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10.1534/g3.120.401288

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles
Cited by: 19
Author(s): H Busra Cagirici, Taner Z. Sen
Software Mentions: 1
Published: over 6 years ago

Improved contiguity of the threespine stickleback genome using long-read sequencing
Cited by: 24
Author(s): Shivangi Nath, Daniel Eric Shaw, Michael A. White
Software Mentions: 1
Published: over 5 years ago

10.1155/2015/230642

Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis
Cited by: 21
Author(s): Jing Shen, Shuang Wang, Abby B. Siegel, Helen Remotti, Qiao Wang, Iryna Sirosh, Regina M. Santella
Software Mentions: 1
Published: over 11 years ago

10.3390/genes2030397

Delineating Chromosomal Breakpoints in Radiation-Induced Papillary Thyroid Cancer
Cited by: 7
Author(s): Heinz‐Ulrich G. Weier, Yuko Ito, Johnson Kwan, Jan Smida, Jingly F. Weier, Ludwig Hieber, Chunmei Lu, Lars Lehmann, Mei Wang, Haig J. Kassabian, Hui Zeng, Benjamin O’Brien
Software Mentions: 1
Published: about 15 years ago

10.3390/genes4020226

High SINE RNA Expression Correlates with Post-Transcriptional Downregulation of BRCA1
Cited by: 1
Author(s): Maureen Peterson, Vicki L. Chandler, Giovanni Bosco
Software Mentions: 1
Published: over 13 years ago

10.3390/genes5010235

Illuminating the Transcriptome through the Genome
Cited by: 5
Author(s): David J. Elliott
Software Mentions: 1
Published: over 12 years ago

10.3390/genes9080405

Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes
Cited by: 22
Author(s): Alex Makunin, Svetlana A. Romanenko, Violetta R. Beklemisheva, Polina L. Perelman, Anna S. Druzhkova, Kristina Petrova, Dmitry Prokopov, Ekaterina Chernyaeva, Jennifer L. Johnson, Anna V. Kukekova, Fengtang Yang, Malcolm A. Ferguson‐Smith, Alexander S. Graphodatsky, Vladimir A. Trifonov
Software Mentions: 1
Published: about 8 years ago

10.3390/genes10030193

Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health
Cited by: 11
Author(s): Esther Walton, Caroline L Relton, Doretta Caramaschi
Software Mentions: 1
Published: over 7 years ago

10.3390/genes10050385

Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration
Cited by: 6
Author(s): Rebekkah J. Hitti, James A. C. Oliver, Ellen Schofield, Anina Bauer, Maria Kaukonen, Oliver P. Forman, Tosso Leeb, Hannes Lohi, Louise M. Burmeister, David R. Sargan, Cathryn S. Mellersh
Software Mentions: 1
Published: over 7 years ago

10.3390/genes10050345

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome
Cited by: 43
Author(s): Radka Symonová
Software Mentions: 1
Published: over 7 years ago

10.3390/genes11121456

Technologies for Pharmacogenomics: A Review
Cited by: 28
Author(s): Maaike van der Lee, Marjolein Kriek, Henk‐Jan Guchelaar, Jesse J. Swen
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12020141

Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses
Cited by: 13
Author(s): Yan‐Ran Sheng, Shunyu Hou, Wenting Hu, Chunyan Wei, Yukai Liu, Yuyin Liu, Lu Jiang, Jingjing Xiang, Xiaoxi Sun, Lei Chen, Huiling Wang, Xiao‐Yong Zhu
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12020238

Evolution of the IRF Family in Salmonids
Cited by: 7
Author(s): Thomas C. Clark, Pierre Boudinot, Bertrand Collet
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12030430

Hunting for Familial Parkinson’s Disease Mutations in the Post Genome Era
Cited by: 2
Author(s): Steven Bentley, Ilaria Guella, Holly E. Sherman, Hannah M. Neuendorf, Alex M. Sykes, Javed Fowdar, Peter A. Silburn, Stephen A. Wood, Matthew J. Farrer, George D. Mellick
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12040470

Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development
Cited by: 13
Author(s): Jeremy W. Prokop, Caleb Bupp, Austin Frisch, Stephanie M. Bilinovich, Daniel B. Campbell, Daniel Vogt, Chad R. Schultz, Katie Uhl, Elizabeth VanSickle, Surender Rajasekaran, André S. Bachmann
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12050669

Investigating Olfactory Gene Variation and Odour Identification in Older Adults
Cited by: 4
Author(s): Siddharth Raj, Anbupalam Thalamuthu, Nicola J. Armstrong, Margaret J. Wright, John B. Kwok, Julian N. Trollor, David Ames, Peter R. Schofield, Henry Brodaty, Perminder S. Sachdev, Karen A. Mather
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12060877

Cytogenetic and Array-CGH Characterization of a Simple Case of Reciprocal t(3;10) Translocation Reveals a Hidden Deletion at 5q12
Cited by: 0
Author(s): Angelo Cellamare, Nicoletta Coccaro, Maria Cristina Nuzzi, Paola Casieri, Marilina Tampoia, Flavia Angela Maria Maggiolini, Mattia Gentile, Romina Ficarella, Emanuela Ponzi, Maria Rosa Conserva, Laura Cardarelli, Annunziata Panarese, Francesca Antonacci, Antonia Gesario
Software Mentions: 1
Published: about 5 years ago

10.3390/genes12060805

Generation and Genetic Correction of USH2A c.2299delG Mutation in Patient-Derived Induced Pluripotent Stem Cells
Cited by: 13
Author(s): Xuezhong Liu, Justin Lillywhite, Wenliang Zhu, Zaohua Huang, Andrew E. Clark, Nicholas C. Gosstola, Colin T. Maguire, Derek M. Dykxhoorn, Zheng-Yi Chen, Jun Yang
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12060822

Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants
Cited by: 6
Author(s): Tingting Zhang, Yang Yang, Xiaoyu Song, Xinyu Gao, Xianliang Zhang, Junjie Zhao, Kehai Zhou, Chun-Chao Zhao, Wei Li, Daigang Yang, Xiongfeng Ma, Zhong-Hu Li
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12081284

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool
Cited by: 18
Author(s): M. de la Puente, Jorge Ruiz-Ramírez, A. Ambroa-Conde, Catarina Xavier, Jacobo Pardo‐Seco, José Antonio Álvarez‐Dios, Ana Freire-Aradas, Ana Mosquera-Miguel, T.E. Gross, Elaine Y.Y. Cheung, Wojciech Branicki, Michael Nothnagel, Walther Parson, Peter M. Schneider, Manfred Kayser, Ángel Carracedo, Marı́a Victoria Lareu, Christopher Phillips
Software Mentions: 1
Published: about 5 years ago

10.3390/genes12081111

Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of CHM Gene Transcription
Cited by: 2
Author(s): Tiziana Fioretti, Valentina Di Iorio, Barbara Lombardo, Francesca De Falco, Armando Cevenini, Fabio Cattaneo, Francesco Testa, Lucio Pastore, Francesca Simonelli, Gabriella Esposito
Software Mentions: 1
Published: about 5 years ago

10.3390/genes12081140

Multiple Acyl-CoA Dehydrogenase Deficiency with Variable Presentation Due to a Homozygous Mutation in a Bedouin Tribe
Cited by: 1
Author(s): Orna Staretz‐Chacham, Shirly Amar, Shlomo Almashanu, Ben Pode‐Shakked, Ann Saada, Ohad Wormser, Eli Hershkovitz
Software Mentions: 1
Published: about 5 years ago

10.1002/gcc.21943

The miR‐17‐92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification
Cited by: 93
Author(s): Antoîne Italiano, Rachael Thomas, Matthew Breen, Lei Zhang, Aimeé M. Crago, Samuel Singer, Raya Khanin, Robert G. Maki, Aleksandra Mihailović, Markus Hafner, Tom Tuschl, Cristina R. Antonescu
Software Mentions: 1
Published: over 14 years ago

10.1002/dvg.22008

From expression cloning to gene modeling: The development ofXenopusgene sequence resources
Cited by: 19
Author(s): Michael J. Gilchrist
Software Mentions: 1
Published: over 14 years ago

10.1590/1678-4685-GMB-2018-0173

Integrated analysis of the critical region 5p15.3–p15.2 associated with cri-du-chat syndrome
Cited by: 13
Author(s): Thiago Corrêa, Bruno César Feltes, Mariluce Riegel
Software Mentions: 1
Published: over 7 years ago

10.4061/2011/976398

Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports
Cited by: 5
Author(s): Jing Liu, François Bernier, Julie Lauzon, R. Brian Lowry, Judy Chernos
Software Mentions: 1
Published: about 15 years ago

10.1186/gb-2006-7-s1-s12

Cited by: 507
Author(s): Danielle Thierry-Mieg, Jean Thierry‐Mieg
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2007-8-3-r41

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
Cited by: 97
Author(s): Kerrin S. Small, Michael Brudno, M. Manuela Hill, Arend Sidow
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2007-8-7-r129

FlyMine: an integrated database for Drosophila and Anopheles genomics
Cited by: 345
Author(s): Rachel Lyne, Richard J. Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, P.G. McLaren, Philip North, Rana Debashis, T. V. Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn S. Lilley, Steven Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2007-8-7-r152

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome
Cited by: 84
Author(s): Brian P. Dalrymple, Ewen F. Kirkness, Mikhail Nefedov, Sean McWilliam, Abhirami Ratnakumar, Wes Barris, Shaying Zhao, Jyoti Shetty, J F Maddox, Margaret O'Grady, F. W. Nicholas, A. M. Crawford, Ted Smith, Pieter J. de Jong, John C. McEwan, V. H. Oddy, Noelle E. Cockett
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2008-9-2-r34

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
Cited by: 88
Author(s): Pär G. Engström, David Fredman, Boris Lenhard
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2008-9-2-r37

Sequence context affects the rate of short insertions and deletions in flies and primates
Cited by: 47
Author(s): Amos Tanay, Eric D. Siggia
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2007-8-8-r167

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
Cited by: 58
Author(s): Boris Adryan, Gertrud Woerfel, Ian Birch-Machin, Shan Gao, Marie Quick, Lisa Meadows, Steven Russell, Robert A. White
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2008-9-6-r104

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Cited by: 15
Author(s): Thorsten Schmidt, Dmitrij Frishman
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2009-10-2-r14

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
Cited by: 51
Author(s): Christoph Bock, Konstantin Halachev, Joachim Büch, Thomas Lengauer
Software Mentions: 1
Published: over 17 years ago

10.1186/gb-2009-10-8-r86

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
Cited by: 25
Author(s): Xianjun Dong, David Fredman, Boris Lenhard
Software Mentions: 1
Published: over 17 years ago

10.1186/gb-2010-11-7-r70

Contrasting chromatin organization of CpG islands and exons in the human genome
Cited by: 101
Author(s): Jung Kyoon Choi
Software Mentions: 1
Published: over 16 years ago

10.1186/gb-2011-12-9-r86

Mutation discovery in mice by whole exome sequencing
Cited by: 102
Author(s): Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R. Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J. Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy B. Rowe, Frank J. Probst, David E. Bergstrom, Stephen A. Murray, Carol J. Bult, Joel E. Richardson, Benjamin T. Kile, Ivo Gut, Jörg Hager, Snaevar Sigurðsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad‐Toh, Michael L. Cunningham, Timothy C. Cox, Monica J. Justice, Mona S. Spector, Scott W. Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey A. Jeddeloh, Jay Shendure
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-s1-p3

COSMIC: the catalogue of somatic mutations in cancer
Cited by: 5
Author(s): Nidhi Bindal, Simon Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Chai Yin Kok, Mingming Jia, Sally Bamford, Charlotte G. Cole, Sari Ward, Jon W. Teague, Michael R. Stratton, Peter J. Campbell, Andrew Futreal
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-s1-p24

Identification of functional genetic variants associated with prostate cancer through analysis of genome-wide genetic and epigenetic datasets
Cited by: 0
Author(s): McAnthony Tarway, Wei Tang, Ludmila Prokunina–Olsson
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2012-13-7-r66

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation
Cited by: 201
Author(s): Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A. Gutowska, Juliane Wolf, Sonja Verena Bergner, Markus B. Schilhabel, Ulrich C. Klostermeier, Robert G. Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2012-13-10-r84

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
Cited by: 141
Author(s): Duncan Sproul, Robert Kitchen, Colm E. Nestor, JM Dixon, Andrew H. Sims, David J. Harrison, Bernard Ramsahoye, Richard R. Meehan
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2013-14-5-r45

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing
Cited by: 115
Author(s): Shivendra Kishore, Andreas Gruber, Dominik J. Jedlinski, Afzal Pasha Syed, Hadi Jorjani, Mihaela Zavolan
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2013-14-3-r25

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes
Cited by: 199
Author(s): James P. Reddington, Sara Maria Perricone, Colm E. Nestor, Judith Reichmann, Neil A. Youngson, Masako Suzuki, Diana Reinhardt, Donncha S. Dunican, James Prendergast, Heidi K. Mjoseng, Bernard Ramsahoye, Emma Whitelaw, John M. Greally, Ian R. Adams, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2014-15-1-r5

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome
Cited by: 146
Author(s): Yishay Pinto, Haim Y. Cohen, Erez Y. Levanon
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2013-14-7-r79

PARma: identification of microRNA target sites in AGO-PAR-CLIP data
Cited by: 52
Author(s): Florian Erhard, Lars Dölken, Łukasz Jaśkiewicz, Ralf Zimmer
Software Mentions: 1
Published: over 13 years ago

10.1186/s13059-015-0672-7

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression
Cited by: 130
Author(s): Ruslan Strogantsev, Felix Krueger, Kazuki Yamazawa, Hui Shi, Poppy A. Gould, Megan Goldman-Roberts, Kirsten McEwen, Bowen Sun, Roger A. Pedersen, Anne C. Ferguson-Smith
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-015-0768-0

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells
Cited by: 175
Author(s): A. Rasim Barutcu, Bryan R. Lajoie, Rachel Patton McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, André J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-015-0842-7

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction
Cited by: 106
Author(s): Joseph L. McClay, Andrey A. Shabalin, Mikhail G. Dozmorov, Daniel E. Adkins, Gaurav Kumar, Srilaxmi Nerella, Shaunna L. Clark, Sarah E. Bergen, Christina M. Hultman, Patrik K. E. Magnusson, Patrick F. Sullivan, Karolina A. Åberg, Edwin J. C. G. van den Oord
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-016-0876-5

The contribution of Alu exons to the human proteome
Cited by: 36
Author(s): Lan Lin, Peng Jiang, Juw Won Park, Jinkai Wang, Zhi-xiang Lu, Maggie P. Y. Lam, Peipei Ping, Yi Xing
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-017-1185-3

Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
Cited by: 141
Author(s): John Cole, Neil Robertson, Mohammed Iqbal Rather, John P. Thomson, Tony McBryan, Duncan Sproul, Tina Wang, Claire Brock, William Clark, Trey Ideker, Richard R. Meehan, Richard A. Miller, Holly M. Brown–Borg, Peter D. Adams
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-017-1226-y

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
Cited by: 30
Author(s): Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Li, Jin‐Xing Zhou, Joe Ogas, Jian‐Kang Zhu, Xin‐Jian He, Heng Zhang
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-017-1225-z

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements
Cited by: 21
Author(s): Cristina Vicente-García, Bárbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter Rigby, Damien P. Devos, José Luis Gómez-Skármeta, Jaime J. Carvajal
Software Mentions: 1
Published: about 9 years ago

10.1186/gb-2004-6-1-r9

Cited by: 253
Author(s): Frank Desiere, Eric W. Deutsch, Alexey I. Nesvizhskii, Parag Mallick, Nichole L. King, Jimmy K. Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson Fausto, Ernst Hafen, Lee Hood, Michael G. Katze, Kathleen A. Kennedy, Floyd Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeffrey A. Ranish, David J. Rawlings, Lawrence E. Samelson, Yuzuru Shiio, Julian D. Watts, Bernd Wollscheid, M. Wright, Wei Yan, Lizhu Yang, Eugene C. Yi, Hui Zhang, Ruedi Aebersold
Software Mentions: 1
Published: over 22 years ago

10.1186/s13059-018-1393-5

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages
Cited by: 30
Author(s): Eugenia D’Atanasio, Beniamino Trombetta, Maria Di Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth E. Watson, Alfredo Coppa, Paolo Anagnostou, Jean‐Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto, Fulvio Cruciani
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-018-1434-0

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
Cited by: 73
Author(s): Luís Zapata, Oriol Pich, Luís Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-018-1493-2

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons
Cited by: 16
Author(s): Yuan Yuan, Shirley Xie, Jennifer C. Darnell, Andrew J. Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth A. Murphy, Chaolin Zhang, Tom Maniatis, Robert B. Darnell
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-018-1491-4

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
Cited by: 181
Author(s): Michaël Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert, Philippe Leroy, Nicolas Guilhot, Jérôme Salse, Catherine Feuillet, Etienne Paux, Kellye Eversole, Anne-Françoise Adam-Blondon, Hadi Quesneville
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-018-1544-8

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Cited by: 40
Author(s): Joana Damas, Jaebum Kim, Marta Farré, Darren K. Griffin, Denis M. Larkin
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13059-019-1889-7

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
Cited by: 28
Author(s): Huizhong Fan, Qi Wu, Fuwen Wei, Fengtang Yang, Bee Ling Ng, Yibo Hu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-019-1897-7

PASTMUS: mapping functional elements at single amino acid resolution in human cells
Cited by: 6
Author(s): Xinyi Zhang, Di Yue, Yinan Wang, Yan Zhou, Ying Liu, Yu Qiu, Feng Tian, Ying Yu, Zhuo Zhou, Wensheng Wei
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-020-02017-z

ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Cited by: 91
Author(s): Egor Dolzhenko, Mark F Bennett, Phillip A. Richmond, Brett Trost, Sai Chen, Joke J.F.A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew M. Gross, Bryan R. Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David Bentley, Ryan K. C. Yuen, Melanie Bahlo, Michael A. Eberle
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-020-02184-z

Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus
Cited by: 7
Author(s): Prithvi Raj, Ran Song, Honglin Zhu, Linley Riediger, Dong Jae Jun, Chao Liang, Carlos Arana, Bo Zhang, Yajing Gao, Benjamin Wakeland, Igor Dozmorov, Jianuan Zhou, Jennifer A. Kelly, Bernard Lauwerys, Joel M. Guthridge, Nancy J. Olsen, Swapan K. Nath, Chandrashekhar Pasare, Nicolai S. C. van Oers, Gary S. Gilkeson, Betty P. Tsao, Patrick M. Gaffney, Peter K. Gregersen, Judith A. James, Xiaoxia Zuo, David R. Karp, Quan Zhen Li, Edward K. Wakeland
Software Mentions: 1
Published: almost 6 years ago

10.1093/gbe/evu139

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome
Cited by: 54
Author(s): Samuel H. Aeschlimann, Franziska Jönsson, Jan Postberg, Nicholas A. Stover, Robert L. Petera, Hans-Joachim Lipps, Mariusz Nowacki, Estienne C. Swart
Software Mentions: 1
Published: about 12 years ago

10.1093/gbe/evv012

The Role of DNA Insertions in Phenotypic Differentiation between Humans and Other Primates
Cited by: 4
Author(s): Elizabeth Hellen, Andrew D. Kern
Software Mentions: 1
Published: over 11 years ago

10.1093/gbe/evv142

A Genome-Wide Landscape of Retrocopies in Primate Genomes
Cited by: 44
Author(s): Fábio C. P. Navarro, Pedro A. F. Galante
Software Mentions: 1
Published: about 11 years ago

10.1093/gbe/evv161

Comparative Genomics of Environmental and ClinicalStenotrophomonas maltophiliaStrains with Different Antibiotic Resistance Profiles
Cited by: 72
Author(s): Benjamin Youenou, Sabine Favre-Bonté, Josselin Bodilis, Elisabeth Brothier, Audrey Dubost, Daniel Müller, Sylvie Nazaret
Software Mentions: 1
Published: about 11 years ago

10.1093/gbe/evx237

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine
Cited by: 9
Author(s): Eran Elhaik, Leeban Yusuf, Ainan I J Anderson, Mehdi Pirooznia, Dimitrios Arnellos, Gregory Vilshansky, Gunes Ercal, Yontao Lu, Teresa A. Webster, Michael L. Baird, Umberto Esposito
Software Mentions: 1
Published: almost 9 years ago

10.1093/gbe/evy199

Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets
Cited by: 7
Author(s): Fabrizio Mafessoni, Rashmi B. Prasad, Leif Groop, Ola Hansson, Kay Prüfer
Software Mentions: 1
Published: almost 8 years ago

10.1093/gbe/evz228

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Cited by: 69
Author(s): Yutaka Satou, Ryohei Nakamura, Dejie Yu, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evz254

Genome Assembly of the Dogface Butterfly Zerene cesonia
Cited by: 7
Author(s): Luis Rodriguez-Caro, Jennifer Fenner, Caleb Benson, Steven M. Van Belleghem, Brian A. Counterman
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evaa045

Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
Cited by: 9
Author(s): Michael Emmett Kartje, Peicheng Jing, Bret A. Payseur
Software Mentions: 1
Published: over 6 years ago

10.1186/2041-9414-2-6

Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
Cited by: 7
Author(s): George E. Liu, Yali Hou, James M. Robl, Yoshimi Kuroiwa, Zhongde Wang
Software Mentions: 1
Published: over 15 years ago

10.1186/gm137

Collaboratively charting the gene-to-phenotype network of human congenital heart defects
Cited by: 28
Author(s): Roland Barriot, Jeroen Breckpot, Bernard Thienpont, Sylvain Brohée, Steven Van Vooren, Bert Coessens, Léon-Charles Tranchevent, Peter Van Loo, Marc Gewillig, Koenraad Devriendt, Yves Moreau
Software Mentions: 1
Published: over 16 years ago

10.1186/s13073-017-0427-z

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories
Cited by: 24
Author(s): Kenneth D. Doig, Andrew Fellowes, Anthony Bell, Andrei Seleznev, Dávid Ma, Jason Ellul, Jason Li, Maria A. Doyle, Ella R. Thompson, Amit Kumar, Luis F. Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T. Papenfuss, Stephen B. Fox
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-017-0453-x

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells
Cited by: 20
Author(s): Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen, Markku Laakso
Software Mentions: 1
Published: about 9 years ago

10.1016/j.ygeno.2009.10.004

Genome-wide end-sequenced BAC resources for the NOD/MrkTac☆ and NOD/ShiLtJ☆☆ mouse genomes
Cited by: 15
Author(s): Charles A. Steward, Sean Humphray, Bob Plumb, Matthew C. Jones, Michael A. Quail, Stephen V. Rice, Tony Cox, Robert M. Davies, James K. Bonfield, Thomas M. Keane, Michael Nefedov, Pieter J. de Jong, Paul Lyons, Linda S. Wicker, John A. Todd, Yoshihide Hayashizaki, Omid M. Gulban, Jayne S. Danska, Jennifer Harrow, Tim Hubbard, Jane Rogers, David J. Adams
Software Mentions: 1
Published: over 16 years ago

10.1016/j.gpb.2019.03.006

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production
Cited by: 34
Author(s): Lin Zhang, Meilan Liu, Hongxu Long, Wei Dong, Asher Pasha, Eddi Esteban, Wenying Li, Xiaoming Yang, Ze Li, Aixia Song, Duo Ran, Guang Zhao, Yanwei Zeng, Hao Chen, Ming Zou, Jingjing Li, Fan Liang, Meili Xie, Jiang Hu, Depeng Wang, Heping Cao, Nicholas J. Provart, Liangsheng Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1186/2047-217X-3-13

Annotated features of domestic cat – Felis catus genome
Cited by: 30
Author(s): Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alex Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasov, Anton Svitin, Klaus‐Peter Koepfli, Joan Pontius, Carlos A. Driscoll, Kevin Blackistone, Cristina Barr, David Goldman, Agostinho Antunes, Javier Quilez, Belén Lorente-Galdós, Can Alkan, Tomàs Marquès‐Bonet, Marylin Menotti-Raymond, Victor A. David, Kristina Narfström, Stephen J. O’Brien
Software Mentions: 1
Published: about 12 years ago

10.1093/gigascience/gix085

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
Cited by: 150
Author(s): Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason T. Howard, Josée Audet, Lindsey J. Cantin, Erich D. Jarvis
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-18378-8

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca
Cited by: 27
Author(s): Shigekatsu Suzuki, Rikiya Endoh, Ri-ichiroh Manabe, Moriya Ohkuma, Yoshihisa Hirakawa
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19744-w

Aminode: Identification of Evolutionary Constraints in the Human Proteome
Cited by: 31
Author(s): K. T. Chang, Junyan Guo, Alberto di Ronza, Marco Sardiello
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-20004-0

Depletion of HDAC1, 7 and 8 by Histone Deacetylase Inhibition Confers Elimination of Pancreatic Cancer Stem Cells in Combination with Gemcitabine
Cited by: 57
Author(s): Mao-Hua Cai, Xiaogang Xu, Shili Yan, Ze Sun, Ying Yin, Baikui Wang, Yuexing Tu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19201-8

Loss-of-function uORF mutations in human malignancies
Cited by: 42
Author(s): Julia Schulz, Nancy Mah, Martin Neuenschwander, Tabea Kischka, Richard Ratei, Peter M. Schlag, Esmeralda Castaños‐Vélez, Iduna Fichtner, Per‐Ulf Tunn, Carsten Denkert, Oliver Klaas, Wolfgang E. Berdel, Jens Peter von Kries, Wojciech Makałowski, Miguel A. Andrade‐Navarro, Achim Leutz, Klaus Wethmar
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-20781-8

Accelerated invagination of vacuoles as a stress response in chronically heat-stressed yeasts
Cited by: 13
Author(s): Ayane Ishii, Masahito Kawai, Haruka Noda, Hiroyuki Kato, Kohei Takeda, K. Asakawa, Yoshinobu Ichikawa, Tomohiro Sasanami, Keiji Tanaka, Yoko Kimura
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-21330-z

A heading date QTL, qHD7.2, from wild rice (Oryza rufipogon) delays flowering and shortens panicle length under long-day conditions
Cited by: 23
Author(s): Jing Li, Rui Xu, Chunchao Wang, Qi Liu, Xiaoming Zheng, Wensheng Wang, Ye Ding, Lizhen Zhang, Yanyan Wang, Yunlian Cheng, Lifang Zhang, Weihua Qiao, Qing Yang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-22010-8

Egr2-dependent microRNA-138 is dispensable for peripheral nerve myelination
Cited by: 11
Author(s): Hsin Pin Lin, Idil Oksuz, John Svaren, Rajeshwar Awatramani
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-23289-3

The transcriptional profiles and functional implications of long non-coding RNAs in the unfolded protein response
Cited by: 9
Author(s): Hongyang Quan, Qianqian Fan, Chuang Li, Yanying Wang, Lin Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25001-x

Application of droplet digital PCR in the analysis of genome integration and organization of the transgene in BAC transgenic mice
Cited by: 2
Author(s): Ayumi Nakagaki, Asuka Urakawa, Shiori Hirano, Takeru Anami, Tatsuya Kishino
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25290-2

Bidirectional regulation of bone formation by exogenous and osteosarcoma-derived Sema3A
Cited by: 6
Author(s): Daniëlle de Ridder, Silvia Marino, Ryan T. Bishop, Nathalie Renema, Chantal Chenu, Dominique Heymann, Aymen I. Idris
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-27104-x

Blocking the 5′ splice site of exon 4 by a morpholino oligomer triggers APOL1 protein isoform switch
Cited by: 9
Author(s): Amber M. Cheatham, Shamara E. Davis, Atanu K. Khatua, Waldemar Popik
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-27360-x

Male mice with large inversions or deletions of X-chromosome palindrome arms are fertile and express their associated genes during post-meiosis
Cited by: 9
Author(s): Alyssa N. Kruger, Quinn Ellison, Michele Brogley, Emma R. Gerlinger, Jacob L. Mueller
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-30238-7

Identification and characterization of TP53 gene Allele Dropout in Li-Fraumeni syndrome and Oral cancer cohorts
Cited by: 5
Author(s): Mohammed Moquitul Haque, Pradnya Kowtal, Rajiv Sarin
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-31968-4

Investigation of hindbrain activity during active locomotion reveals inhibitory neurons involved in sensorimotor processing
Cited by: 24
Author(s): Kristen E. Severi, Urs Lucas Böhm, Claire Wyart
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-31785-9

The acetylation of cyclin-dependent kinase 5 at lysine 33 regulates kinase activity and neurite length in hippocampal neurons
Cited by: 17
Author(s): Juhyung Lee, Yeon Uk Ko, Yuhyun Chung, Nuri Yun, Myung-Jin Kim, Kyungjin Kim, Young Jun Oh
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-33235-y

An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3
Cited by: 3
Author(s): Yuri S. Odaka, Takahide Tohmonda, Atsushi Toyoda, Jun Aruga
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-34078-3

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
Cited by: 27
Author(s): Craig W. Duffy, Alfred Amambua-Ngwa, Ambroise D. Ahouidi, Mahamadou Diakité, Gordon A. Awandare, Hampâté Bâ, Sarah J. Tarr, Lee G. Murray, Lindsay B. Stewart, Umberto D’Alessandro, Thomas D. Otto, Dominic Kwiatkowski, David J. Conway
Software Mentions: 1
Published: almost 8 years ago

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