Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: Lumpy
https://packages.ecosyste.ms/registries/pypi.org/packages/Lumpy
7 versions
Latest release: over 8 years ago
153 downloads last month
Papers Mentioning Lumpy 60
10.1186/s12859-019-3145-2
MoMI-G: modular multi-scale integrated genome graph browserCited 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 cattleCited 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 pearsCited 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 CitrusCited by: 2
Author(s): Carles Borredà, Estela Pérez-Román, Victoria Ibáñez, Javier Terol, Manuel Talón
Software Mentions: 5
Published: about 5 years ago
10.1093/ve/vez060
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA virusesCited 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 pigsCited 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 OgyeCited 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 genomeCited 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-alignmentCited 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 samplesCited 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 dataCited 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 evolutionCited 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 sequencingCited 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 readsCited 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: about 9 years ago
10.1038/s41598-018-25022-6
DNAp: A Pipeline for DNA-seq Data AnalysisCited 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 MedicineCited 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 variationsCited 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 diagnosesCited 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 predictionsCited 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 readsCited 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 dataCited 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 cancerCited 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 ConsequenceCited 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 sequencingCited 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 bifidaCited 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 sequencingCited 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 samplesCited 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 MacaquesCited 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 eventsCited 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 fishCited 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 miningCited 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 medicineCited 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 dataCited 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 detectionCited 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 pigsCited 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 DiseasesCited 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 RegionCited 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 dataCited 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 metastasesCited 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 scaleCited 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 platformsCited 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 dyskinesiaCited 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 dataCited 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 GoatsCited 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 cruziCited 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 MutantsCited 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 embryosCited 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 callersCited 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 genomesCited 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 networkCited 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 ChickenCited 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 bearsCited 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 dataCited 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 editingCited 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: almost 6 years ago
10.3390/genes12081267
Whole-Genome Sequencing Improves the Diagnosis of DFNB1 Monoallelic PatientsCited by: 4
Author(s): Anaïs Le Nabec, Mégane Collobert, Cédric Le Maréchal, R. Marianowski, Claude Férec, Stéphanie Moisan
Software Mentions: 1
Published: over 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 TitsCited 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 MappingCited 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