pypi: pysam | Projects | Ecosyste.ms: Papers

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: almost 8 years ago

NanoPack: visualizing and processing long-read sequencing data
Cited 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 vertebrates
Cited 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 software
Cited 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 data
Cited 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 reads
Cited 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: almost 7 years ago

10.1111/1755-0998.13030

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Cited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pcbi.1004873

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
Cited 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 FPA
Cited 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 plants
Cited 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 Collisions
Cited 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 sequencing
Cited 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 Toxoplasma
Cited 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: about 3 years ago

10.12688/wellcomeopenres.14306.1

CoverView: a sequence quality evaluation tool for next generation sequencing data
Cited 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 reads
Cited 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 genomes
Cited 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 classifier
Cited 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 pest
Cited 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: about 3 years ago

10.1371/journal.pgen.1007784

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Cited 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 Factor
Cited 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 processing
Cited 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 Drosophila
Cited 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: over 11 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited 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: over 4 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited 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: almost 3 years ago

10.3390/ijms22158123

HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data
Cited by: 0
Author(s): Anna Macioszek, Bartek Wilczyński
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2020.00523

Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
Cited 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 interactions
Cited by: 19
Author(s): Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon, Yves Poirier
Software Mentions: 6
Published: about 5 years ago

10.1002/1878-0261.12786

Allele‐specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (TERT) associates with TERT expression in multiple cancers
Cited 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 transcripts
Cited 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 architecture
Cited by: 57
Author(s): Athma A. Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B. Burge
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giaa054

Fcirc: A comprehensive pipeline for the exploration of fusion linear and circular RNAs
Cited 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 filtering
Cited 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 sequencing
Cited 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 Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-76

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology
Cited by: 16
Author(s): Marcin Cieślik, Stefan Bekiranov
Software Mentions: 5
Published: over 10 years ago

10.1093/gigascience/giaa158

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Cited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-020-0888-2

Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells
Cited by: 21
Author(s): Soyeong Jun, Hee‐Jung Lim, Honggu Chun, Ji Hyun Lee, Duhee Bang
Software Mentions: 4
Published: over 4 years ago

10.1186/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

10.1186/s12864-018-4912-6

Shoelaces: an interactive tool for ribosome profiling processing and visualization
Cited by: 13
Author(s): Åsmund Birkeland, Katarzyna Chyżyńska, Eivind Valen
Software Mentions: 4
Published: about 6 years ago

10.12688/f1000research.22400.2

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX
Cited 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: almost 4 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: almost 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 trial
Cited 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 spread
Cited 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 urchins
Cited by: 11
Author(s): Kord M. Kober, Grant H. Pogson
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1007588

Numerous recursive sites contribute to accuracy of splicing in long introns in flies
Cited 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 parsing
Cited 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 evolution
Cited 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 GMO
Cited 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 data
Cited 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 technology
Cited by: 20
Author(s): Xuefang Zhao, Alexandra M. Weber, Ryan E. Mills
Software Mentions: 4
Published: about 7 years ago

10.1007/s00294-020-01096-6

Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality
Cited 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: about 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 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: over 11 years ago

10.1186/1471-2105-15-180

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
Cited 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 variants
Cited 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 regulation
Cited 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 assemblies
Cited 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 data
Cited 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 data
Cited 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 humans
Cited 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 study
Cited 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 Epidemic
Cited 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 Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation
Cited 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 disease
Cited 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 BTV
Cited 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 sequencing
Cited by: 173
Author(s): Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1008815

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Cited 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 sets
Cited 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 disorders
Cited 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 fates
Cited 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 Stress
Cited by: 25
Author(s): Martha L. Slattery, Daniel F. Pellatt, Lila E. Mullany, Roger K. Wolff
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0165375

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage
Cited by: 33
Author(s): Luke R. Thompson, Qinglu Zeng, Sallie W. Chisholm
Software Mentions: 3
Published: almost 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 Sequencing
Cited 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: over 5 years ago

10.1186/s13059-020-02142-9

RNA G-quadruplex structures exist and function in vivo in plants
Cited 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 platform
Cited 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 alignment
Cited 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 bioinformatics
Cited 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 data
Cited 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: about 9 years ago

10.1038/s41598-019-44457-z

Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction
Cited 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 phasing
Cited 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 Communities
Cited 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: almost 5 years ago

10.7554/eLife.60608

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut
Cited 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 Containers
Cited 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 populations
Cited 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 sequencing
Cited by: 2
Author(s): Seung-Ho Shin, Woong-Yang Park, Donghyun Park
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-13-206

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Cited 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 pathways
Cited 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 devices
Cited 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: almost 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 information
Cited by: 2
Author(s): Francisco Pina‐Martins, Bruno Miguel Vieira, Sofia G. Seabra, Dora Batista, Octávio S. Paulo
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-020-6585-1

InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining
Cited 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 disorders
Cited 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: about 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 Miseq
Cited 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: almost 3 years ago

10.1186/s13029-016-0058-6

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing
Cited 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 crescentus
Cited 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 sclerotiorum
Cited by: 33
Author(s): Carolyn Graham-Taylor, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0154177

MicroRNA Seed Region Length Impact on Target Messenger RNA Expression and Survival in Colorectal Cancer
Cited 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 kodakarensis
Cited 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 Annotations
Cited by: 350
Author(s): Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron R. Quinlan
Software Mentions: 2
Published: about 11 years ago

10.3389/fneur.2020.573560

RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's Disease
Cited 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

Projects: pypi: pysam

Papers Mentioning pysam 130