bioconductor: VariantAnnotation | Projects

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago

10.1038/s41598-021-88209-4

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-019-41601-7

Characteristics and homogeneity of N6-methylation in human genomes
Cited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: over 5 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: about 8 years ago

10.7554/eLife.55862

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pcbi.1006596

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer
Cited by: 43
Author(s): Deena M.A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra E. Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Pinjiang Cao, Lincoln Stein, Julie M. Wilson, John M.S. Bartlett, Ming‐Sound Tsao, Neesha C. Dhani, David W. Hedley, Steven Gallinger, Benjamin Haibe‐Kains
Software Mentions: 9
Published: almost 6 years ago

10.1038/s42003-020-01174-y

Chemically induced mutations in a MutaMouse reporter gene inform mechanisms underlying human cancer mutational signatures
Cited by: 12
Author(s): Marc A. Beal, Matthew J. Meier, Danielle P. LeBlanc, Clotilde Maurice, Jason M. O’Brien, Carole L. Yauk, Francesco Marchetti
Software Mentions: 7
Published: over 4 years ago

10.1186/s13058-020-01379-3

Acquired mutations and transcriptional remodeling in long-term estrogen-deprived locoregional breast cancer recurrences
Cited by: 19
Author(s): Nolan Priedigkeit, Kai Ding, William Horne, Jay K. Kolls, Tian Du, Peter C. Lucas, Jens-Uwe Blohmer, Carsten Denkert, A Machleidt, Barbara Ingold-Heppner, Steffi Oesterreich, Adrian V. Lee
Software Mentions: 7
Published: almost 4 years ago

10.3390/genes11091107

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
Cited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-019-2899-x

Efficient estimation of grouped survival models
Cited by: 0
Author(s): Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew S. Allen, Kouros Owzar
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-017-1165-7

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Cited by: 20
Author(s): Inês de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 6
Published: over 7 years ago

10.1002/ece3.5516

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs
Cited by: 18
Author(s): Jóhannes Guðbrandsson, Kalina H. Kapralova, Sigríður Rut Franzdóttir, Þóra Margrét Bergsveinsdóttir, Völundur Hafstað, Zophonı́as O. Jónsson, Sigurður S. Snorrason, Arnar Pálsson
Software Mentions: 6
Published: about 5 years ago

10.1111/jfb.14349

Identification of male heterogametic sex‐determining regions on the Atlantic herring <scp><i>Clupea harengus</i></scp> genome
Cited by: 5
Author(s): Sunnvør í Kongsstovu, Hans Atli Dahl, Hannes Gislason, Eydna í Homrum, Jan Arge Jacobsen, Paul Flicek, Svein‐Ole Mikalsen
Software Mentions: 5
Published: over 4 years ago

10.1111/tpj.14193

Kernel size‐related genes revealed by an integrated<scp>eQTL</scp>analysis during early maize kernel development
Cited by: 30
Author(s): Junling Pang, Junjie Fu, Na Zong, Jing Wang, Dandan Song, Xia Zhang, Cheng He, Ting Fang, Hongwei Zhang, Yanting Fan, Guoying Wang, Jun Zhao
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0230253

Comparing genome-scale DNA methylation and CNV marks between adult human cultured ITGA6+ testicular cells and seminomas to assess in vitro genomic stability
Cited by: 8
Author(s): Robert B. Struijk, Lambert C. J. Dorssers, Peter Henneman, Martin A. Rijlaarsdam, Andrea Venema, Aldo Jongejan, Marcel M.A.M. Mannens, Leendert H. J. Looijenga, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0208371

Genetic resistance to DEHP-induced transgenerational endocrine disruption
Cited by: 17
Author(s): Ludwig Stenz, Rita Rahban, Julien Prados, Serge Nef, Ariane Paoloni-Giacobino
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2021.694727

The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance
Cited by: 3
Author(s): Laxmi S. Mishra, Sanatkumar Mishra, Daniel Caddell, Devin Coleman‐Derr, Christiane Funk
Software Mentions: 5
Published: over 3 years ago

10.1534/g3.120.401452

Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
Cited by: 10
Author(s): Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean‐Marc Audergon, Jean‐Luc Regnard
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13742-016-0131-8

Gigwa—Genotype investigator for genome-wide analyses
Cited by: 18
Author(s): Guilhem Sempéré, Philippe Florian, Alexis Dereeper, Manuel Ruiz, Gautier Sarah, Pierre Larmande
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-021-07627-w

Draft genome of a biparental beetle species, Lethrus apterus
Cited by: 0
Author(s): Nikolett Nagy, R. Rácz, Oliver Rimington, Szilárd Póliska, Pablo Orozco‐terWengel, Michael William Bruford, Zoltán Barta
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.61562

Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans
Cited by: 40
Author(s): Alice V. Easton, Shenghan Gao, Scott P Lawton, Sasisekhar Bennuru, Asis Khan, Eric Dahlstrom, Rita G. Oliveira, Stella Kepha, Stephen F. Porcella, Joanne P. Webster, Roy M. Anderson, Michael E. Grigg, Richard E. Davis, Jianbin Wang, Thomas B. Nutman
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0075495

A Single Nucleotide Polymorphism Associated with Hepatitis C Virus Infections Located in the Distal Region of the IL28B Promoter Influences NF-κB-Mediated Gene Transcription
Cited by: 23
Author(s): Sreedhar Chinnaswamy, Snehajyoti Chatterjee, Ramachandran Boopathi, Shuvolina Mukherjee, Samsiddhi Bhattacharjee, Tapas K. Kundu
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1004137

Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning
Cited by: 97
Author(s): Gad Abraham, Jason A. Tye‐Din, Oneil G. Bhalala, Adam Kowalczyk, Justin Zobel, Michael Inouye
Software Mentions: 4
Published: almost 11 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

10.18632/oncotarget.26533

Imbalanced sphingolipid signaling is maintained as a core proponent of a cancerous phenotype in spite of metabolic pressure and epigenetic drift
Cited by: 5
Author(s): Monique M.P. Speirs, Adam Swensen, Tsz Yin Chan, Peter M. Jones, John C. Holman, McCall B. Harris, J. Alan Maschek, James E. Cox, Richard H. Carson, John E. Hill, Joshua L. Andersen, John T. Prince, John C. Price
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-020-07240-3

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions
Cited by: 11
Author(s): Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till, Hanna Bolibok-Brągoszewska
Software Mentions: 4
Published: almost 4 years ago

10.1093/ve/veaa012

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Cited by: 13
Author(s): Florent Lassalle, Mathew A. Beale, Tehmina Bharucha, Charlotte A. Williams, Rachel Williams, Juliana Cudini, Richard A. Goldstein, Tanzina Haque, Daniel P. Depledge, Judith Breuer
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms22062826

Role of Genetic Variation in Cytochromes P450 in Breast Cancer Prognosis and Therapy Response
Cited by: 4
Author(s): Viktor Hlaváč, Radka Václavíková, Veronika Brynychová, Pavel Ostašov, Renata Koževnikovová, Kateřina Kopečková, David Vrána, Jiří Gatěk, Pavel Souček
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.11892

Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies
Cited by: 20
Author(s): Andrew J. Colebatch, Leon Di Stefano, Stephen Q. Wong, Ross D. Hannan, Paul Waring, Alexander Dobrovic, Grant A. McArthur, Anthony T. Papenfuss
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-015-1700-4

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants
Cited by: 0
Author(s): Aléxandre Kuhn, Yao Min Ong, Stephen R. Quake, William F. Burkholder
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-32198-4

Experimental Adaptation of the Yellow Fever Virus to the Mosquito Aedes albopictus and Potential risk of urban epidemics in Brazil, South America
Cited by: 26
Author(s): Fadila Amraoui, Adrien Pain, Géraldine Piorkowski, Marie Vazeille, Dinair Couto-Lima, Xavier de Lamballerie, Ricardo Lourenço‐de‐Oliveira, Anna‐Bella Failloux
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-81030-z

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika
Cited by: 4
Author(s): Christoph Fischer, Stephan Koblmüller, Christine Börger, Gabriele Michelitsch, Slave Trajanoski, Christian Schlötterer, Christian Godballe, Gerhard Thallinger, Christian Sturmbauer
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-52614-7

Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance
Cited by: 14
Author(s): Robert P. Adelson, Alan E. Renton, Wentian Li, Nir Barzilai, Gil Atzmon, Alison M. Goate, Peter Davies, Yun Freudenberg-Hua
Software Mentions: 2
Published: about 5 years ago

10.3390/genes12050660

Sorghum Brown Midrib19 (Bmr19) Gene Links Lignin Biosynthesis to Folate Metabolism
Cited by: 7
Author(s): Adedayo Adeyanju, Scott E. Sattler, Patrick J. Rich, Luis A. Rivera-Burgos, Xiaochen Xu, Gebisa Ejeta
Software Mentions: 2
Published: over 3 years ago

10.1155/2020/8531502

Exploring the Consistency of the Quality Scores with Machine Learning for Next-Generation Sequencing Experiments
Cited by: 5
Author(s): Erdal Coşgun, Min Kyu Oh
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-016-1066-1

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
Cited by: 827
Author(s): Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter L. Molloy, Susan Van Djik, Beverly S. Mühlhäusler, Clare Stirzaker, Susan J. Clark
Software Mentions: 2
Published: about 8 years ago

10.1093/bioinformatics/bty976

Detection of rare disease variants in extended pedigrees using RVS
Cited by: 5
Author(s): Thomas D. Sherman, Jack Fu, Robert B. Scharpf, Alexandre Bureau, Ingo Ruczinski
Software Mentions: 2
Published: almost 6 years ago

10.3390/pathogens10070910

Molecular Characterization of the env Gene of Bovine Leukemia Virus in Cattle from Pakistan with NGS-Based Evidence of Virus Heterogeneity
Cited by: 4
Author(s): Marzena Rola–Łuszczak, Sakhawat Ali, Aneta Pluta, Anna Ryło, Arkadiusz Bomba, Nazia Bibi, Jacek Kuźmak
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0115449

Differing Evolutionary Histories of the ACTN3*R577X Polymorphism among the Major Human Geographic Groups
Cited by: 23
Author(s): Carlos Eduardo G. Amorim, Víctor Acuña-Alonzo, Francisco M. Salzano, María Cátira Bortolini, Tábita Hünemeier
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0087090

A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila
Cited by: 13
Author(s): Cem Sievers, Federico Comoglio, Makiko Seimiya, Gunter Merdes, Renato Paro
Software Mentions: 1
Published: almost 11 years ago

10.3892/mmr.2019.10303

Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay
Cited by: 7
Author(s): Markéta Wayhelová, Jan Oppelt, Jan Smetana, Eva Hladílková, Hana Filková, Eva Makaturová, Petra Nikolova, Rastislav Beharka, Renata Gaillyová, Petr Kuglík
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-25280-4

Genetic variation in 117 myelination-related genes in schizophrenia: Replication of association to lipid biosynthesis genes
Cited by: 10
Author(s): Tomasz Stokowy, Tatiana Polushina, Ida Elken Sønderby, Robert Karlsson, Sudheer Giddaluru, Stéphanie Le Hellard, Sarah E. Bergen, Patrick F. Sullivan, Ole A. Andreassen, Srdjan Djurovic, Christina M. Hultman, Vidar M. Steen
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-59214-w

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
Cited by: 13
Author(s): Jessica Nordlund, Yanara Marincevic-Zuniga, Lucia Cavelier, Amanda Raine, Tom Martin, Anders Lundmark, Jonas Abrahamsson, Ulrika Norén‐Nyström, Gudmar Lönnerholm, Ann‐Christine Syvänen
Software Mentions: 1
Published: almost 5 years ago

10.1007/s00253-017-8717-3

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger
Cited by: 13
Author(s): Morgann C. Reilly, Joonhoon Kim, Jed Lynn, Blake A. Simmons, John M. Gladden, Jon Magnuson, Scott E. Baker
Software Mentions: 1
Published: almost 7 years ago

Projects: bioconductor: VariantAnnotation

Papers Mentioning VariantAnnotation 47