pypi: liftover | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.640242

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects
Cited by: 7
Author(s): Dustin Miller, Stephen R. Piccolo
Software Mentions: 11
Published: over 3 years ago

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity
Cited by: 37
Author(s): Pierre Khoueiry, Charles Girardot, Lucia Ciglar, Pei-Chen Peng, E. Hilary Gustafson, Saurabh Sinha, Eileen E. M. Furlong
Software Mentions: 7
Published: over 7 years ago

10.1016/j.ebiom.2021.103383

Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.35471

Genetics of trans-regulatory variation in gene expression
Cited by: 133
Author(s): Frank W. Albert, Joshua S. Bloom, Jake J. Siegel, Laura Day, Leonid Kruglyak
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.649168

Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers
Cited by: 3
Author(s): Gang Liu, Zhenhao Liu, Xiaomeng Sun, Xiaoqiong Xia, Yunhe Liu, Lei Liu
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2020.00496

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
Cited by: 55
Author(s): HueyTyng Lee, Harmeet Singh Chawla, Christian Obermeier, Felix Dreyer, Amine Abbadi, Rod J. Snowdon
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02036-w

Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance
Cited by: 38
Author(s): Isaac Kremsky, Victor G. Corcés
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-5529-0

Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal
Cited by: 5
Author(s): Pere Gelabert, Manuel Ferrando-Bernal, Toni de-Dios, Benedetta Mattorre, Elena Campoy, Amaya Gorostiza, Étienne Patin, Antonio González-Martı́n, Carles Lalueza-Fox
Software Mentions: 3
Published: over 5 years ago

10.1186/s12862-016-0819-5

Resolving Cypriniformes relationships using an anchored enrichment approach
Cited by: 95
Author(s): Carla C. Stout, Milton Tan, Alan R. Lemmon, Emily Moriarty Lemmon, Jonathan W. Armbruster
Software Mentions: 3
Published: about 8 years ago

10.1186/gb-2010-11-5-r47

Computational challenges in the analysis of ancient DNA
Cited by: 112
Author(s): Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Edward Green
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pgen.1008673

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin
Cited by: 30
Author(s): Yuh Chwen G. Lee, Yuki Ogiyama, Nuno M. C. Martins, Brian J. Beliveau, David Acevedo, Chao-ting Wu, Giacomo Cavalli, Gary H. Karpen
Software Mentions: 3
Published: over 4 years ago

10.1038/srep08957

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development
Cited by: 84
Author(s): Weimin Zhao, Yulian Mu, Lei Ma, Chen Wang, Zhonglin Tang, Shulin Yang, Rong Zhou, Xiaoju Hu, Menghua Li, Kui Li
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-12-11

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis
Cited by: 142
Author(s): Xuefeng Fang, Jae-Geun Yoon, Lisha Li, Wei Yu, Jiaofang Shao, Dasong Hua, Suiping Zheng, Leroy Hood, David R. Goodlett, Gregory Foltz, Biaoyang Lin
Software Mentions: 3
Published: almost 14 years ago

10.1186/s13073-020-0712-0

A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data
Cited by: 37
Author(s): Ramakrishnan Rajagopalan, Jill R. Murrell, Minjie Luo, Laura K. Conlin
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-57811-3

Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE data
Cited by: 14
Author(s): Γεώργιος Γεωργακίλας, Nikos Perdikopanis, Artemis G. Hatzigeorgiou
Software Mentions: 3
Published: almost 5 years ago

10.1093/database/bax020

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
Cited by: 52
Author(s): Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R. Laird, Ian Longden, G Proctor, Steve Searle, Daniel M. Staines, Kieron Taylor, Alessandro Vullo, Andy Yates, Daniel R. Zerbino, Paul Flicek
Software Mentions: 3
Published: almost 8 years ago

10.1093/gbe/evaa046

A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals
Cited by: 16
Author(s): Niko Popitsch, Christian D. Huber, Ilana Buchumenski, Eli Eisenberg, Michael F. Jantsch, Arndt von Haeseler, Miguel Gallach
Software Mentions: 3
Published: over 4 years ago

10.1186/s12915-021-01011-6

Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis
Cited by: 5
Author(s): Dandan Zong, Beibei Huang, Young Li, Yichen Lu, Nan Xiang, Chuang Guo, Qian Liu, Qing Sha, Pengcheng Du, Qiaoni Yu, Wen Zhang, Pengfei Cai, Yanping Sun, Jin‐Hui Tao, Xiaomei Li, Shanbao Cai, Kun Qu
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-24219-z

A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver
Cited by: 51
Author(s): Tobias Strunz, Felix Graßmann, Javier Gayán, Satu Nahkuri, Débora C. Souza-Costa, Cyrille Maugeais, Sascha Fauser, Everson Nogoceke, Bernhard H. F. Weber
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5854-3

hg19KIndel: ethnicity normalized human reference genome
Cited by: 12
Author(s): Harsh Shukla, Pushpinder Bawa, Subhashini Srinivasan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008485

The impact of genetic adaptation on chimpanzee subspecies differentiation
Cited by: 15
Author(s): Joshua M. Schmidt, Marc de Manuel, Tomàs Marquès‐Bonet, Sergi Castellano, Aida M. Andrés
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0126125

Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization
Cited by: 32
Author(s): Stefanie Kaufmann, Christiane Fuchs, Mariya Gonik, Ekaterina E. Khrameeva, Andrey A. Mironov, Dmitrij Frishman
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2019.00714

The Length of the Expressed 3′ UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases
Cited by: 18
Author(s): Elisa Mariella, Federico Marotta, Elena Grassi, Stefano Gilotto, Paolo Provero
Software Mentions: 2
Published: over 5 years ago

10.1093/gbe/evz071

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World
Cited by: 37
Author(s): Daniel N. Harris, Ingo Ruczinski, Lisa R. Yanek, Lewis C. Becker, Diane M. Becker, Heinner Guio, Tao Cui, Floyd H. Chilton, Rasika A. Mathias, Timothy D. O’Connor
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-020-00803-9

dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs
Cited by: 245
Author(s): Xiaoming Liu, Chang Li, Chengcheng Mou, Yibo Dong, Yi-Cheng Tu
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-14-345

Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods
Cited by: 13
Author(s): Fan Gao, Zong Wei, Wange Lu, Kai Wang
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0059251

Fine Mapping for Weaver Syndrome in Brown Swiss Cattle and the Identification of 41 Concordant Mutations across NRCAM, PNPLA8 and CTTNBP2
Cited by: 19
Author(s): Matthew McClure, Euisoo Kim, Derek M. Bickhart, D.J. Null, T.A. Cooper, J.B. Cole, G.R. Wiggans, Paolo Ajmone‐Marsan, Licia Colli, Enrico Santus, George E. Liu, Steven G. Schroeder, Lakshmi K. Matukumalli, Curtis P. Van Tassell, Tad S. Sonstegard
Software Mentions: 1
Published: over 11 years ago

10.1098/rstb.2012.0366

Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts
Cited by: 8
Author(s): Chih-Hao Hsu, Ivan Ovcharenko
Software Mentions: 1
Published: over 11 years ago

10.1186/1742-4690-10-90

HIV latency and integration site placement in five cell-based models
Cited by: 98
Author(s): Scott Sherrill-Mix, Mary K. Lewinski, Marylinda Famiglietti, Alberto Bosque, Nirav Malani, Karen E. Ocwieja, Charles C. Berry, David J. Looney, Liang Shan, Luis M. Agosto, Matthew Pace, Robert F. Siliciano, Una O’Doherty, John Guatelli, Vicente Planelles, Frederic D. Bushman
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1006933

Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
Cited by: 86
Author(s): Qiongshi Lu, Ryan L. Powles, Sarah B. Abdallah, Derek Ou, Qian Wang, Yiming Hu, Yisi Lu, Wei Liu, Boyang Li, Shubhabrata Mukherjee, Paul K. Crane, Hongyu Zhao
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pbio.1000435

Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification
Cited by: 84
Author(s): Stein Aerts, Xiao‐Jiang Quan, Annelies Claeys, Marina Naval-Sánchez, Phillip Tate, Jiekun Yan, Bassem A. Hassan
Software Mentions: 1
Published: over 14 years ago

10.3389/fgene.2021.654887

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes
Cited by: 3
Author(s): Bo Gao, Michael Baudis
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pbio.1000026

Hotspots of Biased Nucleotide Substitutions in Human Genes
Cited by: 139
Author(s): J. Andrew Berglund, Katherine S. Pollard, Matthew T. Webster
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12864-019-6394-6

Enhanced genome assembly and a new official gene set for Tribolium castaneum
Cited by: 64
Author(s): Nic Herndon, Jennifer Shelton, Lizzy Gerischer, Panos Ioannidis, Maria Ninova, Jürgen Dönitz, Robert M. Waterhouse, Chun Liang, Carsten Damm, Janna Siemanowski, Peter Kitzmann, Julia Ulrich, Stefan Dippel, Georg Oberhofer, Yonggang Hu, Jonas Schwirz, Magdalena Ines Schacht, Sabrina Lehmann, Alice Montino, Nico Posnien, Daniela Gurská, Thorsten Horn, Jan Seibert, Iris M. Vargas Jentzsch, Kristen A. Panfilio, Jianwei Li, Ernst A. Wimmer, Dominik Stappert, Siegfried Roth, Reinhard Schröder, Yoonseong Park, Michael Schoppmeier, Ho Ryun Chung, Martin Klingler, Sebastian Kittelmann, Markus Friedrich, Rui Chen, Boran Altincicek, Andreas Vilcinskas, Evgeny M. Zdobnov, Sam Griffiths‐Jones, Matthew Ronshaugen, Mario Stanke, Susan J. Brown, Gregor Bucher
Software Mentions: 1
Published: almost 5 years ago

Ecosyste.ms: Papers

Projects: pypi: liftover

Papers Mentioning liftover 34