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: pysam
https://packages.ecosyste.ms/registries/pypi.org/packages/pysam
Package for reading, manipulating, and writing genomic data
51 versions
Latest release: about 1 year ago
269 dependent packages
382,212 downloads last month
Papers Mentioning pysam 130
10.1186/s13072-016-0095-z
EpiMINE, a computational program for mining epigenomic dataCited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: about 8 years ago
10.1093/bioinformatics/bty149
NanoPack: visualizing and processing long-read sequencing dataCited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago
10.12688/f1000research.51477.2
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebratesCited by: 2
Author(s): Ann Mc Cartney, Medhat Mahmoud, Michael D. Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K. Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M. Khayat, Maximillian G. Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jimin Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. Sedlazeck
Software Mentions: 14
Published: about 3 years ago
10.12688/f1000research.15140.2
Recommendations for the packaging and containerizing of bioinformatics softwareCited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago
10.1186/s12859-021-04057-z
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing dataCited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: over 3 years ago
10.1099/mgen.0.000131
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing readsCited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago
10.1111/1755-0998.13030
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element compositionCited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: over 5 years ago
10.1371/journal.pcbi.1004873
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA SequencingCited by: 1,141
Author(s): Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian
Software Mentions: 9
Published: over 8 years ago
10.7554/eLife.65537
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPACited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 3 years ago
10.1111/tpj.15190
Subgenome evolution in allotetraploid plantsCited by: 19
Author(s): Matteo Schiavinato, Alexandrina Bodrug‐Schepers, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 9
Published: over 3 years ago
10.1016/j.celrep.2020.108546
RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription CollisionsCited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: almost 4 years ago
10.15252/msb.202010060
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencingCited by: 11
Author(s): Liang Fang, Guipeng Li, Zhiyuan Sun, Qionghua Zhu, Huanhuan Cui, Yunfei Li, Jingwen Zhang, Weizheng Liang, Wencheng Wei, Yuhui Hu, Wei Chen
Software Mentions: 8
Published: over 3 years ago
10.7554/eLife.68312
A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in ToxoplasmaCited by: 12
Author(s): Dayana C Farhat, Matthew W. Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed‐Ali Hakimi, Christopher Swale
Software Mentions: 8
Published: over 3 years ago
10.12688/wellcomeopenres.14306.1
CoverView: a sequence quality evaluation tool for next generation sequencing dataCited by: 7
Author(s): Márton Münz, Shazia Mahamdallie, Shawn Yost, Andrew Rimmer, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Elise Ruark, Nazneen Rahman
Software Mentions: 8
Published: over 6 years ago
10.1186/s12864-019-5624-2
ALFA: annotation landscape for aligned readsCited by: 9
Author(s): Mathieu Bahin, Benoît Noël, Valentine Murigneux, Charles Bernard, Leïla Bastianelli, Hervé Le Hir, Alice Lebreton, Auguste Genovesio
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pgen.1009324
Virus-derived variation in diverse human genomesCited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 3 years ago
10.1186/s12859-021-03986-z
MSIFinder: a python package for detecting MSI status using random forest classifierCited by: 6
Author(s): Tao Zhou, Libin Chen, Jing Guo, Mengmeng Zhang, Yanrui Zhang, Shanbo Cao, Li Feng, Haijun Wang
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pgen.1009422
High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pestCited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pgen.1007784
Maternal and zygotic gene regulatory effects of endogenous RNAi pathwaysCited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 5 years ago
10.1128/mBio.03221-19
A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis FactorCited by: 24
Author(s): Guy E. Townsend, Weiwei Han, Nathan D. Schwalm, Xinyu Hong, Natasha A. Bencivenga-Barry, Andrew L. Goodman, Eduardo A. Groisman
Software Mentions: 7
Published: over 4 years ago
10.1186/s13059-015-0831-x
HiC-Pro: an optimized and flexible pipeline for Hi-C data processingCited by: 1,430
Author(s): Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Éric Viara, Chong Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
Software Mentions: 7
Published: almost 9 years ago
10.1186/gb-2013-14-2-r18
The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in DrosophilaCited by: 29
Author(s): Tobias Kockmann, Moritz Gerstung, Tommy Beat Schlumpf, Zhu Xhinzhou, Daniel Heß, Niko Beerenwinkel, Christian Beisel, Renato Paro
Software Mentions: 7
Published: almost 12 years ago
10.7554/eLife.49658
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modificationCited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: almost 5 years ago
10.1186/s12864-021-07974-8
SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq dataCited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: about 3 years ago
10.3390/ijms22158123
HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq DataCited by: 0
Author(s): Anna Macioszek, Bartek Wilczyński
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2020.00523
Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat StressCited by: 13
Author(s): Carolin Riedel, Konrad U. Förstner, Christoph Püning, Thomas Alter, Cynthia M. Sharma, Greta Gölz
Software Mentions: 6
Published: over 4 years ago
10.1186/s12864-019-5946-0
Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactionsCited by: 19
Author(s): Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon, Yves Poirier
Software Mentions: 6
Published: over 5 years ago
10.1002/1878-0261.12786
Allele‐specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (<i>TERT</i>) associates with <i>TERT</i> expression in multiple cancersCited by: 20
Author(s): Teisha J. Rowland, Andrew J. Bonham, Thomas R. Cech
Software Mentions: 6
Published: about 4 years ago
10.1016/j.molcel.2021.02.034
POINT technology illuminates the processing of polymerase-associated intact nascent transcriptsCited by: 44
Author(s): Rui Sousa-Luís, Geneviève Dujardin, Inna Zukher, Hiroshi Kimurâ, Carika Weldon, Maria Carmo‐Fonseca, Nick J. Proudfoot, Takayuki Nojima
Software Mentions: 6
Published: over 3 years ago
10.7554/eLife.32537
The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architectureCited by: 57
Author(s): Athma A. Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B. Burge
Software Mentions: 5
Published: almost 7 years ago
10.1093/gigascience/giaa054
Fcirc: A comprehensive pipeline for the exploration of fusion linear and circular RNAsCited by: 5
Author(s): Zhaoqing Cai, Hongzhang Xue, Yue Xu, Jens Köhler, Xiaoyu Cheng, Yanjun Dai, Jie Zheng, Haiyun Wang
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-021-02380-5
Samplot: a platform for structural variant visual validation and automated filteringCited by: 40
Author(s): Jonathan R Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael Cormier, Aaron R. Quinlan, Ryan M. Layer
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-021-02296-0
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencingCited by: 12
Author(s): Matthew T Parker, Katarzyna Knop, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-018-36768-4
Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across DatasetsCited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: almost 6 years ago
10.1186/1471-2164-15-76
Combinatorial epigenetic patterns as quantitative predictors of chromatin biologyCited by: 16
Author(s): Marcin Cieślik, Stefan Bekiranov
Software Mentions: 5
Published: almost 11 years ago
10.1093/gigascience/giaa158
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome dataCited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: almost 4 years ago
10.1038/s42003-020-0888-2
Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cellsCited by: 21
Author(s): Soyeong Jun, Hee‐Jung Lim, Honggu Chun, Ji Hyun Lee, Duhee Bang
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-018-4671-4
Indel detection from DNA and RNA sequencing data with transIndelCited by: 23
Author(s): Rendong Yang, Jamie L. Van Etten, Scott M. Dehm
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-018-4912-6
Shoelaces: an interactive tool for ribosome profiling processing and visualizationCited by: 13
Author(s): Åsmund Birkeland, Katarzyna Chyżyńska, Eivind Valen
Software Mentions: 4
Published: over 6 years ago
10.12688/f1000research.22400.2
Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IXCited by: 1
Author(s): Aikaterini Alexaki, Jacob Kames, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Ryan Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 4
Published: about 4 years ago
10.1038/s41598-020-72818-6
Detection of genomic alterations in breast cancer with circulating tumour DNA sequencingCited 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
10.1002/1878-0261.12776
Fine‐needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next‐generation sequencing in cancer patients included in the SHIVA02 trialCited by: 9
Author(s): Célia Dupain, Julien Masliah‐Planchon, Céline Gu, Elodie Girard, Pierre Gestraud, Pauline du Rusquec, Édith Borcoman, Diana Bello, Francesco Ricci, Ségolène Hescot, Marie‐Paule Sablin, Patricia Tresca, Alexandre de Moura, Delphine Loirat, Maxime Frélaut, Anne Vincent‐Salomon, Charlotte Lecerf, Céline Callens, Samantha Antonio, Coralie Franck, Odette Mariani, Ivan Bièche, Maud Kamal, Christophe Le Tourneau, Vincent Servois
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.ppat.1009824
pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spreadCited by: 12
Author(s): Tomasz H. Benedyk, Julia Muenzner, Viv Connor, Yue Han, Katherine A. Brown, Kaveesha J. Wijesinghe, Yunhui Zhuang, Susanna Colaco, Guido A. Stoll, Owen S. Tutt, Stanislava Svobodova, Dmitri I. Svergun, Neil Bryant, Janet E. Deane, Andrew E. Firth, Cy M. Jeffries, Colin M. Crump, Stephen C. Graham
Software Mentions: 4
Published: about 3 years ago
10.1186/s12864-017-3944-7
Genome-wide signals of positive selection in strongylocentrotid sea urchinsCited by: 11
Author(s): Kord M. Kober, Grant H. Pogson
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pgen.1007588
Numerous recursive sites contribute to accuracy of splicing in long introns in fliesCited by: 17
Author(s): Athma A. Pai, Joseph M. Paggi, Paul Yan, Karen Adelman, Christopher B. Burge
Software Mentions: 4
Published: about 6 years ago
10.12688/wellcomeopenres.11640.1
ClinVar data parsingCited by: 18
Author(s): Xiaolei Zhang, Eric Vallabh Minikel, Anne O’Donnell-Luria, Daniel G. MacArthur, James S. Ware, Ben Weisburd
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pgen.1009409
Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolutionCited by: 24
Author(s): Santiago Sánchez‐Ramírez, Jörg G Weiss, Cristel G. Thomas, Asher D. Cutter
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-018-26259-x
Nanopore sequencing technology: a new route for the fast detection of unauthorized GMOCited by: 22
Author(s): Marie‐Alice Fraiture, Assia Saltykova, Stefan Hoffman, Raf Winand, Dieter Deforce, Kevin Vanneste, Sigrid C. J. De Keersmaecker
Software Mentions: 4
Published: over 6 years ago
10.1186/s12859-016-1355-4
SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence dataCited by: 40
Author(s): Sang-Young Chun, Caitlin M. Rodriguez, Peter K. Todd, Ryan E. Mills
Software Mentions: 4
Published: almost 8 years ago
10.1093/gigascience/gix061
A recurrence-based approach for validating structural variation using long-read sequencing technologyCited by: 20
Author(s): Xuefang Zhao, Alexandra M. Weber, Ryan E. Mills
Software Mentions: 4
Published: over 7 years ago
10.1007/s00294-020-01096-6
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentialityCited by: 11
Author(s): Anton Levitan, Andrew N. Gale, Emma Dallon, Darby W. Kozan, Kyle W. Cunningham, Roded Sharan, Judith Berman
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1003219
Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative MutationsCited 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
10.1186/1471-2105-15-180
PBHoney: identifying genomic variants via long-read discordance and interrupted mappingCited by: 135
Author(s): Adam C. English, William Salerno, Jeffrey G. Reid
Software Mentions: 4
Published: over 10 years ago
10.1093/gigascience/giy064
SV-plaudit: A cloud-based framework for manually curating thousands of structural variantsCited by: 27
Author(s): Jonathan R Belyeu, Thomas J. Nicholas, Brent S. Pedersen, Thomas A Sasani, James M Havrilla, Stephanie N. Kravitz, Megan E Conway, Brian K. Lohman, Aaron R. Quinlan, Ryan M. Layer
Software Mentions: 3
Published: over 6 years ago
10.1186/s12859-019-2865-7
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulationCited by: 11
Author(s): Nathan Ungerleider, Erik K. Flemington
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2105-15-281
BESST - Efficient scaffolding of large fragmented assembliesCited by: 136
Author(s): Kristoffer Sahlin, Francesco Vezzi, Björn Nystedt, Joakim Lundeberg, Lars Arvestad
Software Mentions: 3
Published: about 10 years ago
10.1186/1471-2105-12-119
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing dataCited by: 259
Author(s): Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel
Software Mentions: 3
Published: over 13 years ago
10.1186/s12859-017-1985-1
pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing dataCited by: 6
Author(s): Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck, Geert Vandeweyer
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12864-019-6332-7
SMaSH: Sample matching using SNPs in humansCited by: 7
Author(s): Maximillian S. Westphal, David Frankhouser, Carmine M. Sonzone, Peter G. Shields, Pearlly S. Yan, Ralf Bundschuh
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12920-016-0181-x
Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control studyCited by: 29
Author(s): Lila E. Mullany, Jennifer S. Herrick, Roger K. Wolff, Matthew F. Buas, Martha L. Slattery
Software Mentions: 3
Published: over 8 years ago
10.1093/molbev/msab246
Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 EpidemicCited by: 21
Author(s): Jesse D. Bloom
Software Mentions: 3
Published: about 3 years ago
10.1111/mmi.14237
Systematic analysis of Type I‐E <i>Escherichia coli</i> CRISPR‐Cas PAM sequences ability to promote interference and primed adaptationCited by: 26
Author(s): Olga Musharova, Vasily Sitnik, Marnix Vlot, Ekaterina Savitskaya, Kirill A. Datsenko, Andrey Krivoy, Ivan Fedorov, Ekaterina Semenova, Stan J. J. Brouns, Konstantin Severinov
Software Mentions: 3
Published: over 5 years ago
10.1186/s13024-018-0274-4
Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human diseaseCited by: 90
Author(s): Mark T. W. Ebbert, Stefan L. Farrugia, Jonathon P. Sens, Karen Jansen-West, Tania F. Gendron, Mercedes Prudencio, Ian McLaughlin, Brett Bowman, Matthew G. Seetin, Mariely DeJesus-Hernandez, Jazmyne L. Jackson, Patricia E. Brown, Dennis W. Dickson, Marka van Blitterswijk, Rosa Rademakers, Leonard Petrucelli, John Denis Fryer
Software Mentions: 3
Published: about 6 years ago
10.3390/v11050481
Attenuation of Bluetongue Virus (BTV) in an in ovo Model Is Related to the Changes of Viral Genetic Diversity of Cell-Culture Passaged BTVCited by: 4
Author(s): Fabian Z. X. Lean, Matthew J. Neave, John R. White, Jean Payne, Teresa Eastwood, Jemma Bergfeld, Antonio Di Rubbo, Vittoria Stevens, Kelly R. Davies, Joanne M. Devlin, David T. Williams, John Bingham
Software Mentions: 3
Published: over 5 years ago
10.7717/peerj.201
Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencingCited by: 173
Author(s): Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pcbi.1008815
Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyperCited by: 0
Author(s): Phillip A. Richmond, Alice M. Kaye, Godfrain Jacques Kounkou, Tamar V. Av-Shalom, Wyeth W. Wasserman
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1006080
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data setsCited by: 6
Author(s): Soroush Samadian, Jeff Bruce, Trevor J. Pugh
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1005520
Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disordersCited by: 9
Author(s): Raony G C C L Cardenas, Natália Duarte Linhares, Raquel L. Ferreira, Sérgio D.J. Pena
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pgen.1007419
Differential strengths of molecular determinants guide environment specific mutational fatesCited by: 26
Author(s): Rohan Dandage, Rajesh Pandey, Gopal Gunanathan Jayaraj, Manish Kumar, David Berger, Kausik Chakraborty
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0134406
Differential Gene Expression in Colon Tissue Associated With Diet, Lifestyle, and Related Oxidative StressCited by: 25
Author(s): Martha L. Slattery, Daniel F. Pellatt, Lila E. Mullany, Roger K. Wolff
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0165375
Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by CyanophageCited by: 33
Author(s): Luke R. Thompson, Qinglu Zeng, Sallie W. Chisholm
Software Mentions: 3
Published: about 8 years ago
10.12688/f1000research.15841.2
The signs of adaptive mutations identified in the chloroplast genome of the algae endosymbiont of Baikal sponge.Cited by: 1
Author(s): Sergey Feranchuk, Natalia Belkova, Lubov Chernogor, Ulyana Potapova, С. И. Беликов
Software Mentions: 3
Published: over 4 years ago
10.3390/genes10010062
A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio SequencingCited by: 105
Author(s): Sarah B. Kingan, Haynes Heaton, Juliana Cudini, Christine Lambert, Primo Baybayan, Brendan D. Galvin, Richard Durbin, Jonas Korlach, Mara K. N. Lawniczak
Software Mentions: 3
Published: almost 6 years ago
10.1186/s13059-020-02142-9
RNA G-quadruplex structures exist and function in vivo in plantsCited by: 63
Author(s): Xiaofei Yang, Jitender Cheema, Yueying Zhang, Huiyong Deng, Susan Duncan, Mubarak Ishaq Umar, Jieyu Zhao, Qi Liu, Xiaofeng Cao, Chun Kit Kwok, Yiliang Ding
Software Mentions: 3
Published: about 4 years ago
10.1093/gigascience/giab033
BiSulfite Bolt: A bisulfite sequencing analysis platformCited by: 21
Author(s): Colin Farrell, Michael J. Thompson, Anela Tosevska, Adewale Oyetunde, Matteo Pellegrini
Software Mentions: 3
Published: over 3 years ago
10.1093/gigascience/giab063
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignmentCited by: 12
Author(s): Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J. Sedlazeck, Todd J. Treangen
Software Mentions: 3
Published: about 3 years ago
10.1007/s00251-014-0820-3
Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformaticsCited by: 15
Author(s): Wouter J. Veneman, Jan de Sonneville, Kees-Jan van der Kolk, Anita Ordas, Zaid Al-Ars, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 3
Published: almost 10 years ago
10.1038/srep11534
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing dataCited by: 35
Author(s): Michael Förster, Silke Szymczak, David Ellinghaus, Georg Hemmrich, Malte Rühlemann, Lars Kraemer, Sören Mucha, Lars Wienbrandt, Martin Stanulla, André Franke
Software Mentions: 3
Published: over 9 years ago
10.1038/s41598-019-44457-z
Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correctionCited by: 53
Author(s): Hengyi Xu, Jun Yao, Douglas C. Wu, Alan M. Lambowitz
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-019-54446-x
High throughput barcoding method for genome-scale phasingCited by: 13
Author(s): David Redin, Tobias Frick, Hooman Aghelpasand, Max Käller, Erik Borgström, Remi‐André Olsen, Afshin Ahmadian
Software Mentions: 3
Published: almost 5 years ago
10.1128/mSystems.00587-19
The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial CommunitiesCited by: 2
Author(s): Thomas Yssing Michaelsen, Jakob Brandt, Caitlin M. Singleton, Rasmus Hansen Kirkegaard, Johanna Wiesinger, Nicola Segata, Mads Albertsen
Software Mentions: 3
Published: over 4 years ago
10.7554/eLife.47301
Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'Cited by: 6
Author(s): Ben Auxier, Anna Bazzicalupo
Software Mentions: 3
Published: about 5 years ago
10.7554/eLife.60608
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gutCited by: 44
Author(s): Martial Marbouty, Agnès Thierry, Gaël A. Millot, Romain Koszul
Software Mentions: 3
Published: over 3 years ago
10.1021/acs.jproteome.0c00904
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and ContainersCited by: 16
Author(s): Jinwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaíno, Pablo Moreno-Ger, Björn Grüning, Olivier Sallou, Yasset Perez‐Riverol
Software Mentions: 3
Published: over 3 years ago
10.1186/s12711-020-00536-8
Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populationsCited by: 27
Author(s): Roger Ros‐Freixedes, Andrew Whalen, Ching-Yi Chen, Gregor Gorjanc, William Herring, Alan J. Mileham, John M. Hickey
Software Mentions: 2
Published: over 4 years ago
10.1186/s12920-021-01040-8
Characterization of DNA lesions associated with cell-free DNA by targeted deep sequencingCited by: 2
Author(s): Seung-Ho Shin, Woong-Yang Park, Donghyun Park
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2105-13-206
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomesCited by: 39
Author(s): Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart Watt, Paul M. Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E. Branton, Vincent Ferretti
Software Mentions: 2
Published: about 12 years ago
10.1186/s12916-015-0292-9
Improved survival among colon cancer patients with increased differentially expressed pathwaysCited by: 17
Author(s): Martha L. Slattery, Jennifer S. Herrick, Lila E. Mullany, Jason Gertz, Roger K. Wolff
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-018-5094-y
Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devicesCited by: 98
Author(s): Nicholas D. Sanderson, Teresa Street, Dona Foster, Jeremy Swann, Bridget L. Atkins, Andrew Brent, Martin McNally, Sarah Oakley, Adrian Taylor, Tim E. A. Peto, Derrick W. Crook, David W Eyre
Software Mentions: 2
Published: about 6 years ago
10.1186/s12859-016-0892-1
4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain informationCited by: 2
Author(s): Francisco Pina‐Martins, Bruno Miguel Vieira, Sofia G. Seabra, Dora Batista, Octávio S. Paulo
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12864-020-6585-1
InvBFM: finding genomic inversions from high-throughput sequence data based on feature miningCited by: 3
Author(s): Zhongjia Wu, Yufeng Wu, Juan Gao
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-021-92381-y
Assessment of the gene mosaicism burden in blood and its implications for immune disordersCited by: 5
Author(s): Manuel Solís-Moruno, Anna Mensa‐Vilaró, Laura Batlle-Masó, Irene Lobón, Núria Bonet, Tomàs Marqués-Bonet, Juan I. Aróstegui, Ferrán Casals
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-98318-9
High concordance in preimplantation genetic testing for aneuploidy between automatic identification via Ion S5 and manual identification via MiseqCited by: 3
Author(s): Tsu-Hwang Chuang, Zih-Huei Wu, Chin-Sheng Kuan, Meng-Ju Lee, Chu‐Chin Hsieh, Huai-Lin Wang, Hsing-Hua Lai, Yu-Jen Chang, Shee–Uan Chen
Software Mentions: 2
Published: about 3 years ago
10.1186/s13029-016-0058-6
cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processingCited by: 4
Author(s): Takuji Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
Software Mentions: 2
Published: about 8 years ago
10.1128/mBio.02415-19
A CRISPR Interference System for Efficient and Rapid Gene Knockdown in Caulobacter crescentusCited by: 21
Author(s): Mathilde Guzzo, Lennice K. Castro, Christopher R Reisch, Monica S. Guo, Michael T. Laub
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-019-6424-4
A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorumCited by: 33
Author(s): Carolyn Graham-Taylor, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0154177
MicroRNA Seed Region Length Impact on Target Messenger RNA Expression and Survival in Colorectal CancerCited by: 49
Author(s): Lila E. Mullany, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery
Software Mentions: 2
Published: over 8 years ago
10.3389/fmicb.2021.681150
Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensisCited by: 9
Author(s): Travis J. Sanders, Fahad Ullah, Alexandra M. Gehring, Brett W. Burkhart, Robert L. Vickerman, Sudili Fernando, Andrew F. Gardner, Asa Ben‐Hur, Thomas J. Santangelo
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1003153
GEMINI: Integrative Exploration of Genetic Variation and Genome AnnotationsCited by: 350
Author(s): Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron R. Quinlan
Software Mentions: 2
Published: over 11 years ago
10.3389/fneur.2020.573560
RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's DiseaseCited by: 6
Author(s): Miguel A. Andrade‐Navarro, Katja Mühlenberg, Eike J. Spruth, Nancy Mah, Adrián González-López, Tommaso Andreani, Jenny Russ, Matthew R. Huska, Enrique M. Muro, Jean-Fred Fontaine, Vyacheslav Amstislavskiy, Alexei Soldatov, Wilfried Nietfeld, Erich E. Wanker, Josef Priller
Software Mentions: 2
Published: almost 4 years ago