bioconductor: deepSNV | Projects | Ecosyste.ms: Papers

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
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

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pcbi.1003703

Inferring Clonal Composition from Multiple Sections of a Breast Cancer
Cited by: 104
Author(s): Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Joshua D. Smith, Deborah A. Nickerson, Chang Woo Song, Daniela Witten, C. Anthony Blau, William Stafford Noble
Software Mentions: 5
Published: over 10 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

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-015-0812-9

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Cited by: 5
Author(s): Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
Software Mentions: 3
Published: about 9 years ago

10.1186/s12920-019-0557-9

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data
Cited by: 10
Author(s): Dimitrios Kleftogiannis, Marco Punta, Anuradha Jayaram, Shahneen Sandhu, Stephen Q. Wong, Delila Gasi Tandefelt, Vincenza Conteduca, Daniel Wetterskog, Gerhardt Attard, Stefano Lise
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.12848

Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance
Cited by: 61
Author(s): Marieke I.G. Raaijmakers, Daniel Widmer, Apurva Narechania, Ossia M. Eichhoff, Sandra N. Freiberger, Judith Wenzina, Phil F. Cheng, Daniela Mihic‐Probst, Rob DeSalle, Reinhard Dummer, Mitchell P. Levesque
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1007001

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data
Cited by: 32
Author(s): Niedzica Camacho, Peter Van Loo, Sandra E. Edwards, Jonathan Kay, Lucy Matthews, Kerstin Haase, Jeremy Clark, Nening M. Dennis, Sarah Thomas, Bárbara Kremeyer, Jorge Zamora, Adam Butler, Gunes Gundem, Sue Merson, Hayley J. Luxton, Steve Hawkins, Mohammed Ghori, Luke Marsden, Adam Lambert, Katalin Karászi, Paul Gill, Charles E. Massie, Zsofia Kóte-Jarai, Keiran Raine, David R. Jones, William J. Howat, Steven Hazell, Naomi Livni, Cyril Fisher, Christopher Ogden, Pardeep Kumar, Alan Thompson, David Nicol, Erik Mayer, Tim Dudderidge, Yu Ye, Hongwei Zhang, Nimish Shah, Vincent Gnanapragasam, William B. Isaacs, Tapio Visakorpi, Freddie C. Hamdy, Daniel M. Berney, Clare Verrill, Anne Y. Warren, David C. Wedge, Andy G. Lynch, Christopher S. Foster, Yong Lu, G. Steven Bova, Hayley C. Whitaker, Ultan McDermott, David E. Neal, Rosalind Eeles, Christopher S. Cooper, Daniel Brewer
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0129280

Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC
Cited by: 35
Author(s): Xiaobei Zhao, Anyou Wang, Vonn Walter, Nirali M. Patel, David A. Eberhard, Michele C. Hayward, Ashley H. Salazar, Heejoon Jo, Matthew G. Soloway, Matthew D. Wilkerson, Joel S. Parker, Xiaoying Yin, Guosheng Zhang, Marni B. Siegel, Gary B. Rosson, H. Shelton Earp, Norman E. Sharpless, Margaret L. Gulley, Karen E. Weck, D. Neil Hayes, Stergios J. Moschos
Software Mentions: 2
Published: over 9 years ago

10.3390/cancers11111725

Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology
Cited by: 22
Author(s): Áron Bartha, Balázs Győrffy
Software Mentions: 2
Published: about 5 years ago

10.3390/genes10080561

SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data
Cited by: 8
Author(s): Luca Ferretti, Chandana Tennakoon, Adrian Silesian, Graham Freimanis andPaolo Ribeca
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-019-0666-2

Best practices for bioinformatic characterization of neoantigens for clinical utility
Cited by: 126
Author(s): Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Malachi Griffith
Software Mentions: 2
Published: about 5 years ago

10.1136/gutjnl-2015-310748

Evolution of oesophageal adenocarcinoma from metaplastic columnar epithelium without goblet cells in Barrett's oesophagus
Cited by: 34
Author(s): Danielle L. Lavery, Pierre Martinez, Biancastella Cereser, Marco Novelli, Manuel Rodriguez–Justo, Sybren L. Meijer, Trevor A. Graham, Stuart McDonald, Nicholas A. Wright, Marnix Jansen
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-016-1417-7

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers
Cited by: 36
Author(s): Ariane Leoni Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-019-1659-6

Analysis of error profiles in deep next-generation sequencing data
Cited by: 179
Author(s): Xiaotu Ma, Ying Shao, Liqing Tian, Diane A. Flasch, Heather L. Mulder, Michael N. Edmonson, Yu Liu, Xiang Chen, Scott Newman, Joy Nakitandwe, Yongjin Li, Benshang Li, Shuhong Shen, Zhaoming Wang, Sheila Shurtleff, Leslie L. Robison, Shawn Levy, John Easton, Jinghui Zhang
Software Mentions: 1
Published: over 5 years ago

10.1093/bioinformatics/btt750

Subclonal variant calling with multiple samples and prior knowledge
Cited by: 119
Author(s): Moritz Gerstung, Elli Papaemmanuil, Peter J. Campbell
Software Mentions: 1
Published: almost 11 years ago

10.1002/ijc.33327

The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder
Cited by: 11
Author(s): Thomas van Doeveren, J. Alberto Nakauma-González, Andrew S. Mason, Geert J.L.H. van Leenders, Tahlita C.M. Zuiverloon, Ellen C. Zwarthoff, Isabelle C. Meijssen, Angelique Cj Van Der Made, Antoine G. van der Heijden, Kees Hendricksen, Bas W.G. van Rhijn, Charlotte S. Voskuilen, Job van Riet, Winand N.M. Dinjens, Hendrikus J. Dubbink, Harmen J.G. van de Werken, Joost L. Boormans
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.ppat.1008009

A robust human norovirus replication model in zebrafish larvae
Cited by: 99
Author(s): Jana Van Dycke, Annelii Ny, Nádia Conceição-Neto, Jan Maes, Myra Hosmillo, Arno Cuvry, Ian Goodfellow, Tatiane C Nogueira, Erik Verbeken, Jelle Matthijnssens, Peter de Witte, Johan Neyts, Joana Rocha‐Pereira
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0119145

Deconvoluting the Composition of Low-Frequency Hepatitis C Viral Quasispecies: Comparison of Genotypes and NS3 Resistance-Associated Variants between HCV/HIV Coinfected Hemophiliacs and HCV Monoinfected Patients in Japan
Cited by: 12
Author(s): Masato Ogishi, Hiroshi Yotsuyanagi, Takeshi Tsutsumi, Hiroyuki Gatanaga, Hirotaka Ode, Wataru Sugiura, Kyoji Moriya, Shinichi Oka, Satoshi Kimura, Kazuhiko Koike
Software Mentions: 1
Published: over 9 years ago

10.1093/sysbio/syu081

Cancer Evolution: Mathematical Models and Computational Inference
Cited by: 280
Author(s): Niko Beerenwinkel, Roland F. Schwarz, Moritz Gerstung, Florian Markowetz
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0186175

Comprehensive benchmarking of SNV callers for highly admixed tumor data
Cited by: 12
Author(s): Regina Bohnert, Sonia Vivas, Gunther Jansen
Software Mentions: 1
Published: about 7 years ago

10.1128/mBio.00042-17

Lethal Consequences of Overcoming Metabolic Restrictions Imposed on a Cooperative Bacterial Population
Cited by: 12
Author(s): Eunhye Goo, Yong-Cheol Kang, Jae Yun Lim, Hyeonheui Ham, Ingyu Hwang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41436-018-0274-3

Frequency and signature of somatic variants in 1461 human brain exomes
Cited by: 18
Author(s): Wei Wei, Michael J. Keogh, Juvid Aryaman, Zoe J. Golder, Peter Kullar, I. J. Wilson, Kevin Talbot, Martin R Turner, Chris-Anne McKenzie, Claire Troakes, Johannes Attems, Colin Smith, Safa Al Sarraj, Christopher M. Morris, Olaf Ansorge, Nick Jones, James W. Ironside, Patrick F. Chinnery
Software Mentions: 1
Published: over 5 years ago

10.1534/genetics.118.301817

Rpd3L Contributes to the DNA Damage Sensitivity ofSaccharomyces cerevisiaeCheckpoint Mutants
Cited by: 9
Author(s): Belén Gómez-González, Harshil Patel, Anne Early, John F.X. Diffley
Software Mentions: 1
Published: almost 6 years ago

Ecosyste.ms: Papers

Projects: bioconductor: deepSNV

Papers Mentioning deepSNV 26