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)
1 version
Latest release: about 4 years ago
170 downloads last month

Papers Mentioning bwa 989

10.1186/gb-2011-12-9-r90
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice
Cited by: 22
Author(s): Jennifer Hilton, Morag A. Lewis, M’hamed Grati, Neil J. Ingham, Selina Pearson, Roman A. Laskowski, David J. Adams, Karen P. Steel
Software Mentions: 2
Published: almost 14 years ago
10.1038/s41598-020-77835-z
Specific capture and whole-genome phylogeography of Dolphin morbillivirus
Cited by: 8
Author(s): Francesco Cerutti, Federica Giorda, Carla Grattarola, Walter Mignone, Chiara Beltramo, Nicolas Keck, Alessio Lorusso, Di Francesco G, Ludovica Di Renzo, Giovanni Di Guardo, Maria Goria, Loretta Masoero, Pier Luigi Acutis, Cristina Casalone, Simone Peletto
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-020-69822-1
Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis
Cited by: 19
Author(s): Karlijn Hasaart, Freek Manders, Marie-Louise van der Hoorn, Mark Verheul, Tomasz Poplonski, Ewart Kuijk, Susana M. Chuva de Sousa Lopes, Ruben van Boxtel
Software Mentions: 2
Published: over 4 years ago
10.1186/gb-2010-11-12-r125
Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
Cited by: 83
Author(s): Peter L. Chang, Brian P. Dilkes, Michelle M. McMahon, Luca Comai, Sergey V. Nuzhdin
Software Mentions: 2
Published: almost 15 years ago
10.1038/s41598-020-62990-0
Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis
Cited by: 15
Author(s): Yuichi I. Naito, Ioana N. Meleg, Marius Robu, Marius Vlaicu, Dorothée G. Drucker, Christoph Wißing, Michael Hofreiter, Axel Barlow, Hervé Bocherens
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-14-268
Centroid based clustering of high throughput sequencing reads based on n-mer counts
Cited by: 17
Author(s): Alexander Solovyov, W. Ian Lipkin
Software Mentions: 2
Published: about 11 years ago
10.1111/1755-0998.12891
Using <scp>DNA</scp> metabarcoding for simultaneous inference of common vampire bat diet and population structure
Cited by: 62
Author(s): Kristine Bohmann, Shyam Gopalakrishnan, Martin Nielsen, Luisa dos Santos Bay Nielsen, Gareth Jones, Daniel G. Streicker, M. Thomas P. Gilbert
Software Mentions: 2
Published: over 6 years ago
10.1128/genomeA.01243-16
Complete Genome Sequence of a Vaccinal Newcastle Disease Virus Strain Isolated from an Owl ( Rhinoptynx clamator )
Cited by: 2
Author(s): Steven Van Borm, Laís Santos Rizotto, Leila Sabrina Ullmann, Guilherme Pereira Scagion, Camila Dantas Malossi, Raphael Mausbach Simão, João Pessoa Araújo, Izabelle M. Cordeiro, Lara Borges Keid, Tiago Marcelo Oliveira, Rodrigo Martins Soares, Matheus Cavalheiro Martini, Maria Ângela Orsi, Clarice Weis Arns, Helena Lage Ferreira
Software Mentions: 2
Published: almost 8 years ago
10.1099/mgen.0.000114
Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing
Cited by: 23
Author(s): Catherine Ludden, Sandra Reuter, Kim Judge, Theodore Gouliouris, Beth Blane, Francesc Español i Coll, Plamena Naydenova, Martin Hunt, Alan S. Tracey, Katie L. Hopkins, Nicholas M. Brown, Neil Woodford, Julian Parkhill, Sharon J. Peacock
Software Mentions: 2
Published: over 7 years ago
10.1242/dmm.034561
Cancer modeling by Transgene Electroporation in Adult Zebrafish (TEAZ)
Cited by: 37
Author(s): Scott J. Callahan, Stephanie Tepan, Yan M. Zhang, Helen Lindsay, Alexa Burger, Nathaniel R. Campbell, Isabella S. Kim, Travis J. Hollmann, Lorenz Studer, Christian Mosimann, Richard M. White
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pbio.3000582
Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
Cited by: 57
Author(s): Yalin Liu, Handong Su, Jing Zhang, Yang Liu, Chao Feng, Fangpu Han
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-018-2124-3
CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing
Cited by: 15
Author(s): Angel Mojarro, Julie Hachey, Gary Ruvkun, M. T. Zuber, Christopher E. Carr
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-020-07226-1
Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears
Cited by: 6
Author(s): Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan, Wu Jun
Software Mentions: 2
Published: about 4 years ago
10.3390/plants8100375
A Novel Stay-Green Mutant of Rice with Delayed Leaf Senescence and Better Harvest Index Confers Drought Tolerance
Cited by: 20
Author(s): M. K. Ramkumar, S. Kumar, Kishor Gaikwad, Ravi P. Pandey, Viswanathan Chinnusamy, Nagendra Singh, Ashok Kumar Singh, Trilochan Mohapatra, Amitha Mithra Sevanthi
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-019-48229-7
Analysis of head and neck carcinoma progression reveals novel and relevant stage-specific changes associated with immortalisation and malignancy
Cited by: 29
Author(s): Ratna Veeramachaneni, Thomas D. J. Walker, Timothée Revil, Antoine DeWeck, Dunarel Badescu, James O’Sullivan, Catherine L. Higgins, Louise Elliott, Triantafillos Liloglou, Janet M. Risk, Richard Shaw, Lynne Hampson, Ian N. Hampson, Simon Dearden, Robert Woodwards, Stephen S. Prime, Keith D. Hunter, Eric Kenneth Parkinson, Jiannis Ragoussis, Nalin Thakker
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-45760-5
SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia
Cited by: 9
Author(s): Brian M. Forde, Lauren J. McAllister, James C. Paton, Adrienne W. Paton, Scott A. Beatson
Software Mentions: 2
Published: over 5 years ago
10.1002/ece3.6340
Fine‐scale structure among mesophotic populations of the great star coral <i>Montastraea cavernosa</i> revealed by SNP genotyping
Cited by: 9
Author(s): Crawford Drury, Rocío Pérez‐Portela, Xaymara M. Serrano, Marjorie F. Oleksiak, Andrew C. Baker
Software Mentions: 2
Published: over 4 years ago
10.1002/ece3.5646
Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species
Cited by: 21
Author(s): Sara Kurland, Christopher W. Wheat, Maria de la Paz Celorio‐Mancera, Verena E. Kutschera, Jason Hill, Anastasia Andersson, Carl-Johan Rubin, Leif Andersson, Nils Ryman, Linda Laikre
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-019-43292-6
Identification of regulatory variants associated with genetic susceptibility to meningococcal disease
Cited by: 3
Author(s): Lisa Borghini, Eileen Png, Alexander Binder, Victoria J. Wright, Ellie Pinnock, Ronald de Groot, Jan A. Hazelzet, Marieke Emonts, Michiel van der Flier, Luregn J Schlapbach, Suzanne T. Anderson, Fatou Secka, Antonio Salas, Colin G. Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan Coin, Taco W. Kuijpers, Federico Martinón‐Torres, Werner Zenz, Michael Levin, Martin L. Hibberd, Sonia Dávila
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-018-34812-x
A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Cited by: 35
Author(s): Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2164-13-284
Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct
Cited by: 85
Author(s): Hao Hu, Pradip K. Bandyopadhyay, Baldomero M. Olivera, Mark Yandell
Software Mentions: 2
Published: over 12 years ago
10.1534/g3.118.200798
A<i>Very Oil Yellow1</i>Modifier of the<i>Oil Yellow1-N1989</i>Allele Uncovers a Cryptic Phenotypic Impact of<i>Cis</i>-regulatory Variation in Maize
Cited by: 8
Author(s): Rajdeep S. Khangura, Sandeep Marla, Bala P. Venkata, Nicholas Heller, Gurmukh S. Johal, Brian P. Dilkes
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12862-020-1580-3
The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster
Cited by: 31
Author(s): Shiqi Luo, Hong Zhang, Yuange Duan, Xuesong Yao, Andrew G. Clark, Jian Lü
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12864-015-1681-3
Interlocus gene conversion explains at least 2.7 % of single nucleotide variants in human segmental duplications
Cited by: 17
Author(s): Beth L. Dumont
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2164-13-673
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings
Cited by: 31
Author(s): Thomas Müller, Ingo Ensminger, Karl Schmid
Software Mentions: 2
Published: almost 12 years ago
10.1038/s41598-018-31081-6
No association between resistance mutations, empiric antibiotic, and mortality in ceftriaxone-resistant Escherichia coli and Klebsiella pneumoniae bacteremia
Cited by: 7
Author(s): Shi Thong Heng, Swaine L. Chen, Joshua Wong, David C. Lye, Tat Ming Ng
Software Mentions: 2
Published: over 6 years ago
10.1002/ece3.3924
Ancient pathogen DNA in human teeth and petrous bones
Cited by: 35
Author(s): Ashot Margaryan, Henrik Hansen, Simon Rasmussen, Martin Sikora, Vyacheslav Moiseyev, Alexandr Khoklov, Andrey Epimakhov, Levon Yepiskoposyan, Айвар Крийска, Liivi Varul, Lehti Saag, Niels Lynnerup, Eske Willerslev, Morten E. Allentoft
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-23342-1
Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
Cited by: 8
Author(s): Sarun Sereewattanawoot, Ayako Suzuki, Masahide Seki, Yoshitaka Sakamoto, Takashi Kohno, Sumio Sugano, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 2
Published: over 6 years ago
10.1002/ece3.4603
Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden
Cited by: 8
Author(s): Audrey Rohfritsch, Maxime Galan, Mathieu Gautier, Karim Gharbi, Gert E. Olsson, Bernhard Gschloessl, Caroline Zeimes, Sophie Vanwambeke, Renaud Vitalis, Nathalie Charbonnel
Software Mentions: 2
Published: about 6 years ago
10.7717/peerj.1508
Reproducibility of SNV-calling in multiple sequencing runs from single tumors
Cited by: 3
Author(s): Dakota Z. Derryberry, Matthew C. Cowperthwaite, Claus O. Wilke
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12864-021-08037-8
A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum
Cited by: 8
Author(s): Eduardo Sousa Varela, Michaël Bekaert, Luciana Nakaghi Ganeco-Kirschnik, Lucas Simon Torati, L. Shiotsuki, Fernanda L. de Almeida, L. C. V. Villela, Fabrício Pereira Rezende, Aurisan da Silva Barroso, Luiz Eduardo Lima de Freitas, John B. Taggart, Hervé Migaud
Software Mentions: 2
Published: about 3 years ago
10.1038/srep08248
Whole-genome sequencing reveals that mutations in myosin-5 confer resistance to the fungicide phenamacril in Fusarium graminearum
Cited by: 58
Author(s): Zong‐Ping Zheng, Yiping Hou, Yiqiang Cai, Yu Zhang, Yanjun Li, Mingguo Zhou
Software Mentions: 2
Published: almost 10 years ago
10.1080/22221751.2019.1637702
Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles
Cited by: 59
Author(s): Yuki Matsumoto, Takeshi Kinjo, Daisuke Motooka, Daijiro Nabeya, Nicolas Jung, Kohei Uechi, Toshihiro Horii, Tetsuya Iida, Jiro Fujita, Shota Nakamura
Software Mentions: 2
Published: almost 6 years ago
10.1038/srep43613
Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus
Cited by: 41
Author(s): Junko Yoshida, Keiko Akagi, Ryo Misawa, Chikara Kokubu, Junji Takeda, Kyoji Horie
Software Mentions: 2
Published: over 7 years ago
10.1099/mgen.0.000343
Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture
Cited by: 5
Author(s): George C. Russell, Ruth N. Zadoks, Kim Willoughby, Claudia Bachofen
Software Mentions: 2
Published: over 4 years ago
10.1186/s13072-021-00389-5
A cookbook for DNase Hi-C
Cited by: 9
Author(s): Maria Gridina, Evgeniy A. Mozheiko, Э. С. Валеев, Л. П. Назаренко, М. Е. Лопаткина, Ж. Г. Маркова, M. I. Yablonskaya, Viktoria Yu Voinova, N.V. Shilova, I. N. Lebedev, Veniamin Fishman
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-016-1417-7
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers
Cited by: 36
Author(s): Ariane Leoni Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
Software Mentions: 2
Published: almost 8 years ago
10.1038/srep38639
Transient appearance of circulating tumor DNA associated with de novo treatment
Cited by: 7
Author(s): Kikuya Kato, Junji Uchida, Yoji Kukita, Toru Kumagai, Kazumi Nishino, Tomio Inoue, Masashi Kimura, Fumio Imamura
Software Mentions: 2
Published: almost 8 years ago
10.3390/pathogens9020100
Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae
Cited by: 14
Author(s): Evgeny S. Gerasimov, Ksenia A Zamyatnina, Nadezda S Matveeva, Yulia A. Rudenskaya, Natalya Kraeva, Alexander Kolesnikov, Vyacheslav Yurchenko
Software Mentions: 2
Published: almost 5 years ago
10.1099/mgen.0.000325
Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events
Cited by: 8
Author(s): Mariana G. López, John B. Dogba, Manuela Torres-Puente, Galo A. Goig, Miguel Moreno-Molina, Luis M Villamayor, Simeon Cadmus, Iñaki Comas
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41431-018-0266-4
Exploring rare and low-frequency variants in the Saguenay–Lac-Saint-Jean population identified genes associated with asthma and allergy traits
Cited by: 9
Author(s): Andréanne Morin, Anne-Marie Madore, Tony Kwan, Masashi Ban, Jukka Partanen, Lars Rönnblom, Ann‐Christine Syvänen, Stephen Sawcer, Hendrik G. Stunnenberg, Mark Lathrop, Tomi Pastinen, Catherine Laprise
Software Mentions: 2
Published: about 6 years ago
10.1534/g3.119.400853
Synaptonemal Complex-Deficient<i>Drosophila melanogaster</i>Females Exhibit Rare DSB Repair Events, Recurrent Copy-Number Variation, and an Increased Rate of<i>de Novo</i>Transposable Element Movement
Cited by: 7
Author(s): Danny E. Miller
Software Mentions: 2
Published: almost 5 years ago
10.1038/srep25486
Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles
Cited by: 91
Author(s): Raphatphorn Navakanitworakul, Wei Ting Hung, Sumedha Gunewardena, John S. Davis, Wilaiwan Chotigeat, Lane K. Christenson
Software Mentions: 2
Published: over 8 years ago
10.3390/genes12030412
Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations
Cited by: 7
Author(s): Mariya A. Kusliy, Nadezhda V. Vorobieva, Alexey A. Tishkin, Alex Makunin, Anna S. Druzhkova, Vladimir A. Trifonov, Tumur-O. Iderkhangai, Alexander S. Graphodatsky
Software Mentions: 2
Published: over 3 years ago
10.3390/pathogens9090686
Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission
Cited by: 7
Author(s): Jakob Thannesberger, Nicolás Rascovan, Anna Eisenmann, Ingeborg Klymiuk, Carina Zittra, Hans‐Peter Fuehrer, T Scantlebury-Manning, Marquita Gittens–St. Hilaire, Shane Austin, R. Clive Landis, Christoph Steininger
Software Mentions: 2
Published: over 4 years ago
10.3897/zookeys.697.15124
A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling
Cited by: 47
Author(s): Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jésus E. Maldonado
Software Mentions: 2
Published: about 7 years ago
10.1038/srep11444
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Cited by: 67
Author(s): Thomas Nordahl Petersen, Simon Rasmussen, Henrik Hasman, Christian Carøe, Jacob Bælum, Anna Charlotte Schultz, Lasse Bergmark, Christina Aaby Svendsen, Ole Lund, Thomas Sicheritz-Pontén, Frank Møller Aarestrup
Software Mentions: 2
Published: over 9 years ago
10.1111/eva.13254
Response to selection for parasitism of a suboptimal, low‐preference host in an aphid parasitoid
Cited by: 7
Author(s): Keith R. Hopper, Kameron T Wittmeyer, Kristen L. Kuhn, Kathryn A. Lanier
Software Mentions: 2
Published: over 3 years ago
10.1099/mgen.0.000506
Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction
Cited by: 0
Author(s): Madikay Senghore, Peggy-Estelle Tientcheu, Archibald Worwui, Sheikh Jarju, Catherine Okoi, Sambou M. S. Suso, Ebenezer Foster-Nyarko, Chinelo Ebruke, Mohamadou Sonko, Mamdou Hama Kourna, Joseph Agossou, Enyonam Tsolenyanu, Lorna Renner, Daniel Ansong, Bakary Sanneh, Cathérine Boni Cissé, Angeline Boula, Berthe Miwanda, Stephanie Lo, Rebecca A. Gladstone, Stephanie Schwartz, Paulina A. Hawkins, Lesley McGee, Keith P. Klugman, Robert F. Breiman, Stephen D. Bentley, Jason M. Mwenda, Brenda Kwambana-Adams, Martín Antonio
Software Mentions: 2
Published: over 3 years ago
10.1111/eva.12918
Fine‐scale barriers to connectivity across a fragmented South‐East Asian landscape in six songbird species
Cited by: 9
Author(s): Emilie Cros, Elize Y. X. Ng, Rachel Rui Ying Oh, Qian Tang, Suzan Benedick, David P. Edwards, Suzanne Tomassi, Martin Irestedt, Per G. P. Ericson, Frank E. Rheindt
Software Mentions: 2
Published: over 4 years ago
10.1093/molbev/msu320
Patterns of Linkage Disequilibrium and Long Range Hitchhiking in Evolving Experimental<i>Drosophila melanogaster</i>Populations
Cited by: 76
Author(s): Susanne U. Franssen, Viola Nolte, Raymond Tobler, Christian Schlötterer
Software Mentions: 2
Published: about 10 years ago
10.1038/sdata.2016.119
Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection
Cited by: 49
Author(s): Feng Cheng, Jian Wu, Chengcheng Cai, Lixia Fu, Jiansheng Liang, Theo Borm, Mu Zhuang, Yangyong Zhang, Fenglan Zhang, Guusje Bonnema, Xiaowu Wang
Software Mentions: 2
Published: almost 8 years ago
10.1002/evl3.59
Recent admixture between species of the fungal pathogen <i>Histoplasma</i>
Cited by: 27
Author(s): Colin S. Maxwell, Victoria E. Sepúlveda, David A. Turissini, William E. Goldman, Daniel R. Matute
Software Mentions: 2
Published: over 6 years ago
10.3390/genes12010089
The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed
Cited by: 21
Author(s): Alexandra K. Fraik, John McMillan, Martin Liermann, Todd Bennett, Michael L. McHenry, Garrett J. McKinney, Abigail Wells, Gary A. Winans, Joanna L. Kelley, George R. Pess, Krista M. Nichols
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12284-016-0111-8
Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition
Cited by: 64
Author(s): Matthew R. Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
Software Mentions: 2
Published: over 8 years ago
10.12688/f1000research.23214.2
CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets
Cited by: 1
Author(s): Sandeep Kasaragod, Varshasnata Mohanty, Ankur Tyagi, Santosh Kumar Behera, Arun H. Patil, Sneha M. Pinto, T. S. Keshava Prasad, Prashant Kumar Modi, Harsha Gowda
Software Mentions: 2
Published: about 4 years ago
10.1534/g3.116.030452
Improved Placement of Multi-mapping Small RNAs
Cited by: 217
Author(s): Nathan Johnson, Jonathan M. Yeoh, Ceyda Çoruh, Michael J. Axtell
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-015-1715-x
Runs of homozygosity and distribution of functional variants in the cattle genome
Cited by: 135
Author(s): Qianqian Zhang, Bernt Guldbrandtsen, Mirte Bosse, Mogens Sandø Lund, Goutam Sahana
Software Mentions: 2
Published: over 9 years ago
10.12688/f1000research.22954.3
QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing
Cited by: 3
Author(s): Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, F. Elizabeth Martin, Michael T. McManus, Philippe Hupé
Software Mentions: 2
Published: about 4 years ago
10.12688/f1000research.6617.2
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut
Cited by: 21
Author(s): Sandeep Chakraborty, Monica Britton, Jill L. Wegrzyn, Timothy Butterfield, Pedro J. Martínez-García, Russell L. Reagan, Basuthkar J. Rao, Charles A. Leslie, Mallikarjuna Aradhaya, David B. Neale, Keith Woeste, Abhaya M. Dandekar
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.ppat.1008594
Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma
Cited by: 8
Author(s): Jan Clement Santiago, Jason D. Goldman, Hong Zhao, Alec Pankow, Fred Okuku, Michael Schmitt, Lennie H. Chen, Catherine A. Hill, Corey Casper, Warren Phipps, James I. Mullins
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.ppat.1007903
Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis
Cited by: 5
Author(s): David F. Read, Edmond Atindaana, Kalyani Pyaram, Feng Yang, Sarah B. Emery, Anna Cheong, Katherine R. Nakama, Cleo Burnett, Erin T. Larragoite, Emilie Battivelli, Eric Verdin, Vicente Planelles, Ching-Pin Chang, Alice Telesnitsky, Jeffrey M. Kidd
Software Mentions: 2
Published: about 5 years ago
10.1186/1471-2156-12-27
PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
Cited by: 10
Author(s): Ram Vinay Pandey, Robert Kofler, Pablo Orozco‐terWengel, Viola Nolte, Christian Schlötterer
Software Mentions: 2
Published: over 13 years ago
10.1093/femsle/fnaa185
High-density transposon libraries utilising outward-oriented promoters identify mechanisms of action and resistance to antimicrobials
Cited by: 3
Author(s): Chris Coward, Gopujara Dharmalingham, Omar Abdulle, Tim Avis, Stephan Beisken, Elena B. M. Breidenstein, Natasha Carli, Luís F. de Figueiredo, David Jones, Nawaz Khan, Sara Malara, Joana Martins, Nabeetha A. Nagalingam, A. Keith Turner, John Wain, David J. Williams, David J. Powell, Clive Mason
Software Mentions: 2
Published: about 4 years ago
10.3389/fbioe.2020.00513
Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology
Cited by: 24
Author(s): Jestin George, Tim Kahlke, Raffaela M. Abbriano, Unnikrishnan Kuzhiumparambil, Peter J. Ralph, Michele Fabris
Software Mentions: 2
Published: over 4 years ago
10.3389/fcell.2019.00264
TRIBE Uncovers the Role of Dis3 in Shaping the Dynamic Transcriptome in Malaria Parasites
Cited by: 9
Author(s): Meng Liu, Binbin Lu, Yanting Fan, Xiaohong He, Shijun Shen, Cizhong Jiang, Qingfeng Zhang
Software Mentions: 2
Published: about 5 years ago
10.1128/AEM.02762-20
Harnessing CRISPR-Cas9 for Genome Editing in Streptococcus pneumoniae D39V
Cited by: 6
Author(s): Dimitra Synefiaridou, Jan‐Willem Veening
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.ppat.1004447
Programmed Ribosomal Frameshift Alters Expression of West Nile Virus Genes and Facilitates Virus Replication in Birds and Mosquitoes
Cited by: 30
Author(s): Ezequiel Balmori Melian, Sonja Hall‐Mendelin, Du Fangyao, Nick S. Owens, Angela M. Bosco‐Lauth, Tomoko Nagasaki, Stephen Rudd, Aaron C. Brault, Richard A. Bowen, Roy A. Hall, Andrew F. van den Hurk, Alexander A. Khromykh
Software Mentions: 2
Published: about 10 years ago
10.3389/fcell.2021.612581
Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum: Identification of Novel Candidate Modifier Genes and Disease Pathways Through Mixture of Effects Analysis
Cited by: 5
Author(s): Eva Y.G. De Vilder, Ludovic Martin, Georges Lefthériotis, Paul Coucke, Filip Van Nieuwerburgh, Olivier Vanakker
Software Mentions: 2
Published: over 3 years ago
10.3390/v12080879
Tomato Brown Rugose Fruit Virus Contributes to Enhanced Pepino Mosaic Virus Titers in Tomato Plants
Cited by: 20
Author(s): Chen Klap, Neta Luria, Elisheva Smith, Lior Hadad, Elena Bakelman, Noa Sela, Eduard Belausov, Oded Lachman, Diana Leibman, Aviv Dombrovsky
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.ppat.1003984
ChIP-Seq and RNA-Seq Reveal an AmrZ-Mediated Mechanism for Cyclic di-GMP Synthesis and Biofilm Development by Pseudomonas aeruginosa
Cited by: 135
Author(s): Chris J. Jones, David E. Newsom, Benjamin J. Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak
Software Mentions: 2
Published: over 10 years ago
10.3389/fgene.2017.00180
Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach
Cited by: 45
Author(s): Tokurou Shimizu, Yasuhiro Tanizawa, Takako Mochizuki, Hideki Nagasaki, Terutaka Yoshioka, Atsushi Toyoda, Asao Fujiyama, Eli Kaminuma, Yasukazu Nakamura
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41438-021-00614-y
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
Cited by: 22
Author(s): Kai‐Hua Jia, Hui Liu, Rengang Zhang, Jie Xu, Shanshan Zhou, Si-Qian Jiao, Xuemei Yan, Xue Tian, Tian-Le Shi, Hang Luo, Zhichao Li, Yu-Tao Bao, Shuai Nie, Jing‐Fang Guo, Ilga Porth, Yousry A. El‐Kassaby, Xiaoru Wang, Charles Chen, Yves Van de Peer, Zhao Wang, Jian‐Feng Mao
Software Mentions: 2
Published: about 3 years ago
10.3389/fgene.2021.660366
UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction
Cited by: 4
Author(s): Maria Tsagiopoulou, Μαρία Μανιού, Nikolaos Pechlivanis, Anastasis Togkousidis, Michaela Kotrová, Tobias Hutzenlaub, Ilias Kappas, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 2
Published: over 3 years ago
10.1186/s41065-020-00120-6
STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
Cited by: 4
Author(s): Dong Wang, Ruiyang Tao, Zhiqiang Li, Dun Pan, Zhuo Wang, Chengtao Li, Yongyong Shi
Software Mentions: 2
Published: over 4 years ago
10.3389/fgene.2019.00275
Chromosome-Level Assembly of the Chinese Seabass (Lateolabrax maculatus) Genome
Cited by: 19
Author(s): Baohua Chen, Yun Li, Wenzhu Peng, Zhixiong Zhou, You Shi, Fei Pu, Xuan Luo, Chen Lin, Peng Xu
Software Mentions: 2
Published: over 5 years ago
10.1186/1757-4749-4-20
Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia
Cited by: 8
Author(s): Ramani Baddam, Narender Kumar, Sabiha Shaik, Suma Tiruvayipati, Soo Tein Ngoi, Kwai Lin Thong, Niyaz Ahmed
Software Mentions: 2
Published: almost 12 years ago
10.3389/fgene.2020.00482
Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts
Cited by: 7
Author(s): Rupert Mazzucco, Viola Nolte, Thapasya Vijayan, Christian Schlötterer
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-12-557
Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping
Cited by: 68
Author(s): Bin Zhan, João Fadista, Bo Thomsen, Jakob Hedegaard, Frank Panitz, Christian Berthou
Software Mentions: 2
Published: about 13 years ago
10.1186/s40168-018-0611-4
Signatures within the esophageal microbiome are associated with host genetics, age, and disease
Cited by: 92
Author(s): Nandan P. Deshpande, Stephen M. Riordan, Natalia Castaño‐Rodríguez, Marc R. Wilkins, Nadeem O. Kaakoush
Software Mentions: 2
Published: almost 6 years ago
10.1080/19490976.2020.1854967
Gene variations in Autism Spectrum Disorder are associated with alternation of gut microbiota, metabolites and cytokines
Cited by: 24
Author(s): Zhi Li, Xuhua Mao, Dan Zhou, Peng Yang, Rui Xu, Mengchen Guo, Kangjian Liu, Faming Zhang, Junyu Chen, Chuan Su, Yaoyao Zhuang, Jun‐Ming Tang, Yankai Xia, Lianhong Qin, Zhibin Hu, Xingyin Liu
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2021.625564
Case Report: Whole Exome Sequencing Revealed Disease-Causing Variants in Two Genes in a Patient With Autism Spectrum Disorder, Intellectual Disability, Hyperactivity, Sleep and Gastrointestinal Disturbances
Cited by: 8
Author(s): Maria Cerminara, Giovanni Spirito, Livia Pisciotta, Margherita Squillario, Martina Servetti, Maria Teresa Divizia, Margherita Lerone, Bianca Berloco, Silvia Boeri, Lino Nobili, Diego Vozzi, Remo Sanges, Stefano Gustincich, Aldamaria Puliti
Software Mentions: 2
Published: almost 4 years ago
10.1534/g3.116.030411
First Draft Assembly and Annotation of the Genome of a California Endemic Oak<i>Quercus lobata</i>Née (Fagaceae)
Cited by: 83
Author(s): Victoria L. Sork, Sorel Fitz‐Gibbon, Daniela Puiu, Marc W. Crepeau, Paul F. Gugger, Rachel M. Sherman, Kristian Stevens, Charles H. Langley, Matteo Pellegrini, Steven L. Salzberg
Software Mentions: 2
Published: about 8 years ago
10.3390/v5041042
Interpreting the Epstein-Barr Virus (EBV) Epigenome Using High-Throughput Data
Cited by: 43
Author(s): Aaron Arvey, Italo Tempera, Paul M. Lieberman
Software Mentions: 2
Published: over 11 years ago
10.3389/fmicb.2018.02553
Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors
Cited by: 30
Author(s): Robert Lasek, Magdalena Szuplewska, Monika Mitura, Przemysław Decewicz, Cora Chmielowska, Aleksandra Pawłot, Dorota Sentkowska, Jakub Czarnecki, Dariusz Bartosik
Software Mentions: 2
Published: about 6 years ago
10.1093/g3journal/jkaa009
Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells
Cited by: 2
Author(s): Sibylle C. Vonesch, Shengdi Li, Chelsea Szu-Tu, Bianca P. Hennig, Nikolay Dobrev, Lars M. Steinmetz, M Steinmetz Lars
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pgen.1003984
Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs
Cited by: 196
Author(s): Adam Auton, Ying Rui Li, Jeffrey M. Kidd, Kyle C. Oliveira, Julie Nadel, J. Kim Holloway, Jessica J. Hayward, Paula E. Cohen, John M. Greally, Jun Wang, Carlos D. Bustamante, Adam R. Boyko
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pgen.1003968
Elevated Mutagenesis Does Not Explain the Increased Frequency of Antibiotic Resistant Mutants in Starved Aging Colonies
Cited by: 30
Author(s): Sophia Katz, Ruth Hershberg
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pgen.1003809
The Highly Prolific Phenotype of Lacaune Sheep Is Associated with an Ectopic Expression of the B4GALNT2 Gene within the Ovary
Cited by: 68
Author(s): Laurence Drouilhet, Camille Mansanet, Julien Sarry, Tabet Kamila, Philippe Bardou, Florent Woloszyn, Jérôme Lluch, Grégoire Harichaux, Catherine Viguié, Danielle Monniaux, Loýs Bodin, Philippe Mulsant, Stéphane Fabre
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pgen.1007503
No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice
Cited by: 101
Author(s): Vivek Iyer, Katharina Boroviak, Mark Thomas, Brendan Doe, Laura Riva, Edward Ryder, David J. Adams
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pgen.1006162
Fragment Length of Circulating Tumor DNA
Cited by: 472
Author(s): Hunter R. Underhill, Jacob O. Kitzman, Sabine Hellwig, Noah C. Welker, Riza M. Daza, David Baker, Keith M. Gligorich, Robert Rostomily, Mary P. Bronner, Jay Shendure
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-019-5920-x
Pea genomic selection for Italian environments
Cited by: 28
Author(s): Paolo Annicchiarico, Nelson Espinoza N., L. Pecetti, Massimo Romani, Luigi Russi
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pgen.1003698
Ras-Induced Changes in H3K27me3 Occur after Those in Transcriptional Activity
Cited by: 43
Author(s): Masaki Hosogane, Ryo Funayama, Yuichiro Nishida, Takeshi Nagashima, Keiko Nakayama
Software Mentions: 2
Published: about 11 years ago
10.1534/g3.115.026898
Transcriptome Sequencing of Diverse Peanut (<i>Arachis</i>) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability
Cited by: 17
Author(s): Ratan Chopra, Gloria Burow, C. E. Simpson, Jennifer Chagoya, Joann Mudge, Mark D. Burow
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12864-016-3115-2
Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis
Cited by: 25
Author(s): Si Qiu, Wenhui Li, Heng Xiong, Dongbing Liu, Yang Bai, Kui Wu, Xiuqing Zhang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pgen.1006537
Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers
Cited by: 91
Author(s): Samantha N. McNulty, José F. Tort, Gabriel Rinaldi, Kerstin Fischer, Bruce A. Rosa, Pablo Smircich, Santiago Fontenla, Young Jun Choi, Rahul Tyagi, Kymberlie Hallsworth-Pepin, Victoria H. Mann, Lakshmi Kammili, Patricia S. Latham, Nicolás Dell’Oca, Fernanda Domínguez, Carlos Carmona, Peter U. Fischer, Paul J. Brindley, Makedonka Mitreva
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pgen.1004785
Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization
Cited by: 156
Author(s): Danelle Seymour, Daniel Koenig, Joerg Hagmann, Claude Becker, Detlef Weigel
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pgen.1006275
Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions
Cited by: 10
Author(s): Lai Hong Wong, Sunita Sinha, Julien R. C. Bergeron, Joseph Mellor, Guri Giaever, Patrick Flaherty, Corey Nislow
Software Mentions: 2
Published: about 8 years ago
10.1186/s12864-019-5710-5
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2
Cited by: 8
Author(s): Giorgio Gonnella, Nicole Adam, Mirjam Perner
Software Mentions: 2
Published: over 5 years ago
10.1186/s12859-018-2154-x
ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
Cited by: 31
Author(s): Egon A. Ozer
Software Mentions: 2
Published: over 6 years ago