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

10.1099/mgen.0.000334
Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK
Cited by: 21
Author(s): Daniel Yara, David R. Greig, David L. Gally, Timothy J. Dallman, Claire Jenkins
Software Mentions: 1
Published: over 4 years ago
10.1099/mgen.0.000226
Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building
Cited by: 4
Author(s): Sophia David, M. Mentasti, Sandra Lai, Lalita Vaghji, Derren Ready, Victoria J. Chalker, Julian Parkhill
Software Mentions: 1
Published: about 6 years ago
10.1099/mgen.0.000300
A survey of Fusobacterium nucleatum genes modulated by host cell infection
Cited by: 14
Author(s): Kyla Cochrane, Avery Robinson, Robert A. Holt, Emma Allen‐Vercoe
Software Mentions: 1
Published: almost 5 years ago
10.1099/mgen.0.000468
Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7
Cited by: 1
Author(s): Alexander Bolotin, Benoît Quinquis, Hugo Roume, Michel Gohar, Didier Lereclus, Alexeï Sorokin
Software Mentions: 1
Published: almost 4 years ago
10.1099/mgen.0.000278
Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries
Cited by: 3
Author(s): Koji Kikuchi, Ken-ichi Lee, Hiroyuki Ueno, Kentaro Tomari, Sumie Kobori, Akihiko Kaetsu, Mari Matsui, Satowa Suzuki, Tsuyoshi Sekizuka, Makoto Kuroda, Motonobu Miyazaki, Makoto Ohnishi
Software Mentions: 1
Published: over 5 years ago
10.1002/mbo3.1191
Optimized bacterial DNA isolation method for microbiome analysis of human tissues
Cited by: 16
Author(s): Carlijn E. Bruggeling, Daniel Garza, Soumia Achouiti, Wouter Mes, Bas E. Dutilh, Annemarie Boleij
Software Mentions: 1
Published: over 3 years ago
10.1099/mic.0.000948
Antibacterial activity and mode of action of potassium tetraborate tetrahydrate against soft-rot bacterial plant pathogens
Cited by: 3
Author(s): Yingyu Liu, Melanie J. Filiatrault
Software Mentions: 1
Published: about 4 years ago
10.1128/MRA.00560-20
Near-Complete Genome Sequences of a <i>Wolbachia</i> Strain Isolated from Diaphorina citri Kuwayama ( <i>Hemiptera</i> : <i>Liviidae</i> )
Cited by: 5
Author(s): Surendra Neupane, Sylvia Bonilla, Andrew M. Manalo, Kirsten S. Pelz‐Stelinski
Software Mentions: 1
Published: about 4 years ago
10.1128/MRA.01388-18
Genome Sequencing of Polydrug-, Multidrug-, and Extensively Drug-Resistant Mycobacterium tuberculosis Strains from South India
Cited by: 4
Author(s): Sivakumar Shanmugam, Narender Kumar, Dina Nair, Mohan Natrajan, Srikanth Tripathy, Sharon J. Peacock, Soumya Swaminathan, Uma Devi Ranganathan
Software Mentions: 1
Published: over 5 years ago
10.1128/MRA.00623-19
Draft Genome Sequence of Pseudomonas aeruginosa Strain BWH047, a Sequence Type 235 Multidrug-Resistant Clinical Isolate Expressing High Levels of Colistin Resistance
Cited by: 1
Author(s): Kelly E R Bachta, Egon A. Ozer, Alisha Pandit, Francisco M. Marty, John J. Mekalanos, Alan R. Hauser
Software Mentions: 1
Published: over 5 years ago
10.1186/s40168-017-0234-1
Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details
Cited by: 89
Author(s): Rounak Feigelman, Christian Kahlert, Florent Baty, Frank Rassouli, Rebekka Kleiner, Philipp Köhler, Martin Brutsche, Christian von Mering
Software Mentions: 1
Published: almost 8 years ago
10.3390/microorganisms9040762
Phage Resistance Is Associated with Decreased Virulence in KPC-Producing Klebsiella pneumoniae of the Clonal Group 258 Clade II Lineage
Cited by: 10
Author(s): Lucia Henrici De Angelis, Noemi Poerio, Vincenzo Di Pilato, Federica De Santis, Alberto Antonelli, María Cristina Thaller, Maurizio Fraziano, Gian María Rossolini, Marco Maria D’Andrea
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2020.1831988
Complete mitochondrial genomes of Karchaev goat (<i>Capra hircus</i>)
Cited by: 2
Author(s): Andrey N. Rodionov, Arsen V Dotsev, O. Yu. Fomenko, Nekruz Bakoev, Tatiana Deniskova, Alexey Shakhin, В. А. Багиров, Elisabeth Kunz, Ivica Međugorac, Stefan Krebs, Gottfried Brem, N. A. Zinovieva
Software Mentions: 1
Published: over 4 years ago
10.1093/molbev/msx098
Loss of Heterozygosity Drives Adaptation in Hybrid Yeast
Cited by: 101
Author(s): Caiti Smukowski Heil, Christopher DeSevo, Dave A. Pai, Cheryl M. Tucker, Margaret L. Hoang, Maitreya J. Dunham
Software Mentions: 1
Published: over 7 years ago
10.1093/molbev/msab001
De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in <i>Arabidopsis arenosa</i>
Cited by: 18
Author(s): Magdalena Bohutínská, Vinzenz Handrick, Levi Yant, Roswitha Schmickl, Filip Kolář, Kirsten Bomblies, Pirita Paajanen
Software Mentions: 1
Published: almost 4 years ago
10.1093/molbev/mst205
Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments
Cited by: 138
Author(s): Raymond Tobler, Susanne U. Franssen, Robert Kofler, Pablo Orozco‐terWengel, Viola Nolte, Joachim Hermisson, Christian Schlötterer
Software Mentions: 1
Published: about 11 years ago
10.1186/s12943-019-1020-4
MED12 exerts an emerging role in actin-mediated cytokinesis via LIMK2/cofilin pathway in NSCLC
Cited by: 16
Author(s): Meng Xu, Fang Wang, Guibo Li, Xiaokun Wang, Xiaona Fang, Haoxuan Jin, Zhen Chen, Jianye Zhang, Liwu Fu
Software Mentions: 1
Published: over 5 years ago
10.1016/j.molcel.2014.01.017
A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation
Cited by: 84
Author(s): Keerthi Thelakkad Chathoth, J. David Barrass, Shaun Webb, Jean D. Beggs
Software Mentions: 1
Published: over 10 years ago
10.1111/mec.12594
Inference of chromosomal inversion dynamics from <scp>P</scp>ool‐<scp>S</scp>eq data in natural and laboratory populations of <i><scp>D</scp>rosophila melanogaster</i>
Cited by: 99
Author(s): Martin Kapun, Hester van Schalkwyk, Bryant F. McAllister, Thomas Flatt, Christian Schlötterer
Software Mentions: 1
Published: almost 11 years ago
10.1111/j.1365-294X.2012.05673.x
Adaptation of <i>Drosophila</i> to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles
Cited by: 202
Author(s): Pablo Orozco‐terWengel, Martin Kapun, VIiola Nolte, Robert Kofler, Thomas Flatt, Christian Schlötterer
Software Mentions: 1
Published: over 12 years ago
10.1111/1755-0998.12432
The impact of library preparation protocols on the consistency of allele frequency estimates in <scp>P</scp> ool‐ <scp>S</scp> eq data
Cited by: 23
Author(s): Robert Kofler, Viola Nolte, Christian Schlötterer
Software Mentions: 1
Published: over 9 years ago
10.1111/1755-0998.13150
Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)
Cited by: 21
Author(s): Zheng Bin Randolph Quek, Sudhanshi S. Jain, Mei Lin Neo, Greg W. Rouse, Danwei Huang
Software Mentions: 1
Published: over 4 years ago
10.1002/mgg3.964
Whole‐exome sequencing provides insights into monogenic disease prevalence in Northwest Russia
Cited by: 21
Author(s): Yury A. Barbitoff, Rostislav K. Skitchenko, Olga I. Poleshchuk, Anton E. Shikov, Elena Serebryakova, Yulia A. Nasykhova, Dmitrii E. Polev, Anna R. Shuvalova, Irina V. Shcherbakova, Mikhail A. Fedyakov, Oleg S. Glotov, Andrey S. Glotov, Alexander V. Predeus
Software Mentions: 1
Published: about 5 years ago
10.1002/mgg3.164
A distinctive oral phenotype points to <i> <scp>FAM</scp> 20A </i> mutations not identified by <scp>S</scp> anger sequencing
Cited by: 7
Author(s): James A. Poulter, Claire E. L. Smith, Gina Murrillo, Sandra Silva, Sally Feather, Marianella Howell, Laura A. Crinnion, David T. Bonthron, Ian Carr, Christopher M. Watson, Chris F. Inglehearn, Alan J. Mighell
Software Mentions: 1
Published: about 9 years ago
10.1002/1878-0261.12539
Detection of mutational patterns in cell‐free <scp>DNA</scp> of colorectal cancer by custom amplicon sequencing
Cited by: 8
Author(s): Simon Herrmann, Tianzuo Zhan, Johannes Betge, Benedikt Rauscher, Sebastian Belle, Tobias Gutting, Nadine Schulte, Ralf Jesenofsky, Nicolai Härtel, Timo Gaiser, Ralf Hofheinz, Matthias Ebert, Michael Boutros
Software Mentions: 1
Published: over 5 years ago
10.15252/msb.20199419
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation
Cited by: 30
Author(s): Carlos Eduardo Flores-Tinoco, Flavia Tschan, Tobias Fuhrer, Céline Margot, Uwe Sauer, Matthias Christen, Beat Christen
Software Mentions: 1
Published: over 4 years ago
10.1038/mt.2013.111
Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients
Cited by: 163
Author(s): David G. Ousterout, Pablo Pérez-Piñera, Pratiksha I. Thakore, Ami M. Kabadi, Matthew T. Brown, Xiao Qin, Olivier Fédrigo, Vincent Mouly, Jacques P. Tremblay, Charles A. Gersbach
Software Mentions: 1
Published: about 11 years ago
10.1038/s41385-019-0220-y
Single-cell RNA-sequencing identifies the developmental trajectory of C-Myc-dependent NK1.1− T-bet+ intraepithelial lymphocyte precursors
Cited by: 10
Author(s): Jonas Hummel, Patrice Zeis, Karolina Ebert, Jonas Fixemer, Philip Konrad, Christian Schachtrup, Sebastian J. Arnold, Dominic Grün, Yakup Tanriver
Software Mentions: 1
Published: over 4 years ago
10.3390/vaccines9040392
Phenotypic and Genetic Evolutions of a Porcine Reproductive and Respiratory Syndrome Modified Live Vaccine after Limited Passages in Pigs
Cited by: 2
Author(s): Julie Eclercy, Patricia Renson, Edouard Hirchaud, Mathieu Andraud, Véronique Béven, Frédéric Paboeuf, Nicolas Rose, Yannick Blanchard, Olivier Bourry
Software Mentions: 1
Published: over 3 years ago
10.1186/1743-422X-10-116
Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain
Cited by: 17
Author(s): Sarah L. Fordyce, Karoline Bragstad, Susanne Juhl Pedersen, Thøger Gorm Jensen, Bente Gahrn‐Hansen, Rod S. Daniels, Alan J. Hay, Marie-Louise Kampmann, Christian Bruhn, J. Víctor Moreno-Mayar, María C. Ávila-Arcos, M. Thomas P. Gilbert, Lars Peter Nielsen
Software Mentions: 1
Published: over 11 years ago
10.3390/v10090451
Characterization of Unknown Orthobunya-Like Viruses from India
Cited by: 9
Author(s): Shannon Whitmer, Pragya D Yadav, Prasad Sarkale, Gouri Chaubal, Alicia Francis, John D. Klena, Stuart T. Nichol, Ute Ströher, Devendra T. Mourya
Software Mentions: 1
Published: about 6 years ago
10.3390/v10110633
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
Cited by: 20
Author(s): Antonin Bal, Clémentine Sarkozy, Laurence Josset, Valérie Cheynet, Guy Oriol, Jérémie Becker, Gaëlle Vilchez, Pierre Sesques, François Mallet, Alexandre Pachot, Florence Morfin, Bruno Lina, Gilles Salles, Frédéric Reynier, Sophie Trouillet‐Assant, Karen Brengel‐Pesce
Software Mentions: 1
Published: about 6 years ago
10.3390/v12030258
The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh
Cited by: 41
Author(s): Dominique L. Chaput, David Bass, Md. Mehedi Alam, Neaz A. Hasan, Grant D. Stentiford, Ronny van Aerle, Karen Moore, John P. Bignell, Mohammad Mahfujul Haque, Charles R. Tyler
Software Mentions: 1
Published: over 4 years ago
10.3390/v12111251
First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region
Cited by: 8
Author(s): Bourèma Kouriba, Angela Dürr, Alexandra Rehn, Abdoul Karim Sangaré, Bréhima Traoré, Malena Bestehorn-Willmann, Judicaël Ouédraogo, Asli Heitzer, Elisabeth Sogodogo, Abderrhamane Maiga, Mathias C. Walter, Fee Zimmermann, Roman Wölfel, Markus Antwerpen
Software Mentions: 1
Published: about 4 years ago
10.3390/v13061152
Emergence of a Novel Dengue Virus 3 (DENV-3) Genotype-I Coincident with Increased DENV-3 Cases in Yangon, Myanmar between 2017 and 2019
Cited by: 6
Author(s): Aung Min Soe, Mya Myat Ngwe Tun, Takeshi Nabeshima, Theingi Win Myat, Moh Moh Htun, Htin Lin, Nang Sarm Hom, Satoshi Inoue, Khine Mya Nwe, Lynn Pa Pa Aye, Mizuki Fukuta, Kyaw Zin Thant, Futoshi Hasebe, Kouichi Morita, Sujan Shresta, Hlaing Myat Thu, Meng Ling Moi
Software Mentions: 1
Published: over 3 years ago
10.3390/v13081492
Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract
Cited by: 12
Author(s): Jose L. Huaman, Carlo Pacioni, Subir Sarker, Mark Doyle, David M. Forsyth, Anthony Pople, Jordan O. Hampton, Teresa G. Carvalho, Karla J. Helbig
Software Mentions: 1
Published: over 3 years ago
10.1186/s13071-019-3748-5
From the feces to the genome: a guideline for the isolation and preservation of Strongyloides stercoralis in the field for genetic and genomic analysis of individual worms
Cited by: 11
Author(s): Siyu Zhou, Dorothee Harbecke, Adrian Streit
Software Mentions: 1
Published: about 5 years ago
10.7717/peerj.3901
Complete mitochondrial genome sequences of the northern spotted owl (<i>Strix occidentalis caurina</i>) and the barred owl (<i>Strix varia</i>; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region
Cited by: 18
Author(s): Zachary R Hanna, James Henderson, Anna B. Sellas, Jérôme Fuchs, Rauri C. K. Bowie, John P. Dumbacher
Software Mentions: 1
Published: about 7 years ago
10.7717/peerj.2023
Genome-scale investigation of phenotypically distinct but nearly clonalTrichodermastrains
Cited by: 3
Author(s): Claudia Lange, Richard J. Weld, Murray P. Cox, Rosie E. Bradshaw, K. L. McLean, Alison Stewart, Johanna M. Steyaert
Software Mentions: 1
Published: over 8 years ago
10.1098/rstb.2019.0582
Evolutionary history of <i>Mycobacterium leprae</i> in the Pacific Islands
Cited by: 12
Author(s): Kelly E. Blevins, Adele Crane, C. Lum, Kanako Furuta, Keolu Fox, Anne C. Stone
Software Mentions: 1
Published: about 4 years ago
10.1111/pbi.13062
A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat
Cited by: 46
Author(s): Yosef Gebrehawaryat Kidane, Cherinet Alem Gesesse, Bogale Nigir Hailemariam, Ermias Abate Desta, Deȷene K. Mengistu, Carlo Fadda, Mario Enrico Pè, Matteo Dell’Acqua
Software Mentions: 1
Published: almost 6 years ago
10.1002/pld3.96
A chromosome‐scale assembly of the model desiccation tolerant grass <i>Oropetium thomaeum</i>
Cited by: 35
Author(s): Robert VanBuren, Ching Man Wai, Jens Keilwagen, Jeremy Pardo
Software Mentions: 1
Published: about 6 years ago
10.1186/s13007-019-0525-6
High-throughput long paired-end sequencing of a Fosmid library by PacBio
Cited by: 4
Author(s): Zhaozhao Dai, Tong Li, Jiadong Li, Han Zhi-jun, Yonglong Pan, Sha Tang, Xianmin Diao, Meizhong Luo
Software Mentions: 1
Published: almost 5 years ago
10.1186/s13007-019-0486-9
A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing
Cited by: 32
Author(s): Miriam Schreiber, Abdellah Barakate, Nicola Uzrek, Malcolm Macaulay, Adeline Sourdille, Jenny Morris, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pbio.1001868
Genome-Wide Stochastic Adaptive DNA Amplification at Direct and Inverted DNA Repeats in the Parasite Leishmania
Cited by: 111
Author(s): Jean-Michel Ubeda, Frédéric Raymond, Avinaba Mukherjee, Marie Plourde, Hélène Gingras, Gaétan Roy, Andréanne Lapointe, Philippe Leprohon, Barbara Papadopoulou, Jacques Corbeil, Marc Ouellette
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pbio.2000618
The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications
Cited by: 54
Author(s): Benoît Sessinou Assogba, Pascal Milesi, Luc Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkhir, Pierrick Labbé, Mylène Weill
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pbio.2006348
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Cited by: 84
Author(s): Shivani Mahajan, Kevin H.-C. Wei, Matthew J. Nalley, Lauren Gibilisco, Doris Bachtrog
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pcbi.1005026
Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data
Cited by: 30
Author(s): Yuheng Lu, Christina Leslie
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1006242
Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development
Cited by: 91
Author(s): Κρινιώ Γιαννίκου, Izabela A. Malinowska, Trevor J. Pugh, Rachel Yan, Yuen-Yi Tseng, Coyin Oh, Jaegil Kim, Magdalena E. Tyburczy, Yvonne Chekaluk, Yang Liu, Nicola Alesi, Geraldine A. Finlay, Chin‐Lee Wu, Sabina Signoretti, Matthew Meyerson, Gad Getz, Jesse S. Boehm, Elizabeth P. Henske, David J. Kwiatkowski
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1004427
Evolution and Genetic Architecture of Chromatin Accessibility and Function in Yeast
Cited by: 19
Author(s): Caitlin Connelly, Jon Wakefield, Joshua M. Akey
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1006461
Mutations in the Heme Exporter FLVCR1 Cause Sensory Neurodegeneration with Loss of Pain Perception
Cited by: 39
Author(s): Deborah Chiabrando, Marco Castori, Maja Di Rocco, Martin Ungelenk, Sebastian Gießelmann, M. Di Capua, Annalisa Madeo, Paola Grammatico, Sophie Bartsch, Christian A. Hübner, Fiorella Altruda, Lorenzo Silengo, Emanuela Tolosano, Ingo Kurth
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pgen.1007849
Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers
Cited by: 58
Author(s): Kerryn Elliott, Martin Boström, Stefan Filges, Markus Lindberg, Jimmy Van den Eynden, Anders Ståhlberg, Anders R. Clausen, Erik Larsson
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pgen.1004353
Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe
Cited by: 86
Author(s): Martin Sikora, Meredith L. Carpenter, Andrés Moreno‐Estrada, Brenna M. Henn, Peter A. Underhill, Federico Sánchez-Quinto, Ilenia Zara, Maristella Pitzalis, Carlo Sidore, Fabio Busonero, Andrea Maschio, Andrea Angius, Chris Jones, Javier Mendoza‐Revilla, Georgi Nekhrizov, Dessislava Dimitrova, Nikola Theodossiev, Timothy T. Harkins, Andreas Keller, Frank Maixner, Albert Zink, Gonçalo R. Abecasis, Serena Sanna, Francesco Cucca, Carlos D. Bustamante
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1004553
EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
Cited by: 74
Author(s): Sara Elgamal, Assaf Katz, Steven J. Hersch, David E. Newsom, Peter White, William Wiley Navarre, Michael Ibba
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1004298
Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome
Cited by: 39
Author(s): Concepción M. Díez, Esteban Meca, Maud I. Tenaillon, Brandon S. Gaut
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1004216
CDKN2D-WDFY2 Is a Cancer-Specific Fusion Gene Recurrent in High-Grade Serous Ovarian Carcinoma
Cited by: 40
Author(s): K. P. Kannan, Cristian Coarfa, Kimal Rajapakshe, Shannon M. Hawkins, Martin M. Matzuk, Aleksandar Milosavljevic, Laising Yen
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1004775
Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila
Cited by: 456
Author(s): Alan O. Bergland, Emily L. Behrman, Katherine R. O’Brien, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pgen.1005637
Mosaic and Intronic Mutations in TSC1/TSC2 Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing
Cited by: 193
Author(s): Magdalena E. Tyburczy, Kira Dies, Jennifer Glass, Susana Camposano, Yvonne Chekaluk, Aaron R. Thorner, Gang Li, Darcy A. Krueger, David Neal Franz, Elizabeth A. Thiele, Mustafa Şahin, David J. Kwiatkowski
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pgen.1005333
Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers
Cited by: 101
Author(s): James B. Stewart, Babak Alaei-Mahabadi, Radhakrishnan Sabarinathan, Tore Samuelsson, Jan Gorodkin, Claes M. Gustafsson, Erik Larsson
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pgen.1002599
Widespread Site-Dependent Buffering of Human Regulatory Polymorphism
Cited by: 67
Author(s): Matthew T. Maurano, Hao Wang, Tanya Kutyavin, J Stamatoyannopoulos
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pgen.1008571
Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
Cited by: 93
Author(s): Andrew C. Read, Matthew J. Moscou, Aleksey V. Zimin, Geo Pertea, Rachel S. Meyer, Michael D. Purugganan, Jan E. Leach, Lindsay R. Triplett, Steven L. Salzberg, Adam J. Bogdanove
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pgen.1008302
The presence and impact of reference bias on population genomic studies of prehistoric human populations
Cited by: 121
Author(s): Torsten Günther, Carl Nettelblad
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pgen.1003381
Comparative Genomics of Wolbachia and the Bacterial Species Concept
Cited by: 157
Author(s): Kirsten Ellegaard, Lisa Klasson, Kristina Näslund, Kostas Bourtzis, Siv G. E. Andersson
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pgen.1006538
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression
Cited by: 64
Author(s): Ian K. Quigley, Chris Kintner
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pgen.1008911
The role of gene dosage in budding yeast centrosome scaling and spontaneous diploidization
Cited by: 5
Author(s): Jingjing Chen, Zhiyong Xiong, Danny E. Miller, Zulin Yu, Scott McCroskey, W. David Bradford, Ann M. Cavanaugh, Sue L. Jaspersen
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pgen.1007526
Ancestral polymorphisms explain the role of chromosomal inversions in speciation
Cited by: 64
Author(s): Zachary L. Fuller, Christopher J. Leonard, Randee E. Young, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pgen.1001236
Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Cited by: 264
Author(s): Joseph K. Pickrell, Athma A. Pai, Yoav Gilad, Jonathan K. Pritchard
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pgen.1005241
Altered Levels of Mitochondrial DNA Are Associated with Female Age, Aneuploidy, and Provide an Independent Measure of Embryonic Implantation Potential
Cited by: 242
Author(s): Elpida Fragouli, K Spath, S Alfarawati, Fiona Kaper, Andrew Craig, Claude-Edouard Michel, Felix Kokocinski, Jacques Cohen, Santiago Munné, Dagan Wells
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pgen.1005607
Mapping of Craniofacial Traits in Outbred Mice Identifies Major Developmental Genes Involved in Shape Determination
Cited by: 67
Author(s): Luisa F. Pallares, Peter Carbonetto, Shyam Gopalakrishnan, Clarissa C. Parker, Cheryl Ackert‐Bicknell, Abraham A. Palmer, Diethard Tautz
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pgen.1007111
Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk
Cited by: 26
Author(s): Rosalie Griffin, Todd M. Darlington, Xiaomu Wei, Michael J. Madsen, Alun Thomas, Karen Curtin, Hilary Coon, Venkatesh Rajamanickam, Justin Musinsky, David Jayabalan, Djordje Atanackovic, S. Vincent Rajkumar, Shaji Kumar, Susan L. Slager, Mridu Middha, Perrine Galia, Delphine Demangel, Mohamed E. Salama, Joseph Vijai, James McKay, Robert J. Klein, Steven M. Lipkin, Charles Dumontet, Celine M. Vachon, Nicola J. Camp
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pgen.1008314
Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba
Cited by: 26
Author(s): Nicholas B. Stewart, Rebekah L. Rogers
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pgen.1006601
Excess of genomic defects in a woolly mammoth on Wrangel island
Cited by: 103
Author(s): Rebekah L. Rogers, Montgomery Slatkin
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pgen.1006685
Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations
Cited by: 37
Author(s): Shantao Li, Brian Shuch, Mark Gerstein
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pntd.0007421
One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia
Cited by: 48
Author(s): Timothy Barkham, Ruth N. Zadoks, Mohammad Noor Amal Azmai, Stephen Baker, Vu Thi Bich, Victoria J. Chalker, Man Ling Chau, David A. B. Dance, Rama Narayana Deepak, H. Rogier van Doorn, Ramona Alikiiteaga Gutiérrez, Mark A. Holmes, Lan Huong, Tse Hsien Koh, Elisabete Martins, Kurosh S. Mehershahi, Paul N. Newton, Lee Ching Ng, Nguyễn Ngọc Phước, Ornuma Sangwichian, Pongpun Sawatwong, Uraiwan Surin, Thean Yen Tan, Wen Tang, Nguyen Vu Thuy, Paul Turner, Manivanh Vongsouvath, Defeng Zhang, Toni Whistler, Swaine L. Chen
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pntd.0002564
Gene Amplification and Point Mutations in Pyrimidine Metabolic Genes in 5-Fluorouracil Resistant Leishmania infantum
Cited by: 22
Author(s): Jean-François Ritt, Frédéric Raymond, Philippe Leprohon, Danielle Légaré, Jacques Corbeil, Marc Ouellette
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pntd.0001811
Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax
Cited by: 65
Author(s): E. Ricky Chan, Didier Ménard, Peter H. David, Arsène Ratsimbasoa, Saorin Kim, Pheaktra Chim, Catherine Do, Benoît Witkowski, Odile Mercereau–Puijalon, Peter A. Zimmerman, David Serre
Software Mentions: 1
Published: about 12 years ago
10.1371/journal.pntd.0001817
Generation of Leishmania Hybrids by Whole Genomic DNA Transformation
Cited by: 11
Author(s): Adriano C. Coelho, Philippe Leprohon, Marc Ouellette
Software Mentions: 1
Published: about 12 years ago
10.1371/journal.pntd.0005091
Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications
Cited by: 42
Author(s): Jessica B. Hostetler, Eugenia Lo, Usheer Kanjee, Chanaki Amaratunga, Seila Suon, Sokunthea Sreng, Sivanna Mao, Delenasaw Yewhalaw, Anjali Mascarenhas, Dominic P. Kwiatkowski, Marcelo U. Ferreira, Pradipsinh K. Rathod, Guiyun Yan, Rick M. Fairhurst, Manoj T. Duraisingh, Julian C. Rayner
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pone.0192377
Prospecting for viral natural enemies of the fire ant Solenopsis invicta in Argentina
Cited by: 21
Author(s): Steven M. Valles, Sanford D. Porter, Luis A. Calcaterra
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0244505
CLK-2/TEL2 is a conserved component of the nonsense-mediated mRNA decay pathway
Cited by: 5
Author(s): Yanwu Guo, Cristina Tocchini, Rafal Ciosk
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0192062
Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks
Cited by: 23
Author(s): Eltohamy A. A. Yousef, Thomas Müller, Andreas Börner, Karl Schmid
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pone.0244228
Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia
Cited by: 5
Author(s): Stanislav Dryomov, Azhar M Nazhmidenova, Elena B. Starikovskaya, Sofia A Shalaurova, Nadin Rohland, Swapan Mallick, Rebecca Bernardos, Anatoly P. Derevianko, David Reich, Rem I. Sukernik
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0215912
Characterization of the Candida orthopsilosis agglutinin-like sequence (ALS) genes
Cited by: 13
Author(s): Lisa Lombardi, Marina Zoppo, Cosmeri Rizzato, Daria Bottai, Álvaro González Hernández, Lois L. Hoyer, Arianna Tavanti
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0105691
Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers
Cited by: 84
Author(s): Yan Shi, Chuan‐Chao Wang, Hou-Feng Zheng, Wei Wang, Zhaoyu Qin, Lan‐Hai Wei, Yi Wang, Xuedong Pan, Wenqing Fu, Yungang He, Lijun Xiong, Wenfei Jin, Shilin Li, Yu An, Hui Li, Jin Li
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0234508
Complete genome analysis and characterization of neurotropic dengue virus 2 cosmopolitan genotype isolated from the cerebrospinal fluid of encephalitis patients
Cited by: 15
Author(s): Mya Myat Ngwe Tun, Rohitha Muthugala, Takeshi Nabeshima, Aung Min Soe, Shyam Prakash Dumre, Lakmali Rajamanthri, Dulani Jayawardana, Shanthi Attanayake, Satoshi Inoue, Kouichi Morita
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0115152
Profiling of Exome Mutations Associated with Progression of HBV-Related Hepatocellular Carcinoma
Cited by: 16
Author(s): Hyun Goo Woo, Soon Sun Kim, Hyunwoo Cho, So Mee Kwon, Hyo Jung Cho, Sung Jun Ahn, Eun Sung Park, Ju Seog Lee, Sung Won Cho, Jae Youn Cheong
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0193928
High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing
Cited by: 10
Author(s): Anh Nhi Tran, Fulya Taylan, Vasilios Zachariadis, Ingegerd Ivanov Öfverholm, Anna Wedell, Francesco Vezzi, Britta Lötstedt, Magnus Nordenskjöld, Ann Nordgren, Daniel Nilsson, Gisela Barbany
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0137690
Molecular Profiling of a Rare Rosette-Forming Glioneuronal Tumor Arising in the Spinal Cord
Cited by: 26
Author(s): Lucas Tadeu Bidinotto, Cristovam Scapulatempo‐Neto, Alan Mackay, Gisele Caravina de Almeida, Bernd W. Scheithauer, Gustavo Nóriz Berardinelli, Raul Torrieri, Carlos Afonso Clara, Leonir Terezinha Feltrin, Marta Viana-Pereira, Marileila Varella‐Garcia, Chris Jones, Rui Manuel Reis
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0208771
Differential gene expression between the vigorous and dwarf litchi cultivars based on RNA-Seq transcriptome analysis
Cited by: 11
Author(s): Fuchu Hu, Zhe Chen, Jiamin Zhao, Xianghe Wang, Weixu Su, Yonghua Qin, Guibing Hu
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0118084
Genetic Investigation of Bisphosphonate-Related Osteonecrosis of Jaw (BRONJ) via Whole Exome Sequencing and Bioinformatics
Cited by: 16
Author(s): Jeehwan Kim, Yong Jae Ko, Jiyoung Kim, Yoonsoo Oh, Jihye Hwang, Sangjin Han, Sanguk Kim, Jae Hoon Lee, Dong‐Hoo Han
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0147749
Genome-Wide Detection of SNP and SV Variations to Reveal Early Ripening-Related Genes in Grape
Cited by: 25
Author(s): Yanshuai Xu, Zhihong Gao, Jianmin Tao, Weihua Jiang, Shijie Zhang, Qiunan Wang, Shenchun Qu
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0251314
Detection of genotype-1 of dengue virus serotype 3 for the first time and complete genome analysis of dengue viruses during the 2018 epidemic in Mandalay, Upper Myanmar
Cited by: 5
Author(s): Mya Myat Ngwe Tun, Aung Kyaw Kyaw, Takeshi Nabeshima, Aung Min Soe, Khine Mya Nwe, Kyaw Ko Ko Htet, Thet Htoo Aung, Thein Thein Htwe, Thidar Aung, Su Su Myaing, Tu Tu Mar, Ei Phyu Lwin, Hlaing Myat Thu, Kyaw Zin Thant, Kouichi Morita
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0196334
Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods
Cited by: 8
Author(s): Lieselot Deleye, Yannick Gansemans, Dieter De Coninck, Filip Van Nieuwerburgh, Dieter Deforce
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0106388
Genetic Diagnosis of Two Dopa-Responsive Dystonia Families by Exome Sequencing
Cited by: 9
Author(s): Zhanfang Sun, Yuhan Zhang, Jifeng Guo, Qiying Sun, Junpu Mei, Hanlin Zhou, Liping Guan, Jing Tian, Zhengmao Hu, Jia‐Da Li, Kun Xia, Xinxiang Yan, Beisha Tang
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0196473
The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis
Cited by: 13
Author(s): Xiaopeng Mu, Pengfei Wang, Junjie Du, Yu Gao, Jiancheng Zhang
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0155508
Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon
Cited by: 12
Author(s): Guido Valverde, María Inés Barreto Romero, Isabel Flores Espinoza, Alan Cooper, Lars Fehren‐Schmitz, Bastien Llamas, Wolfgang Haak
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0210529
Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection
Cited by: 53
Author(s): John Damien Platten, Joshua N. Cobb, Rochelle Endegado Zantua
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0028879
A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
Cited by: 64
Author(s): Gordon Daly, Nick Bexfield, Judith Heaney, Sam Stubbs, Antonia P. Mayer, Anne L. Palser, Paul Kellam, Nizar Drou, Mario Cáccamo, Laurence Tiley, Graeme Alexander, William Bernal, Jonathan L. Heeney
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0139582
Genome-Wide Epigenetic Regulation of Gene Transcription in Maize Seeds
Cited by: 28
Author(s): Xiaoduo Lu, Weixuan Wang, Wen Ren, Zhenguang Chai, Wu Guo, Rumei Chen, Lei Wang, Jun Zhao, Zhihong Lang, Yanting Fan, Jiuran Zhao, Chunyi Zhang
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0251019
Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019
Cited by: 2
Author(s): Alexey V. Danilenko, Natalia Kolosova, Аlexander N. Shvalov, T. N. Ilyicheva, Svetlana V. Svyatchenko, А. Г. Дурыманов, Julia A. Bulanovich, Н. И. Гончарова, Ivan M. Susloparov, Vasiliy Y. Marchenko, Т. В. Трегубчак, Elena V. Gavrilova, Rinat А. Maksyutov, Alexander B. Ryzhikov
Software Mentions: 1
Published: over 3 years ago