pypi: pysam | Projects | Ecosyste.ms: Papers

10.1534/g3.119.400908

BlobToolKit – Interactive Quality Assessment of Genome Assemblies
Cited by: 644
Author(s): Richard Challis, E. G. Richards, Jeena Rajan, Guy Cochrane, Mark Blaxter
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00010-20

A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies
Cited by: 66
Author(s): Peter H. Culviner, Chantal K. Guegler, Michael T. Laub
Software Mentions: 2
Published: over 4 years ago

10.1534/genetics.118.300826

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations
Cited by: 29
Author(s): Elise A. Lucotte, Laurits Skov, James C. Jensen, Moisès Coll Macià, Kasper Munch, Mikkel Heide Schierup
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11845

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA <i>de novo</i> assembly
Cited by: 19
Author(s): Maxime Borry, Alexander Hübner, Adam Ben Rohrlach, Christina Warinner
Software Mentions: 2
Published: over 3 years ago

10.15252/msb.202010025

CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators
Cited by: 15
Author(s): Liang Fang, Wen Wang, Guipeng Li, Li Zhang, Jun Li, Diwen Gan, Yang Jiao, Yisen Tang, Zewen Ding, Min Zhang, Wenhao Zhang, Daqi Deng, Zhenlong Song, Qionghua Zhu, Huanhuan Cui, Yuhui Hu, Wei Chen
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-020-02105-0

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
Cited by: 30
Author(s): Danang Crysnanto, Hubert Pausch
Software Mentions: 2
Published: over 4 years ago

10.1093/gbe/evz229

The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content Within Poaceae
Cited by: 3
Author(s): Nathan Hall, Hui Zhang, Jeffrey P. Mower, J. Scott McElroy, Leslie R. Goertzen
Software Mentions: 2
Published: about 5 years ago

10.1099/mgen.0.000607

SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data
Cited by: 7
Author(s): Einar Gabbassov, Miguel Moreno-Molina, Iñaki Comas, Maxwell W. Libbrecht, Leonid Chindelevitch
Software Mentions: 2
Published: over 3 years ago

10.1093/gigascience/giz054

Software engineering for scientific big data analysis
Cited by: 19
Author(s): Björn Grüning, Samuel Lampa, Marc Vaudel, Daniel Blankenberg
Software Mentions: 2
Published: over 5 years ago

10.3390/biology1020370

Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP
Cited by: 59
Author(s): Michał T. Lorenc, Satomi Hayashi, Jiri Stiller, S. Hong Lee, Sahana Manoli, Pradeep Ruperao, Paul Visendi, Paul J. Berkman, Kaitao Lai, Jacqueline Batley, David Edwards
Software Mentions: 2
Published: about 12 years ago

10.1093/biomethods/bpaa010

ACValidator: A novel assembly-based approach for in silico verification of circular RNAs
Cited by: 4
Author(s): Shobana Sekar, Philipp Geiger, Jonathan Adkins, Erica E. Tassone, Geidy E. Serrano, Thomas G. Beach, Winnie S. Liang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-020-03562-x

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis
Cited by: 21
Author(s): Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò
Software Mentions: 2
Published: over 4 years ago

10.1534/genetics.119.302235

Histone Chaperone Paralogs Have Redundant, Cooperative, and Divergent Functions in Yeast
Cited by: 3
Author(s): Neda Savic, Shawn P Shortill, Misha Bilenky, Joseph M Dobbs, David Dilworth, Martin Hirst, Christopher J. Nelson
Software Mentions: 1
Published: almost 5 years ago

10.1186/gb-2013-14-3-r22

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Cited by: 101
Author(s): Adam D. Ewing, Tracy Ballinger, Dent Earl, Christopher Harris, Ding Li, Richard K. Wilson, David Haussler
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12859-016-1162-y

BAMQL: a query language for extracting reads from BAM files
Cited by: 21
Author(s): Andre P. Masella, Christopher M. Lalansingh, Pragash Sivasundaram, Michael Fraser, Robert G. Bristow, Paul C. Boutros
Software Mentions: 1
Published: over 8 years ago

10.3390/jcm9082349

Mitochondrial DNA: Hotspot for Potential Gene Modifiers Regulating Hypertrophic Cardiomyopathy
Cited by: 7
Author(s): Parisa K Kargaran, Jared M. Evans, Sara Bodbin, James G W Smith, T. J. N. Nelson, Chris Denning, Diogo Mosqueira
Software Mentions: 1
Published: over 4 years ago

10.1186/s13059-019-1673-8

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Cited by: 21
Author(s): Joanna Hård, Ezeddin Al Håkim, Marie Kindblom, Åsa K. Björklund, Bengt Sennblad, Ilke Demirci, Marta Paterlini, Pedro Réu, Erik Borgström, Patrik L. Ståhl, Jakob Michaëlsson, Jeff E. Mold, Jonas Frisén
Software Mentions: 1
Published: over 5 years ago

10.1186/s12711-018-0436-4

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
Cited by: 35
Author(s): Roger Ros‐Freixedes, Mara Battagin, Martin Johnsson, Gregor Gorjanc, Alan J. Mileham, Steve Rounsley, John M. Hickey
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms19020480

CircSMARCA5 Inhibits Migration of Glioblastoma Multiforme Cells by Regulating a Molecular Axis Involving Splicing Factors SRSF1/SRSF3/PTB
Cited by: 133
Author(s): Davide Barbagallo, A Caponnetto, Matilde Cirnigliaro, Duilia Brex, Cristina Barbagallo, Floriana D’Angeli, Antonio Morrone, Rosario Caltabiano, Giuseppe Barbagallo, Marco Ragusa, Cinzia Di Pietro, Thomas B. Hansen, Michele Purrello
Software Mentions: 1
Published: almost 7 years ago

10.1002/mgg3.126

Improved inherited peripheral neuropathy genetic diagnosis by whole‐exome sequencing
Cited by: 53
Author(s): Alexander P. Drew, Danqing Zhu, Aditi Kidambi, Carolyn Ly, Shelisa Tey, Megan H. Brewer, Azlina Ahmad‐Annuar, Garth A. Nicholson, Marina Kennerson
Software Mentions: 1
Published: almost 10 years ago

10.1186/s40168-021-01021-0

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages
Cited by: 10
Author(s): Davide Albanese, Claudia Coleine, Omar Rota‐Stabelli, Silvano Onofri, Susannah G. Tringe, Jason E. Stajich, Laura Selbmann, Claudio Donati
Software Mentions: 1
Published: over 3 years ago

10.1016/j.xpro.2021.100828

Efficient acquisition of tens of thousands of short tandem repeats in single-cell whole-genome-amplified DNA
Cited by: 0
Author(s): Liming Tao, Zipora Marx, Ofir Raz, Ehud Shapiro
Software Mentions: 1
Published: almost 3 years ago

10.1186/s13073-016-0336-6

Assessing the reproducibility of exome copy number variations predictions
Cited by: 44
Author(s): Celine Hong, Larry N. Singh, James C. Mullikin, Leslie G. Biesecker
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0162077

Telomere Length, TERT, and miRNA Expression
Cited by: 13
Author(s): Martha L. Slattery, Jennifer S. Herrick, Andrew J. Pellatt, Roger K. Wolff, Lila E. Mullany
Software Mentions: 1
Published: about 8 years ago

10.1099/mgen.0.000356

Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software
Cited by: 4
Author(s): Charlotte Couchoud, Xavier Bertrand, Benoı̂t Valot, Didier Hocquet
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2021.693088

Maize Inbred Line B96 Is the Source of Large-Effect Loci for Resistance to Generalist but Not Specialist Spider Mites
Cited by: 7
Author(s): Huyen Bui, Robert Greenhalgh, Gunbharpur S. Gill, Meiyuan Ji, Andre H. Kurlovs, Christian Ronnow, Sarah Lee, Ricardo A. Ramirez, Richard M. Clark
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1006315

Multi-nucleotide de novo Mutations in Humans
Cited by: 110
Author(s): Søren Besenbacher, Patrick Sulem, Agnar Helgason, Hannes Helgason, Helgi Kristjansson, Áslaug Jónasdóttir, Aðalbjörg Jónasdóttir, Ólafur Þ. Magnússon, Unnur Þorsteinsdóttir, Gísli Másson, Augustine Kong, Daníel F. Guðbjartsson, Kāri Stefánsson
Software Mentions: 1
Published: about 8 years ago

10.3389/fgene.2019.00753

MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries
Cited by: 22
Author(s): Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-019-6497-0

TP53 and PTEN mutations were shared in concurrent germ cell tumor and acute megakaryoblastic leukemia
Cited by: 15
Author(s): Keiichi Akizuki, Masaaki Sekine, Yasunori Kogure, Takuro Kameda, Kotaro Shide, Junji Koya, Ayako Kamiunten, Yoko Kubuki, Yuki Tahira, Tomonori Hidaka, Takumi Kiwaki, Hiroyuki Tanaka, Yuichiro Sato, Hiroaki Kataoka, Keisuke Kataoka, Kazuya Shimoda
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms21207758

Saliva microRNA Biomarkers of Cumulative Concussion
Cited by: 13
Author(s): Steven D. Hicks, Robert P. Olympia, Cayce Onks, Raymond Y. Kim, Kevin Zhen, Gregory Fedorchak, Samantha DeVita, Aakanksha Rangnekar, Matthew Heller, Hallie Zwibel, Chuck Monteith, Zofia Gagnon, Callan D. McLoughlin, Jason R. Randall, Miguel M. Madeira, Thomas R. Campbell, Elise Fengler, Michael N. Dretsch, Christopher Neville, Frank Middleton
Software Mentions: 1
Published: about 4 years ago

Ecosyste.ms: Papers

Projects: pypi: pysam

Papers Mentioning pysam 130