cran: Platypus | Projects | Ecosyste.ms: Papers

10.15252/msb.20177697

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Cited by: 153
Author(s): Julia Jabs, Franziska Maria Zickgraf, Jeongbin Park, Sven Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut Toprak, Marc A. Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin R. Sprick, Roland Eils, Christian Conrad
Software Mentions: 11
Published: about 7 years ago

10.1186/s12859-018-2296-x

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

10.1186/s13059-021-02316-z

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
Cited by: 24
Author(s): Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd Richmond, Donald J. Johann, Halil Bişğin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee S Basehore, Anne Bergstrom Lucas, Daniel L. Burgess, Daniel Butler, Simon Cawley, Chia Jung Chang, Guangchun Chen, Tao Chen, Yun Ching Chen, Daniel J. Craig, Ángela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, You-Zeng Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff S. Jasper, Giuseppe Jurman, David P. Kreil, Paweł P. Łabaj, Kevin Lai, Jianying Li, Quan Zhen Li, Yulong Li, Chi Kong Li, Zhichao Liu, Mario Solís-López, Kelci Miclaus, Raymond D. Miller, Vinay Kumar Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy M. Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Leming Shi, Joshua Xu
Software Mentions: 10
Published: over 3 years ago

10.1016/j.csbj.2018.01.003

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Cited by: 184
Author(s): Chang Xu
Software Mentions: 9
Published: almost 7 years ago

10.1186/s13059-020-1941-7

Genotyping structural variants in pangenome graphs using the vg toolkit
Cited by: 136
Author(s): Glenn Hickey, David Heller, Jean Monlong, Jonas Andreas Sibbesen, Jouni Sirén, Jordan M. Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pgen.1008671

PEA15 loss of function and defective cerebral development in the domestic cat
Cited by: 3
Author(s): Emily C. Graff, J. Nicholas Cochran, Christopher B. Kaelin, Kenneth Day, Heather L. Gray‐Edwards, Rie Watanabe, Jey W. Koehler, Rebecca A. Falgoust, Jeremy W. Prokop, R Myers, Nancy R. Cox, Gregory S. Barsh, Douglas R. Martin
Software Mentions: 9
Published: about 4 years ago

10.1093/g3journal/jkab238

Whole-genome variation of transposable element insertions in a maize diversity panel
Cited by: 13
Author(s): Yinjie Qiu, Christine H. O’Connor, Rafael Della Coletta, Jonathan S. Renk, Patrick J. Monnahan, Jaclyn M. Noshay, Zhikai Liang, Amanda M. Gilbert, Sarah N. Anderson, Suzanne E. McGaugh, Nathan M. Springer, Candice N. Hirsch
Software Mentions: 9
Published: over 3 years ago

10.1186/s13148-020-00889-3

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
Cited by: 6
Author(s): Holly Russell, Katarzyna Kedzierska, Daniel D. Buchanan, Russell J. Thomas, Emma Tham, Miriam Mints, Anne Keränen, Graham G. Giles, Melissa C. Southey, Roger L. Milne, Ian Tomlinson, David N. Church, Amanda B. Spurdle, Tracy A. O’Mara, Annabelle Lewis
Software Mentions: 8
Published: over 4 years ago

10.3390/genes12030444

Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity
Cited by: 9
Author(s): Amanda T S Albanaz, Evgeny S. Gerasimov, Jeffrey Jon Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Frederik Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko, Vyacheslav Yurchenko
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pbio.2004830

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species
Cited by: 73
Author(s): Reuben W. Nowell, Pedro Almeida, Christopher G. Wilson, Thomas P. Smith, Diego Fontaneto, Alastair Crisp, Gos Micklem, Alan Tunnacliffe, Chiara Boschetti, Timothy G. Barraclough
Software Mentions: 8
Published: over 6 years ago

10.12688/wellcomeopenres.10501.2

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection
Cited by: 35
Author(s): Laura Oikkonen, Stefano Lise
Software Mentions: 8
Published: almost 8 years ago

10.1038/s42003-019-0719-5

Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel
Cited by: 25
Author(s): Katharine R. Grabek, Thomas F. Cooke, L. Elaine Epperson, Kaitlyn Spees, Gleyce Fonseca Cabral, Shirley Sutton, Dana K. Merriman, Sandra L. Martin, Carlos D. Bustamante
Software Mentions: 7
Published: about 5 years ago

10.1534/g3.120.401325

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Cited by: 17
Author(s): Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
Software Mentions: 7
Published: over 4 years ago

10.1111/eva.12852

Temporal variation in spatial genetic structure during population outbreaks: Distinguishing among different potential drivers of spatial synchrony
Cited by: 27
Author(s): Jérémy Larroque, Simon Legault, Rob C. Johns, Lisa M. Lumley, Michel Cusson, Sébastien Renaut, Roger C. Levesque, Patrick M. A. James
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-019-2955-6

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Cited by: 3
Author(s): Akio Miyao, Jianyu Song Kiyomiya, Kei Iida, Koji Doi, Hiroshi Yasue
Software Mentions: 6
Published: over 5 years ago

10.1186/s12920-020-0668-3

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting
Cited by: 3
Author(s): Christian Wünsch, Henrik Banck, Carsten Müller‐Tidow, Martin Dugas
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-020-6455-x

Comparison of multiple algorithms to reliably detect structural variants in pears
Cited by: 14
Author(s): Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang, Wu Jun
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-98414-w

Integrated genomics point to immune vulnerabilities in pleural mesothelioma
Cited by: 7
Author(s): Anca Năstase, Amit Kumar Mandal, Shir Kiong Lu, Hima Anbunathan, Deborah Morris-Rosendahl, Yu Zhi Zhang, Xiaoming Sun, Spyridon Gennatas, Robert C. Rintoul, Matthew Edwards, Alex Bowman, Tatyana Chernova, T. Benepal, Eric Lim, Alison Taylor, Andrew G. Nicholson, Sanjay Popat, Anne E. Willis, Marion MacFarlane, Mark Lathrop, Anne M. Bowcock, Miriam F. Moffatt, William Cookson
Software Mentions: 6
Published: about 3 years ago

10.1007/s00401-021-02300-8

TERT promoter mutation and chromosome 6 loss define a high-risk subtype of ependymoma evolving from posterior fossa subependymoma
Cited by: 12
Author(s): Christian Thomas, Felix Thierfelder, Malte Träger, Patrick Soschinski, Michael Müther, Dominic Edelmann, Alexandra Förster, Carola Geiler, Hee-Yeong Kim, Katharina Filipski, Patrick N. Harter, Jens Schittenhelm, Franziska Eckert, Georgios Ntoulias, Sven-Axel May, Walter Stummer, Julia Onken, Peter Vajkoczy, Ulrich Schüller, Frank L. Heppner, David Capper, Arend Koch, David Kaul, Werner Paulus, Martin Hasselblatt, Leonille Schweizer
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12920-018-0391-5

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine
Cited by: 5
Author(s): Naresh Prodduturi, Aditya Bhagwate, Jean Pierre A. Kocher, Zhifu Sun
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-020-0885-5

Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes
Cited by: 5
Author(s): Peter A. Perrino, Lidiya Talbot, Rose Kirkland, Amanda Hill, Amanda R. Rendall, Hayley S. Mountford, Jenny C. Taylor, Alexzandrea N Buscarello, Nayana Lahiri, Anand Saggar, R. Holly Fitch, Dianne F. Newbury
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0192858

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets
Cited by: 1
Author(s): Piotr Madanecki, Magdalena Bałut, Patrick G. Buckley, J. Renata Ochocka, Rafał Bartoszewski, David K. Crossman, Ludwine Messiaen, Arkadiusz Piotrowski
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2021.661440

Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes
Cited by: 3
Author(s): Jingjia Li, Jason B. West, Alexander Hart, Jill L. Wegrzyn, Matthew A. Smith, Jean‐Christophe Domec, Carol A. Loopstra, Claudio Casola
Software Mentions: 5
Published: over 3 years ago

10.1016/j.ajhg.2021.04.024

Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder
Cited by: 6
Author(s): Holger Hengel, Shabab B. Hannan, Sarah Dyack, Sara MacKay, Ulrich Schatz, Martin Fleger, Andreas Kurringer, Ghassan Balousha, Zaïd Ghanim, Fowzan S. Alkuraya, Hamad Alzaidan, Hessa S. Alsaif, Tadahiro Mitani, Sevcan Tuğ Bozdoğan, Davut Pehlivan, James R. Lupski, Joseph J Gleeson, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Elliott H. Sherr, Kendall C. Parks, Emanuela Argilli, Amber Begtrup, Hamid Galehdari, Osama Balousha, Gholamreza Shariati, Neda Mazaheri, Reza Azizi Malamiri, Alistair T. Pagnamenta, Helen Kingston, Siddharth Banka, Adam Jackson, Mathew Osmond, Angelika Rieß, Tobias B. Haack, Thomas Nägele, Stefanie Schuster, Stefan Hauser, Jakob Admard, Nicolas Casadei, Ana Velić, Boris Maček, Stephan Ossowski, Henry Houlden, Reza Maroofian, Lüdger Schöls
Software Mentions: 5
Published: over 3 years ago

10.1155/2016/7983236

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data
Cited by: 32
Author(s): Jennifer D. Hintzsche, William A. Robinson, Aik Choon Tan
Software Mentions: 5
Published: almost 9 years ago

10.1021/acs.chemrev.0c01266

Performance-Based Screening of Porous Materials for Carbon Capture
Cited by: 99
Author(s): Amir Hajiahmadi Farmahini, Shreenath Krishnamurthy, Daniel Friedrich, Stefano Brandani, Lev Sarkisov
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0126321

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow
Cited by: 36
Author(s): Amit Kawalia, Susanne Motameny, Stephan Wonczak, Holger Thiele, Lech Nieroda, Kamel Jabbari, Stefan Borowski, Vishal Sinha, Wilfried Gunia, Ulrich Lang, Viktor Achter, Peter Nürnberg
Software Mentions: 5
Published: over 9 years ago

10.12688/wellcomeopenres.14754.2

ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series
Cited by: 0
Author(s): Elise Ruark, Esty Holt, Anthony Renwick, Márton Münz, Matthew N. Wakeling, Sian Ellard, Shazia Mahamdallie, Shawn Yost, Nazneen Rahman
Software Mentions: 5
Published: about 6 years ago

10.1002/mgg3.1106

Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate
Cited by: 7
Author(s): Alba Sanchis‐Juan, Marcia Anahí Hasenahuer, James Alexander Baker, Amy McTague, Katy Barwick, Manju A. Kurian, Sofia Duarte, Nihr BioResource, Keren Carss, Janet M. Thornton, F. Lucy Raymond
Software Mentions: 5
Published: over 4 years ago

10.1186/s13073-019-0651-9

Implementation of a genomic medicine multi-disciplinary team approach for rare disease in the clinical setting: a prospective exome sequencing case series
Cited by: 20
Author(s): Jenny C Taylor, Judith Craft, Edward Blair, Sarah Wordsworth, David Beeson, Saleel Chandratre, Judith Cossins, Tracy Lester, Andrea H. Németh, Elizabeth Ormondroyd, Smita Y. Patel, Alistair T. Pagnamenta, Jenny C Taylor, Kate Thomson, Hugh Watkins, Wilkie Aom., Julian C. Knight
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5998-1

Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants
Cited by: 8
Author(s): Marc‐André Lemay, Davoud Torkamaneh, Guillem Rigaill, Brian Boyle, Adrian O. Stec, Robert M. Stupar, François Belzile
Software Mentions: 4
Published: over 5 years ago

10.1186/s13073-020-00791-w

Best practices for variant calling in clinical sequencing
Cited by: 136
Author(s): Daniel C. Koboldt
Software Mentions: 4
Published: about 4 years ago

10.1186/s13073-018-0563-0

Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing
Cited by: 25
Author(s): Annie N. Cowell, Hugo O. Valdivia, Danett K. Bishop, Elizabeth A. Winzeler
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.3000926

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils
Cited by: 23
Author(s): Young Mi Kwon, Kevin Gori, Naomi Park, Nicole Potts, Kate Swift, Jinhong Wang, Maximilian R Stammnitz, Naomi Cannell, Adrian Baez‐Ortega, Sébastien Comte, Samantha Fox, Colette Harmsen, Stewart J. Huxtable, Menna Lloyd Jones, Alexandre Kreiss, C.C. Lawrence, Billie Lazenby, Sarah Peck, Ruth J. Pye, Gregory M. Woods, Mona Zimmermann, David C. Wedge, David Pemberton, Michael R. Stratton, Rodrigo Hamede, Elizabeth P. Murchison
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-016-1279-z

Impact of post-alignment processing in variant discovery from whole exome data
Cited by: 28
Author(s): Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L. Slager
Software Mentions: 4
Published: about 8 years ago

10.1128/mBio.02257-16

Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples
Cited by: 54
Author(s): Annie N. Cowell, Dorothy E. Loy, Sesh A. Sundararaman, Hugo O. Valdivia, Kathleen Fisch, Andrés G. Lescano, G. Christian Baldeviano, Salomón Durand, Vincent R. Gerbasi, Colin J. Sutherland, Debbie Nolder, Joseph M. Vinetz, Beatrice H. Hahn, Elizabeth A. Winzeler
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1003219

Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations
Cited by: 43
Author(s): Katherine Bull, Andrew Rimmer, Owen M. Siggs, Lisa A. Miosge, Carla Roots, Anselm Enders, Edward M. Bertram, Tanya L. Crockford, Belinda Whittle, Paul K. Potter, Michelle Simon, Ann Marie Mallon, Steve Brown, Bruce Beutler, Christopher C. Goodnow, Gerton Lunter, Richard J. Cornall
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12864-018-4671-4

Indel detection from DNA and RNA sequencing data with transIndel
Cited by: 23
Author(s): Rendong Yang, Jamie L. Van Etten, Scott M. Dehm
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ajhg.2015.07.007

Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability
Cited by: 51
Author(s): Stephen R.F. Twigg, Jennifer Forecki, Jacqueline A.C. Goos, Ivy C.A. Richardson, A. Jeannette M. Hoogeboom, Ans M.W. van den Ouweland, Sigrid Swagemakers, Maarten H. Lequin, Daniel Van Antwerp, Simon J. McGowan, Isabelle Westbury, Kerry A. Miller, Steven A. Wall, Peter J. van der Spek, Irene M.J. Mathijssen, Erwin Pauws, Christa Merzdorf, Andrew O.M. Wilkie
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-016-1116-8

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Cited by: 112
Author(s): Shaman Narayanasamy, Yohan Jarosz, Emilie Muller, Anna Heintz‐Buschart, Malte Herold, Anne Kaysen, Cédric Christian Laczny, Nicolás Pinel, Patrick May, Paul Wilmes
Software Mentions: 4
Published: about 8 years ago

10.1093/gigascience/giaa007

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
Cited by: 79
Author(s): Stephen J. Bush, Dona Foster, David W Eyre, Emily L. Clark, Nicola De Maio, Liam P. Shaw, Nicole Stoesser, Tim Peto, Derrick W. Crook, A Sarah Walker
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2019.01384

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies
Cited by: 10
Author(s): Anthony Piot, Julien Prunier, Nathalie Isabel, Jaroslav Klápště, Yousry A. El‐Kassaby, Juan Carlos Villarreal Aguilar, Ilga Porth
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0200423

Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis
Cited by: 6
Author(s): Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen J. O’Brien
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0049110

Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
Cited by: 48
Author(s): Matthew Frampton, Richard S. Houlston
Software Mentions: 4
Published: about 12 years ago

10.1186/s12864-019-6225-9

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance
Cited by: 44
Author(s): Xiaoling Yu, Wen Zhang, Zhiping Zhao, Chengsong Ye, Shao-Lai Zhou, Shaogui Wu, Lijing Han, Zhaofang Han, Hanhui Ye
Software Mentions: 4
Published: about 5 years ago

10.1093/bioinformatics/btz275

NGSEP3: accurate variant calling across species and sequencing protocols
Cited by: 44
Author(s): Daniel Tello, Juanita Gil, Cristian D Loaiza, John J. Riascos, Nicolás Cardozo, Jorge Duitama
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00439

Whole-Exome Sequencing Identifies Somatic Mutations Associated With Mortality in Metastatic Clear Cell Kidney Carcinoma
Cited by: 17
Author(s): Alejandro Mendoza-Álvarez, Beatriz Guillén‐Guío, Adrian Baez‐Ortega, Carolina Hernandez-Perez, Sita Lakhwani-Lakhwani, María-del-Carmen Maeso, José M. Lorenzo-Salazar, Manuel Morales, Carlos Flores
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/bty157

Integrating long-range connectivity information into de Bruijn graphs
Cited by: 56
Author(s): Isaac Turner, Kiran Garimella, Zamin Iqbal, Gil McVean
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0185207

Escape Excel: A tool for preventing gene symbol and accession conversion errors
Cited by: 8
Author(s): Eric A. Welsh, Paul A. Stewart, Brent M. Kuenzi, James A. Eschrich
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-016-1312-2

InDel marker detection by integration of multiple softwares using machine learning techniques
Cited by: 8
Author(s): Jin Yang, Xinyi Shi, Lun Hu, Daipeng Luo, Jing Peng, Shengwu Xiong, Fankai Kong, Baohui Liu, Xiaohui Yuan
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-017-2000-6

A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy
Cited by: 53
Author(s): Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers, Matthew E. Hudson
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pntd.0007919

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus
Cited by: 16
Author(s): Michele Marconcini, Luis Miguel Hernández, Giuseppe Iovino, Vincent Houé, Federica Valerio, Umberto Palatini, Elisa Pischedda, Jacob E. Crawford, Bradley J. White, Teresa Lin, Rebeca Carballar-Lejarazú, Lino Ometto, Federico Forneris, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6126-y

Comparative genomics of Leishmania (Mundinia)
Cited by: 24
Author(s): Anzhelika Butenko, Alexei Y. Kostygov, Jovana Sádlová, Yuliya Kleschenko, Tomáš Bečvář, Lucie Podešvová, Diego H. Macedo, David Žihala, Julius Lukeš, Paul A. Bates, Petr Volf, Frederik Opperdoes, Vyacheslav Yurchenko
Software Mentions: 4
Published: about 5 years ago

10.1186/s40246-015-0042-2

Performance evaluation of indel calling tools using real short-read data
Cited by: 76
Author(s): Mohammad Shabbir Hasan, Xiaowei Wu, Liqing Zhang
Software Mentions: 4
Published: over 9 years ago

10.1002/ece3.5950

Continent‐wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)
Cited by: 19
Author(s): Lisa M. Lumley, Esther Pouliot, Jérôme Laroche, Brian Boyle, Bryan M. T. Brunet, Roger C. Levesque, Felix A. H. Sperling, Michel Cusson
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-72818-6

Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing
Cited by: 6
Author(s): Dimitrios Kleftogiannis, David Ho, Jun Xian Liew, Polly Poon, Anna Gan, Raymond Ng, Benita Kiat‐Tee Tan, Kiang Hiong Tay, Swee Ho Lim, Gek San Tan, Chih Chuan Shih, Tony Kiat-Hon Lim, Ann Siew‐Gek Lee, Iain Beehuat Tan, Yoon Sim Yap, Sarah Ng
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-018-26239-1

A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms
Cited by: 19
Author(s): Ruth Barral-Arca, Jacobo Pardo‐Seco, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-49952-x

The polymorphic variant rs1800734 influences methylation acquisition and allele-specific TFAP4 binding in the MLH1 promoter leading to differential mRNA expression
Cited by: 6
Author(s): Russell J. Thomas, Davide Trapani, Lily Goodyer-Sait, Markéta Tomková, Ceres Fernández–Rozadilla, Nora Sahnane, Connor Woolley, Hayley L. Belnoue-Davis, Laura Chegwidden, Skirmantas Kriaucionis, Tim Maughan, Simon J. Leedham, Claire Palles, Daniela Furlan, Ian Tomlinson, Annabelle Lewis
Software Mentions: 4
Published: over 5 years ago

10.1111/pbi.12645

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application
Cited by: 204
Author(s): Armin Scheben, Jacqueline Batley, David Edwards
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.11724

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
Cited by: 11
Author(s): Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan
Software Mentions: 4
Published: over 3 years ago

10.1038/srep20369

Multidisciplinary investigation links backward-speech trait and working memory through genetic mutation
Cited by: 5
Author(s): Stefan Prekovic, Dušica Filipović Đurđević, Gábor Csifcsák, Olivera Šveljo, Oliver Stojković, Milica M. Janković, Katarina Koprivšek, Laura Covill, Miloš Lučić, Thomas Van den Broeck, Christine Helsen, Fabiola Ceroni, Frank Claessens, Dianne F. Newbury
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-15-948

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle
Cited by: 41
Author(s): C.F. Baes, Marlies Dolezal, James E. Koltes, Beat Bapst, Eric R. Fritz-Waters, Sandra Jansen, Christine Flury, Heidi Signer-Hasler, Christine Stricker, Rohan L. Fernando, R. Fries, J. Moll, Dorian J. Garrick, James M. Reecy, Birgit Gredler
Software Mentions: 4
Published: almost 11 years ago

10.1200/JCO.19.00577

Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma
Cited by: 44
Author(s): Matthias Begemann, Sebastian M. Waszak, Giles Robinson, Natalie Jäger, Tanvi Sharma, Cordula Knopp, Florian Kraft, Olga Moser, Martin Mynarek, Léa Guerrini-Rousseau, Laurence Brugières, Pascale Varlet, Torsten Pietsch, Daniel C. Bowers, Murali Chintagumpala, Felix Sahm, Jan O. Korbel, Stefan Rutkowski, Thomas Eggermann, Amar Gajjar, Paul A. Northcott, Miriam Elbracht, Stefan M. Pfister, Udo Kontny, Ingo Kurth
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-14400-1

UPS-indel: a Universal Positioning System for Indels
Cited by: 6
Author(s): Mohammad Shabbir Hasan, Xiaowei Wu, Layne T. Watson, Liqing Zhang
Software Mentions: 4
Published: about 7 years ago

10.3390/genes12081282

A Novel Missense Mutation in TNNI3K Causes Recessively Inherited Cardiac Conduction Disease in a Consanguineous Pakistani Family
Cited by: 5
Author(s): Shafaq Ramzan, Stephanie Tennstedt, Muhammad Tariq, Sheraz Khan, Hafiza Noor Ul Ayan, Aamir Ali, Matthias Munz, Holger Thiele, Asad Aslam Korejo, Abdul Razzaq Mughal, Syed Zahid Jamal, Peter Nürnberg, Shahid Mahmood Baig, Jeanette Erdmann, Ilyas Ahmad
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-016-2824-x

SPAI: an interactive platform for indel analysis
Cited by: 0
Author(s): Mohammad Shabbir Hasan, Liqing Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-07224-3

Red panda: a novel method for detecting variants in single-cell RNA sequencing
Cited by: 0
Author(s): Adam Cornish, Shrabasti Roychoudhury, Krishna Sarma, Suravi Pramanik, Kishor K. Bhakat, Andrew T. Dudley, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 3
Published: about 4 years ago

10.1016/j.ajhg.2017.03.010

Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability
Cited by: 145
Author(s): Katrina Tatton‐Brown, Chey Loveday, Shawn Yost, Matthew Clarke, Emma Ramsay, Anna Zachariou, Anna Elliott, Harriet Wylie, Anna Ardissone, Olaf Rittinger, Fiona Stewart, I. Karen Temple, Trevor Cole, Shazia Mahamdallie, Sheila Seal, Elise Ruark, Nazneen Rahman
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-018-0606-6

Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing
Cited by: 102
Author(s): Alba Sanchis‐Juan, Jonathan Stephens, Courtney French, Nicholas Gleadall, Karyn Mégy, Christopher J. Penkett, Olga Shamardina, Kathleen Stirrups, Isabelle Delon, Eleanor Dewhurst, Helen Dolling, Marie Erwood, Detelina Grozeva, Luca Stefanucci, Gavin Arno, Andrew R. Webster, Trevor Cole, Topun Austin, Ricardo Garcia Branco, Willem H. Ouwehand, F. Lucy Raymond, Keren Carss
Software Mentions: 3
Published: about 6 years ago

10.1093/gigascience/giz074

Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data
Cited by: 57
Author(s): Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung, Phillip A. Richmond, Whitney Whitford, Melissa A. Wilson
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3045-z

An analytical workflow for accurate variant discovery in highly divergent regions
Cited by: 16
Author(s): Shulan Tian, Huihuang Yan, Claudia Neuhauser, Susan L. Slager
Software Mentions: 3
Published: over 8 years ago

10.1016/j.ccell.2019.05.013

Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer
Cited by: 159
Author(s): Andrew Woolston, Khurum Khan, Georgia Spain, Louise J. Barber, Beatrice Griffiths, Reyes Gonzalez-Exposito, Lisa Hornsteiner, Marco Punta, Yatish Patil, Alice Newey, Sonia Mansukhani, Matthew N. Davies, Andrew Furness, Francesco Sclafani, Clare Peckitt, Mirta Jiménez, Kyriakos Kouvelakis, Romana Ranftl, Ruwaida Begum, Isma Rana, Janet Thomas, Annette Bryant, Sergio A. Quezada, Andrew Wotherspoon, Nasir Khan, Nikolaos Fotiadis, Teresa Marafioti, Thomas Powles, Stefano Lise, Fernando Calvo, Sebastian Guettler, Katharina von Loga, Rao S, David Watkins, Naureen Starling, Ian Chau, Anguraj Sadanandam, David Cunningham, Marco Gerlinger
Software Mentions: 3
Published: over 5 years ago

10.1186/s13073-015-0195-6

CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting
Cited by: 49
Author(s): Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter, Nazneen Rahman
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-13-361

Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species
Cited by: 85
Author(s): Emily A. Hornett, Christopher W. Wheat
Software Mentions: 3
Published: almost 13 years ago

10.1093/gbe/evab126

The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades
Cited by: 9
Author(s): Markus Hiltunen, Sandra Lorena Ament‐Velásquez, Hanna Johannesson
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-015-0251-2

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
Cited by: 39
Author(s): Rendong Yang, Andrew C. Nelson, Christine Henzler, Bharat Thyagarajan, Kevin A.T. Silverstein
Software Mentions: 3
Published: about 9 years ago

10.1038/s41416-020-0797-7

The prognostic significance of immune microenvironment in breast ductal carcinoma in situ
Cited by: 25
Author(s): Michael S. Toss, Asima Abidi, Dorothea Lesche, Chitra Joseph, Sakshi Mahale, Hugo Saunders, Tanjina Kader, Islam M. Miligy, Andrew Green, Kylie L. Gorringe, Emad A. Rakha
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers13061340

Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms
Cited by: 9
Author(s): Adrián Mosquera Orgueira, Marcos Pérez López, Andrés Peleteiro Raíndo, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ángeles Bendaña López, Ayelén Melisa Blanco, Paula Melero Valentín, Roi Ferreiro Ferro, Cristina Santos, Marianela Rodríguez, Marta Sonia González Pérez, Manuel Pérez‐Encinas, José Luis Bello López
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41436-020-01071-z

A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy
Cited by: 9
Author(s): Min Ni, Bushra Afroze, Chao Xing, Chunxiao Pan, Yanqiu Shao, Ling Cai, Brandi L. Cantarel, Jimin Pei, Nick V. Grishin, Stacy Hewson, Devon Knight, Sonal Mahida, Donnice Michel, Mark A. Tarnopolsky, Annapurna Poduri, Alexander Rotenberg, Neal Sondheimer, Ralph J. DeBerardinis
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-1431-9

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
Cited by: 90
Author(s): Davoud Torkamaneh, Jérôme Laroche, Maxime Bastien, Amina Abed, François Belzile
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13073-018-0529-2

From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards
Cited by: 32
Author(s): Júlia Perera-Bel, Barbara Hutter, Christoph Heining, Annalen Bleckmann, Martina Fröhlich, Stefan Fröhling, Hanno Glimm, Benedikt Brors, Tim Beißbarth
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2020.00711

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros
Cited by: 11
Author(s): Charlotte Avanzi, Emmanuel Lecorché, Fetra Angelot Rakotomalala, Andrej Benjak, F. Rapelanoro Rabenja, Lala Soavina Ramarozatovo, B. Cauchoix, Mala Rakoto-Andrianarivelo, Maria Tió-Coma, Thyago Leal-Calvo, Philippe Busso, Stefanie Boy‐Röttger, Aurélie Chauffour, T Rasamoelina, Aina Andrianarison, Fandresena Arilala Sendrasoa, John S. Spencer, Pushpendra Singh, Digambar Dashatwar, Rahul Narang, Jean-Luc Berland, Vincent Jarlier, Cláudio Guedes Salgado, Milton Ozório Moraes, Annemieke Geluk, Andriamira Randrianantoandro, Emmanuelle Cambau, Stewart T. Cole
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0187926

Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans
Cited by: 51
Author(s): Douglas R. Smith, Christine M. Stanley, Theodore Foss, Richard G. Boles, Kevin McKernan
Software Mentions: 3
Published: about 7 years ago

10.3389/fped.2019.00122

Combined Immunodeficiency With Late-Onset Progressive Hypogammaglobulinemia and Normal B Cell Count in a Patient With RAG2 Deficiency
Cited by: 10
Author(s): Mayra B. Dorna, Pamela F. A. Barbosa, A. Rangel-Santos, Krisztián Csomós, Boglárka Ujházi, Joseph Dasso, D.I. Thwaites, Joan Boyes, Sinisa Savic, Jolán E. Walter
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0135800

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification
Cited by: 12
Author(s): Riyue Bao, Kyle M. Hernandez, Lei Huang, Wenjun Kang, Elizabeth T. Bartom, Kenan Onel, Samuel L. Volchenboum, Jorge Andrade
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2021.617935

Screening for Combination Cancer Therapies With Dynamic Fuzzy Modeling and Multi-Objective Optimization
Cited by: 5
Author(s): Simone Spolaor, Martijn Scheve, Murat Fırat, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants
Cited by: 23
Author(s): Gangyi Yang, Wenlong Luo, Jian Zhang, Xian-cheng Yan, Yuguo Du, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 3
Published: about 5 years ago

10.3389/fendo.2021.600682

Whole Genome Sequencing Prioritizes CHEK2, EWSR1, and TIAM1 as Possible Predisposition Genes for Familial Non-Medullary Thyroid Cancer
Cited by: 11
Author(s): Aayushi Srivastava, Sara Galimberti, Diamanto Skopelitou, Benchun Miao, Nagarajan Paramasivam, Chiara Diquigiovanni, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2019.01192

LD-annot: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes
Cited by: 3
Author(s): Julien Prunier, Audrey Lemaçon, Alexandre Bastien, Mohsen Jafarikia, Ilga Porth, Claude Robert, Arnaud Droit
Software Mentions: 3
Published: about 5 years ago

10.1093/bioinformatics/btx753

Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
Cited by: 20
Author(s): Peter A. Audano, Shashidhar Ravishankar, Fredrik Vannberg
Software Mentions: 3
Published: about 7 years ago

10.1093/bioinformatics/btw587

ReliableGenome: annotation of genomic regions with high/low variant calling concordance
Cited by: 5
Author(s): Niko Popitsch, Anna Schuh, Jenny C. Taylor
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0208901

The sequencing and interpretation of the genome obtained from a Serbian individual
Cited by: 3
Author(s): Wazim Mohammed Ismail, Kymberleigh A. Pagel, Vikas Pejaver, Simo V. Zhang, Sofía Casasa, Matthew Mort, David Neil Cooper, Matthew W. Hahn, Predrag Radivojac
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers13071497

An Evaluation of the Diagnostic Accuracy of a Panel of Variants in DPYD and a Single Variant in ENOSF1 for Predicting Common Capecitabine Related Toxicities
Cited by: 12
Author(s): Claire Palles, Susan Fotheringham, Laura Chegwidden, Marie Madeleine Lucas, Rachel Kerr, Guy Mozolowski, Dan Rosmarin, Jenny C. Taylor, Ian Tomlinson, David Kerr
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.01015

Targeting Mutated Plus Germline Epitopes Confers Pre-clinical Efficacy of an Instantly Formulated Cancer Nano-Vaccine
Cited by: 34
Author(s): Mona O. Mohsen, Monique Vogel, Carsten Riether, Julius Müller, Silvia Salatino, Nicola Ternette, Ariane Gomes, Gustavo Cabral-Miranda, Aadil El-Turabi, Christiane Ruedl, Thomas M. Kündig, Said Dermime, Alexander Knuth, Daniel E. Speiser, Martin F. Bachmann
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0216838

Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data
Cited by: 21
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Behnam Abasht, Carl J. Schmidt
Software Mentions: 3
Published: about 5 years ago

10.1186/1756-0500-7-864

Comparison of insertion/deletion calling algorithms on human next-generation sequencing data
Cited by: 54
Author(s): Dalia Ghoneim, Jason R. Myers, Emily Tuttle, Alex R. Paciorkowski
Software Mentions: 3
Published: almost 11 years ago

10.1002/ece3.4778

Near‐complete genome assembly and annotation of the yellow drum ( Nibea albiflora ) provide insights into population and evolutionary characteristics of this species
Cited by: 11
Author(s): Zhaofang Han, Wanbo Li, Weihua Zhu, Sha Sun, Kun Ye, Yangjie Xie, Zhiyong Wang
Software Mentions: 3
Published: about 6 years ago

10.1038/ejhg.2017.32

Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders
Cited by: 60
Author(s): Alistair T. Pagnamenta, Yoshiko Murakami, John M. Taylor, Consuelo Anzilotti, Malcolm F. Howard, Venessa Miller, Diana Johnson, Shereen Tadros, Sahar Mansour, I. Karen Temple, Rachel Firth, Elisabeth Rosser, Rachel Harrison, B Kerr, Niko Popitsch, Taroh Kinoshita, Jenny C Taylor, Usha Kini
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1008102

An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome
Cited by: 12
Author(s): Thomas W. Marchant, Elisabeth Dietschi, Ulrich Rytz, Peter Schawalder, Vidhya Jagannathan, Sheida Hadji Rasouliha, Corinne Gurtner, Andreas Waldvogel, R. S. Harrington, Michaela Drögemüller, Jeffrey M. Kidd, Elaine A. Ostrander, Amanda Warr, Michael Watson, David Argyle, Gert ter Haar, Dylan Clements, Tosso Leeb, Jeffrey J. Schoenebeck
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-020-00803-z

Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data
Cited by: 7
Author(s): Ali Karimnezhad, Gareth Palidwor, Kednapa Thavorn, David J. Stewart, Pearl A. Campbell, Bryan Lo, Theodore J. Perkins
Software Mentions: 3
Published: about 4 years ago

Projects: cran: Platypus

Papers Mentioning Platypus 218