pypi: Lumpy | Projects | Ecosyste.ms: Papers

10.1186/s12859-019-3145-2

MoMI-G: modular multi-scale integrated genome graph browser
Cited by: 20
Author(s): Toshiyuki Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki, Masahiro Kasahara
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pgen.1009331

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Cited by: 20
Author(s): Young Lim Lee, Hitoshi Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Erik Mullaart, Wouter Coppieters, Ruth Appeltant, R.F. Veerkamp, Martien A. M. Groenen, Michel Georges, Mirte Bosse, Tom Druet, A.C. Bouwman, Carole Charlier
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-020-6455-x

Comparison of multiple algorithms to reliably detect structural variants in pears
Cited by: 14
Author(s): Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang, Wu Jun
Software Mentions: 6
Published: almost 5 years ago

10.1093/gbe/evz246

Reprogramming of retrotransposon activity during speciation of the genus Citrus
Cited by: 2
Author(s): Carles Borredà, Estela Pérez-Román, Victoria Ibáñez, Javier Terol, Manuel Talón
Software Mentions: 5
Published: almost 5 years ago

10.1093/ve/vez060

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
Cited by: 23
Author(s): Vincent Loiseau, Elisabeth A. Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian A. Federici, Richard Cordaux, Clément Gilbert
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pgen.1008055

Loss of function mutations in essential genes cause embryonic lethality in pigs
Cited by: 38
Author(s): Martijn F.L. Derks, Arne B. Gjuvsland, Mirte Bosse, Marcos S. Lopes, Maren van Son, B. Harlizius, Beatrice Tan, Hanne Hamland, Eli Grindflek, Martien A. M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy086

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Cited by: 17
Author(s): Jang il Sohn, Kyoungwoo Nam, Hyosun Hong, Jun Mo Kim, Dajeong Lim, Kyung Tai Lee, Yoon Jung, Chang Yeon Cho, Namshin Kim, Han Ha Chai, Jin Wu Nam
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1007661

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
Cited by: 29
Author(s): Martijn F.L. Derks, Marcos S. Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, B. Harlizius, M.A.M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-018-2252-9

npInv: accurate detection and genotyping of inversions using long read sub-alignment
Cited by: 26
Author(s): Haojing Shao, Devika Ganesamoorthy, Tânia Duarte, Minh Duc Cao, Clive Hoggart, Lachlan Coin
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giab065

SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples
Cited by: 4
Author(s): Lanying Wei, Martin Dugas, Sarah Sandmann
Software Mentions: 5
Published: about 3 years ago

10.1093/gigascience/giab046

NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data
Cited by: 4
Author(s): Michael D. Linderman, Crystal Paudyal, Musab Shakeel, William L. Kelley, Ali Kashif Bashir, Bruce D. Gelb
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giy081

SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
Cited by: 14
Author(s): Xia Li, Dongmei Ai, Hojoon Lee, Noemi Andor, Chao Li, Nancy R. Zhang, Hanlee P. Ji
Software Mentions: 4
Published: over 6 years ago

10.1186/s13073-020-00791-w

Best practices for variant calling in clinical sequencing
Cited by: 136
Author(s): Daniel C. Koboldt
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-015-0818-3

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Cited by: 11
Author(s): Xiao Zhu, Ho-fung Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-25022-6

DNAp: A Pipeline for DNA-seq Data Analysis
Cited by: 13
Author(s): Jason Causey, Cody Ashby, Karl Walker, Zhiping Paul Wang, Mary Qu Yang, Yuanfang Guan, Jason H. Moore, Xiuzhen Huang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.8867

intansv: an R package for integrative analysis of structural variations
Cited by: 4
Author(s): Jia Lee, Na Liu, Fangfang Huang, Zhengfu Zhou, Xin He, Haoran Li, Zhizhan Wang, Wen Yao
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giz110

Evaluation of computational genotyping of structural variation for clinical diagnoses
Cited by: 34
Author(s): Varuna Chander, Richard A. Gibbs, Fritz J. Sedlazeck
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008397

Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions
Cited by: 5
Author(s): Riccha Sethi, Julia Powers Becker, Jos de Graaf, Martin Löwer, M Suchan, Uğur Şahin, D. F. Weber
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-020-3414-0

NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
Cited by: 5
Author(s): Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-021-00841-x

ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data
Cited by: 29
Author(s): André E. Minoche, Ben Lundie, Greg Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schönrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger, Mark J. Cowley
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.15802

Next generation mapping reveals novel large genomic rearrangements in prostate cancer
Cited by: 38
Author(s): Weerachai Jaratlerdsiri, Eva Chan, Desiree C. Petersen, Claire C. Yang, Peter I. Croucher, M. S. Bornman, Palak Sheth, Vanessa M. Hayes
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1004572

Wham: Identifying Structural Variants of Biological Consequence
Cited by: 98
Author(s): Zev Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1007285

Global characterization of copy number variants in epilepsy patients from whole genome sequencing
Cited by: 42
Author(s): Jean Monlong, Simon L. Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M. Andrade, Ron G. Lafrenière, Micheline Gravel, Dan Spiegelman, Alexandre Dionne‐Laporte, Cyrus Boelman, Fadi F. Hamdan, Jacques L. Michaud, Guy A. Rouleau, Berge A. Minassian, Guillaume Bourque, Patrick Cossette
Software Mentions: 3
Published: over 6 years ago

10.1038/s41436-021-01126-9

Genome-wide investigation identifies a rare copy-number variant burden associated with human spina bifida
Cited by: 7
Author(s): Paul Wolujewicz, Vanessa Aguiar‐Pulido, Alice AbdelAleem, Vidya Nair, Gaurav Thareja, Karsten Suhre, Gary M. Shaw, Richard H. Finnell, Olivier Elemento, M. Elizabeth Ross
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-019-1720-5

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
Cited by: 288
Author(s): Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo, Yoichiro Kamatani
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-92444-0

Mobile element insertions and associated structural variants in longitudinal breast cancer samples
Cited by: 3
Author(s): Cody J. Steely, Kristi Russell, Julie E. Feusier, Yi Qiao, Sean V. Tavtigian, Gábor Marth, Lynn B. Jorde
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msaa303

Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques
Cited by: 10
Author(s): Gregg W.C. Thomas, Richard J. Wang, Jelena Nguyen, R. Alan Harris, Muthuswamy Raveendran, Jeffrey Rogers, Matthew W. Hahn
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-017-1760-3

CLOVE: classification of genomic fusions into structural variation events
Cited by: 7
Author(s): Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss
Software Mentions: 3
Published: over 7 years ago

10.1186/s12862-019-1484-2

The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish
Cited by: 7
Author(s): Henri van Kruistum, Joost van den Heuvel, Joseph Travis, Ken Kraaijeveld, Bas J. Zwaan, M.A.M. Groenen, Hendrik Jan Megens, Bart J. A. Pollux
Software Mentions: 2
Published: over 5 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

10.1186/s12920-017-0246-5

Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine
Cited by: 14
Author(s): Fang Han, Yiyang Wu, Hui Yang, Margaret S. Yoon, Laura T. Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J. Lyon
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-020-00731-y

MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
Cited by: 2
Author(s): Stefanie Friedrich, Remus Barbulescu, Thomas Helleday, Erik L. L. Sonnhammer
Software Mentions: 2
Published: over 4 years ago

10.1002/mgg3.496

Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception?
Cited by: 10
Author(s): Nehir Edibe Kurtas, Luciano Xumerle, Ursula Giussani, Alessandra Pansa, Laura Cardarelli, Veronica Bertini, Angelo Valetto, Thomas Liehr, María Clara Bonaglia, Edoardo Errichiello, Massimo Delledonne, Orsetta Zuffardi
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0238108

Shiny-SoSV: A web-based performance calculator for somatic structural variant detection
Cited by: 0
Author(s): Ting-Ting Gong, Vanessa M. Hayes, Eva Chan
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0186721

Genome-wide analysis of structural variants reveals genetic differences in Chinese pigs
Cited by: 7
Author(s): Ruifei Yang, Shuai Fang, Jing Wang, Chunyuan Zhang, Ran Zhang, Di Liu, Yiqiang Zhao, Xiaoxiang Hu, Ning Li
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2021.647400

Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
Cited by: 27
Author(s): Xinye Qian, Jun Wang, Meng Wang, Austin D. Igelman, Kaylie Webb‐Jones, Yumei Li, Keqing Wang, Kerry Goetz, David G. Birch, Paul Yang, Mark E. Pennesi, Rui Chen
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12050684

The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes—A Comprehensive Study of the GJB2/DFNB1 Region
Cited by: 8
Author(s): Dana Šafka Brožková, Anna Uhrová Mészárosová, Petra Laššuthová, Lukáš Varga, David Staněk, Silvia Borecká, Jana Laštůvková, Vlasta Čejnová, Dagmar Ras̆ková, Filip Lhota, Daniela Gašperíková, Pavel Seeman
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-019-1909-7

Paragraph: a graph-based structural variant genotyper for short-read sequence data
Cited by: 92
Author(s): Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M. Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David Bentley, Michael C. Schatz, Fritz J. Sedlazeck, Michael A. Eberle
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13073-017-0447-8

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases
Cited by: 53
Author(s): Stephanie Greer, Lincoln Nadauld, Billy T. Lau, Jiamin Chen, Christina Wood-Bouwens, James M. Ford, Calvin J. Kuo, Hanlee P. Ji
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/giaa145

Parliament2: Accurate structural variant calling at scale
Cited by: 46
Author(s): Samantha Zarate, Andrew Carroll, Medhat Mahmoud, Olga Krasheninina, Goo Jun, William Salerno, Michael C. Schatz, Eric Boerwinkle, Richard A. Gibbs, Fritz J. Sedlazeck
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-019-55636-3

Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms
Cited by: 31
Author(s): Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M. Oschwald, Michael C. Zody, Søren Germer, Vaidehi Jobanputra, Jade Carter, Nicolas Robine
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-60589-z

The genetics of situs inversus without primary ciliary dyskinesia
Cited by: 32
Author(s): Merel C. Postema, Amaia Carrion‐Castillo, Simon E. Fisher, Guy Vingerhoets, Clyde Francks
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-017-1802-x

PennCNV in whole-genome sequencing data
Cited by: 9
Author(s): Leandro Lima, Kai Wang
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2018.00449

Trio-Based Deep Sequencing Reveals a Low Incidence of Off-Target Mutations in the Offspring of Genetically Edited Goats
Cited by: 27
Author(s): Chao Li, Shiwei Zhou, Yan Li, Guanwei Li, Yige Ding, Lan Li, Jing Liu, Qu Liu, Tad S. Sonstegard, Xingxu Huang, Yu Jiang, Yulin Chen, Björn Petersen, Xiaolong Wang
Software Mentions: 1
Published: about 6 years ago

10.3389/fcimb.2021.614665

Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi
Cited by: 26
Author(s): Carlos Talavera-López, Louisa A. Messenger, Michael D. Lewis, Matthew Yeo, João Luís Reis-Cunha, Gabriel Machado Matos, Daniella Castanheira Bartholomeu, José E. Calzada, Azäel Saldaña, Juan David Ramírez, Felipe Guhl, Sofía Ocaña-Mayorga, Jaime A. Costales, Rodion Gorchakov, Kathryn M. Jones, Melissa S. Nolan, Santuza Maria Ribeiro Teixeira, Hernán J. Carrasco, María Elena Bottazzi, Peter J. Hotez, Kristy O. Murray, Mario J. Grijalva, Barbara A. Burleigh, Edmundo C. Grisard, Michael A. Miles, Björn Andersson
Software Mentions: 1
Published: over 3 years ago

10.1016/j.gpb.2018.02.003

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants
Cited by: 6
Author(s): Shangang Jia, Kyla J. Morton, Chi Zhang, David R. Holding
Software Mentions: 1
Published: almost 6 years ago

10.1038/s42003-019-0745-3

Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos
Cited by: 39
Author(s): Hye Kyung Lee, Harold E. Smith, Chengyu Liu, Michaela Willi, Lothar Hennighausen
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pcbi.1009186

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers
Cited by: 0
Author(s): Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
Software Mentions: 1
Published: about 3 years ago

10.7717/peerj.3166

Prioritisation of structural variant calls in cancer genomes
Cited by: 17
Author(s): Miika J. Ahdesmäki, Brad Chapman, Pablo Cingolani, Oliver Hofmann, Aleksandr Sidoruk, Zhongwu Lai, Г. А. Захаров, Mikhail Rodichenko, Mikhail Alperovich, D. Graham Jenkins, T. Hedley Carr, Daniel Stetson, Brian Dougherty, J. Carl Barrett, Justin Johnson
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-019-3299-y

DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network
Cited by: 24
Author(s): Lei Cai, Yufeng Wu, Juan Gao
Software Mentions: 1
Published: almost 5 years ago

10.1093/molbev/msaa093

Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken
Cited by: 19
Author(s): Jingyi Li, Mi‐Ok Lee, Brian W. Davis, Sangeet Lamichhaney, Ben Dorshorst, P. B. Siegel, Leif C. Andersson
Software Mentions: 1
Published: over 4 years ago

10.1080/23802359.2017.1318673

Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseudogenes (<i>numts</i>) in bears
Cited by: 4
Author(s): Fritjof Lammers, Axel Janke, Cornelia Rücklé, Vera M. A. Zizka, Maria A. Nilsson
Software Mentions: 1
Published: almost 8 years ago

10.1093/bib/bbaa056

Detection of somatic structural variants from short-read next-generation sequencing data
Cited by: 28
Author(s): Ting-Ting Gong, Vanessa M. Hayes, Eva Chan
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-018-33533-5

Simultaneous targeting of linked loci in mouse embryos using base editing
Cited by: 12
Author(s): Hye Kyung Lee, Michaela Willi, Harold E. Smith, Shannon M. Miller, David R. Liu, Chengyu Liu, Lothar Hennighausen
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12081267

Whole-Genome Sequencing Improves the Diagnosis of DFNB1 Monoallelic Patients
Cited by: 4
Author(s): Anaïs Le Nabec, Mégane Collobert, Cédric Le Maréchal, R. Marianowski, Claude Férec, Stéphanie Moisan
Software Mentions: 1
Published: about 3 years ago

10.1093/g3journal/jkaa048

The crest phenotype in domestic chicken is caused by a 195 bp duplication in the intron of <i>HOXC10</i>
Cited by: 12
Author(s): Jingyi Li, Mi‐Ok Lee, Brian W. Davis, Ping Wu, Shu-Man Hsieh Li, Cheng‐Ming Chuong, Leif Andersson
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms21155197

Epigenetic Regulation of Verticillium dahliae Virulence: Does DNA Methylation Level Play A Role?
Cited by: 3
Author(s): Jorge A. Ramírez-Tejero, Carmen Gómez-Lama Cabanás, Antonio Valverde-Corredor, Jesús Mercado‐Blanco, Francisco Luque
Software Mentions: 1
Published: over 4 years ago

10.1093/gbe/evz106

The Genomic Complexity of a Large Inversion in Great Tits
Cited by: 15
Author(s): Vinícius da Silva, Veronika N. Laine, Mirte Bosse, Lewis G. Spurgin, Martijn F.L. Derks, Kees van Oers, Bert Dibbits, Jon Slate, R.P.M.A. Crooijmans, Marcel E. Visser, M.A.M. Groenen
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2018.00971

Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping
Cited by: 9
Author(s): Yuxuan Yuan, Zbyněk Milec, Philipp E. Bayer, Jan Vrána, Jaroslav Doležel, David Edwards, William Erskine, Parwinder Kaur
Software Mentions: 1
Published: over 6 years ago

Projects: pypi: Lumpy

Papers Mentioning Lumpy 60