, Rene Edgar Condori, Niceta Cunha Costa, Nguyen Van Duc Long, Phạm Quang Minh, Vo Dinh Chuong, Nguyen Dang Tho, Nguyen Tat Thanh, Nguyen Xuan Thin, Nguyễn Thị Hồng Hạnh, Gati Wambura, Frederick Ade, Oscar Mito, Veronicah Chuchu, Mathew Muturi, Athman Mwatondo, Katie Hampson, Samuel M. Thumbi, Byron G Thomae, Victor Hugo de Paz, Sergio Meneses, Peninah Munyua, David Morán, Loren Cadena, Andrew D Gibson, Crystal M. Gigante, Emily G. Pieracci, Li Yu
Software Mentions: 4
Published: about 4 years ago
10.1016/j.gpb.2019.01.006
Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis
Cited by: 3
Author(s): Jun Wang, Xiaowen Chen, Funan He, Xian‐Rong Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su
Software Mentions: 4
Published: over 4 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: over 13 years ago
10.1186/s13059-021-02396-x
Chromosome-level genome assembly of a regenerable maize inbred line A188
Cited by: 28
Author(s): Guifang Lin, Cheng He, Jun Zheng, Dal Hoe Koo, Ha Le, Huakun Zheng, Tej Man Tamang, Jianqing Lin, Yan Liu, Mingxia Zhao, Yangfan Hao, Frank McFraland, Bo Wang, Qin Yang, Haibao Tang, Donald R. McCarty, Hairong Wei, Myeong Je Cho, Sunghun Park, Heidi F. Kaeppler, Shawn M. Kaeppler, Yun-Jun Liu, Nathan M. Springer, Patrick S. Schnable, Guoying Wang, Frank F. White, Sanzhen Liu
Software Mentions: 4
Published: over 3 years ago
10.1093/ve/veaa012
Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Cited by: 13
Author(s): Florent Lassalle, Mathew A. Beale, Tehmina Bharucha, Charlotte A. Williams, Rachel Williams, Juliana Cudini, Richard A. Goldstein, Tanzina Haque, Daniel P. Depledge, Judith Breuer
Software Mentions: 4
Published: almost 5 years ago
10.3389/fmicb.2018.01551
Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
Cited by: 22
Author(s): Pengfei Liu, Yahai Lu
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pbio.1002112
Natural Selection Constrains Neutral Diversity across A Wide Range of Species
Cited by: 270
Author(s): Russell Corbett-Detig, Daniel L. Hartl, Timothy B. Sackton
Software Mentions: 4
Published: over 9 years ago
10.1186/s13015-021-00181-w
Fast lightweight accurate xenograft sorting
Cited by: 8
Author(s): Jens Zentgraf, Sven Rahmann
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-020-02022-2
RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Cited by: 28
Author(s): Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Li Pan, Bao‐Fa Sun, Ying Yang, Ning Zhang, Yongliang Zhao, Hailin Wang, Feng Liu, Qiangfeng Cliff Zhang, Yun‐Gui Yang
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pbio.3000128
Genetic redundancy fuels polygenic adaptation in Drosophila
Cited by: 198
Author(s): Neda Barghi, Raymond Tobler, Viola Nolte, Ana Marija Jakšić, François Mallard, Kerstin Otte, Marlies Dolezal, Thomas Taus, Robert Kofler, Christian Schlötterer
Software Mentions: 4
Published: almost 6 years ago
10.1186/s13059-020-02029-9
Gapless assembly of maize chromosomes using long-read technologies
Cited by: 87
Author(s): Jianing Liu, Arun S. Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Víctor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David Kudrna, Magdy S. Alabady, Candice N. Hirsch, Kevin Fengler, Doreen Ware, Todd P. Michael, Matthew B. Hufford, R. Kelly Dawe
Software Mentions: 4
Published: over 4 years ago
10.1093/jhered/esaa057
Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (<i>Felis catus</i>) and Asian Leopard Cat (<i>Prionailurus bengalensis</i>)
Cited by: 22
Author(s): Kevin R. Bredemeyer, Andrew Harris, Gang Li, Li-Jun Zhao, Nicole M. Foley, Melody Roelke‐Parker, Stephen J. O’Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2148-13-48
Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species
Cited by: 39
Author(s): Yeting Zhang, Mónica Fernández‐Aparicio, Eric Wafula, Mita Das, Yuannian Jiao, Norman J. Wickett, Loren Honaas, Paula E. Ralph, Martin F. Wojciechowski, Michael P. Timko, John I. Yoder, James H. Westwood, Claude W. dePamphilis
Software Mentions: 3
Published: almost 12 years ago
10.1002/1878-0261.12119
Novel landscape of HLA-G isoforms expressed in clear cell renal cell carcinoma patients
Cited by: 62
Author(s): Diana Tronik‐Le Roux, Julie Renard, Jérôme Verine, Victor Renault, Emmanuel Tubacher, Joël LeMaoult, Nathalie Rouas‐Freiss, Jean‐François Deleuze, François Desgrandschamps, Edgardo D. Carosella
Software Mentions: 3
Published: about 7 years ago
10.1186/s13059-015-0696-z
FOXM1 binds directly to non-consensus sequences in the human genome
Cited by: 47
Author(s): Deborah A. Sanders, Michael V. Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0217255
A competence-regulated toxin-antitoxin system in Haemophilus influenzae
Cited by: 3
Author(s): Hailey Findlay Black, Scott Mastromatteo, Sunita Sinha, Rachel Ehrlich, Corey Nislow, Joshua Chang Mell, Rosemary J. Redfield
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12711-015-0111-y
Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs
Cited by: 32
Author(s): Joaquim Corominas, Jorge Augusto Petroli Marchesi, Anna Puig-Oliveras, Manuel Revilla, Jordi Estellé, E. Alves, Josep María Folch, María Ballester
Software Mentions: 3
Published: over 9 years ago
10.1186/s12864-018-4508-1
CoVaCS: a consensus variant calling system
Cited by: 22
Author(s): Matteo Chiara, Silvia Gioiosa, Giovanni Chillemi, Mattia D’Antonio, Tiziano Flati, Ernesto Picardi, Federico Zambelli, David S. Horner, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0065793
Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing
Cited by: 41
Author(s): Alma Brolund, Oscar Franzén, Öjar Melefors, Karin Tegmark-Wisell, Linus Sandegren
Software Mentions: 3
Published: over 11 years ago
10.1186/s13059-016-1056-3
Fitness consequences of polymorphic inversions in the zebra finch genome
Cited by: 41
Author(s): Ulrich Knief, Georg Hemmrich-Stanisak, Michael Wittig, André Franke, Simon C. Griffith, Bart Kempenaers, Wolfgang Forstmeier
Software Mentions: 3
Published: about 8 years ago
10.3390/genes12010092
Contribution of Mitochondrial DNA Heteroplasmy to the Congenital Cardiac and Palatal Phenotypic Variability in Maternally Transmitted 22q11.2 Deletion Syndrome
Cited by: 0
Author(s): Boris Rebolledo‐Jaramillo, María Gabriela Obregón, Victoria Huckstadt, Abel Gomez, Gabriela M. Repetto
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0182392
metaSNV: A tool for metagenomic strain level analysis
Cited by: 93
Author(s): Paul Igor Costea, Robin Munch, Luís Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Software Mentions: 3
Published: over 7 years ago
10.1093/g3journal/jkab211
Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the <i>Ogataea polymorpha</i> species complex
Cited by: 2
Author(s): Sara J. Hanson, Eoin Ó Cinnéide, Letal I. Salzberg, Kenneth H. Wolfe, Jamie McGowan, David A. Fitzpatrick, Kate Matlin
Software Mentions: 3
Published: over 3 years ago
10.3390/genes12030426
Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide
Cited by: 10
Author(s): Jessica Lumian, Anne D. Jungblut, Megan L Dillion, Ian Hawes, Peter T. Doran, Tyler J. Mackey, Gregory J. Dick, Christen L. Grettenberger, D. Y. Sumner
Software Mentions: 3
Published: over 3 years ago
10.1111/mec.14972
Multiple chromosomal rearrangements in a hybrid zone between <i>Littorina saxatilis</i> ecotypes
Cited by: 93
Author(s): Rui Faria, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily Moriarty Lemmon, Marina Rafajlović, Marina Panova, Mark Ravinet, Kerstin Johannesson, Anja M. Westram, Roger K. Butlin
Software Mentions: 3
Published: over 5 years ago