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10.3390/v9070161

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome
Cited by: 10
Author(s): Przemysław Decewicz, Monika Radlińska, Łukasz Dziewit
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-15-1060

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
Cited by: 64
Author(s): Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca E O'Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D. Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin
Software Mentions: 2
Published: almost 12 years ago

10.1002/dvg.22963

Transcriptional regulation of the proto‐oncogeneZfp521by SPI1 (PU.1) and HOXC13
Cited by: 11
Author(s): Ming Yu, Salma Aldallal, Latifa Al‐Haj, Shiraj Panjwani, Akina S. McCartney, Sarah Edwards, Pooja Manjunath, Catherine Walker, Alexander Awgulewitsch, Kathryn E. Hentges
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0082499

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid
Cited by: 30
Author(s): Tianjiao Li, Shuai Wang, Xin-He Meng, Yong-Rui Bao, Shanshan Guan, Bo Liu, Chen Lü, Lei Wang, Xiaorong Ran
Software Mentions: 2
Published: over 12 years ago

10.1186/s12711-020-0528-9

pCADD: SNV prioritisation in Sus scrofa
Cited by: 16
Author(s): Christian Groß, Martijn F.L. Derks, Hendrik Jan Megens, Mirte Bosse, M.A.M. Groenen, Marcel J. T. Reinders, Dick de Ridder
Software Mentions: 2
Published: over 6 years ago

10.1534/genetics.115.185363

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
Cited by: 27
Author(s): Katarzyna B. Hooks, Samina Naseeb, Steven J. Parker, Sam Griffiths-Jones, Daniela Delneri
Software Mentions: 2
Published: about 10 years ago

10.1186/gb-2006-7-7-r58

Cited by: 22
Author(s): Matthew D. Wilkerson, Shannon D. Schlueter, Volker Brendel
Software Mentions: 2
Published: over 20 years ago

10.3390/v13091764

The Evolving Faces of the SARS-CoV-2 Genome
Cited by: 14
Author(s): Maria Schmidt, Mamoona Arshad, Stephan H. Bernhart, Siras Hakobyan, Arsen Arakelyan, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 2
Published: about 5 years ago

10.1186/gb-2006-7-s1-s9

Cited by: 59
Author(s): Jonathan Allen, William H. Majoros, Mihaela Pertea, Steven L. Salzberg
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2148-9-286

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
Cited by: 26
Author(s): Alan M. Moses
Software Mentions: 2
Published: over 17 years ago

10.1007/s00439-017-1838-z

Enrichment of putatively damaging rare variants in the DYX2 locus and the reading-related genes CCDC136 and FLNC
Cited by: 8
Author(s): Andrew Adams, Shelley D. Smith, Dongnhu T. Truong, Erik G. Willcutt, Richard K. Olson, John C. DeFries, Bruce F. Pennington, Jeffrey R. Gruen
Software Mentions: 2
Published: about 9 years ago

10.1007/s00439-014-1454-0

A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs
Cited by: 13
Author(s): Joshua A. Stern, Stephen N. White, Linda B. Lehmkuhl, Yamir Reina-Doreste, Jordan L. Ferguson, Nanette Nascone‐Yoder, Kathryn M. Meurs
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-11-382

Integration and visualization of systems biology data in context of the genome
Cited by: 35
Author(s): J. Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S. Baliga
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2164-16-S8-S2

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Cited by: 68
Author(s): Adam Frankish, Barbara Uszczyńska, Graham R. S. Ritchie, Jose M. Gonzalez, Dmitri D. Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno A. Fonseca, Alvis Brāzma, Roderic Guigó, Jennifer Harrow
Software Mentions: 2
Published: about 11 years ago

10.1002/ece3.2985

Genomic and phenotypic signatures of climate adaptation in an Anolis lizard
Cited by: 24
Author(s): Ariel Rodríguez, Tia Rusciano, Rickeisha Hamilton, Leondra Holmes, Deidra Jordan, Katharina C. Wollenberg Valero
Software Mentions: 2
Published: about 9 years ago

10.1186/s12862-018-1311-1

Rapid microevolution during recent range expansion to harsh environments
Cited by: 26
Author(s): Yiyong Chen, Noa Shenkar, Ping Ni, Ya‐Ping Lin, Shiguo Li, Aibin Zhan
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2008-9-12-r170

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
Cited by: 75
Author(s): Rongrong Chen, Alex Morgan, Joel T. Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, An‐Jen Chiang, Atul J. Butte
Software Mentions: 2
Published: over 18 years ago

10.7717/peerj.6028

Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study
Cited by: 6
Author(s): Qi Mao, Chengjie Chen, Tongxin Xie, Aiping Luan, Chaoyang Liu, Yehua He
Software Mentions: 2
Published: almost 8 years ago

10.18632/oncotarget.25536

Prostate cancer susceptibility gene HIST1H1A is a modulator of androgen receptor signaling and epithelial to mesenchymal transition
Cited by: 6
Author(s): Kendra A. Williams, Minnkyong Lee, Jean M. Winter, Derek Gildea, Carla Calagua, Natasha Curry, Jens Lichtenberg, Huihui Ye, Nigel P.S. Crawford
Software Mentions: 2
Published: about 8 years ago

10.1186/s40246-021-00342-3

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism
Cited by: 11
Author(s): Evin M. Padhi, Tristan J. Hayeck, Cheng Zhang, Satadal Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Bénech, Kévin Uguen, Séverine Audebert‐Bellanger, Cédric Le Marechal, Claude Férec, Stéphanie Efthymiou, Fatima Rahman, Shazia Maqbool, Reza Maroofian, Henry Houlden, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Riana D Hunter, Jennifer A. Akiyama, Lauren Fries, Jeffrey Ng, Elvisa Mehinovic, Nicholas Stong, Andrew S. Allen, Diane E. Dickel, Raphael Bernier, David U. Gorkin, L Pennacchio, Michael C. Zody, Tychele N. Turner
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0243791

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence
Cited by: 9
Author(s): Caitlin Mills, Anushya Muruganujan, Dustin Ebert, Crystal N. Marconett, Juan Pablo Lewinger, Paul D. Thomas
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2010-11-3-r34

Global and unbiased detection of splice junctions from RNA-seq data
Cited by: 87
Author(s): Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Software Mentions: 2
Published: over 16 years ago

10.1186/gb-2010-11-2-r22

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Cited by: 254
Author(s): Guoliang Li, Melissa J. Fullwood, Xu Han, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B. Vega, Pramila Ariyaratne, Yusoff Bin Mohamed, Hong Ooi, Chandana Tennakoon, Chia Lin Wei, Yijun Ruan, Wing-Kin Sung
Software Mentions: 2
Published: over 16 years ago

10.1186/gb-2010-11-4-r36

Optimized design and data analysis of tag-based cytosine methylation assays
Cited by: 76
Author(s): Masako Suzuki, Jun Qiang, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally
Software Mentions: 2
Published: over 16 years ago

10.1186/gb-2010-11-4-r42

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
Cited by: 66
Author(s): Qiang Gan, Dustin E. Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen
Software Mentions: 2
Published: over 16 years ago

10.7717/peerj.11052

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily
Cited by: 13
Author(s): Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal
Software Mentions: 2
Published: over 5 years ago

10.15252/embr.201846255

Ch <scp>IP</scp> ‐Atlas: a data‐mining suite powered by full integration of public Ch <scp>IP</scp> ‐seq data
Cited by: 473
Author(s): Shinya Oki, Toshio Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: over 14 years ago

10.7717/peerj.6230

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
Cited by: 5
Author(s): Jonas S. Almeida, Janos Hajagos, Joel Saltz, Mary Saltz
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0019481

Elevated miR-499 Levels Blunt the Cardiac Stress Response
Cited by: 130
Author(s): Joseph T.C. Shieh, Yu Huang, Jacqueline Gilmore, Deepak Srivastava
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: over 13 years ago

10.1016/j.molcel.2019.10.002

R-Loops Promote Antisense Transcription across the Mammalian Genome
Cited by: 97
Author(s): Sue Mei Tan-Wong, Somdutta Dhir, Nick J. Proudfoot
Software Mentions: 2
Published: almost 7 years ago

10.1093/hmg/ddv272

Homozygous loss-of-function variants in European cosmopolitan and isolate populations
Cited by: 25
Author(s): Vera B. Kaiser, Victoria Svinti, James Prendergast, You-Ying Chau, Archie Campbell, Inga Patarčić, Inês Barroso, Peter K. Joshi, Nicholas D. Hastie, Ana Miljković, Martin S. Taylor, Generation Scotland, Uk K, Stefan Enroth, Yasin Memari, Anja Kolb-Kokocinski, Alan F. Wright, Ulf Gyllensten, Richard Durbin, Igor Rudan, Harry Campbell, Ozren Polašek, Åsa Johansson, Sascha Sauer, David J. Porteous, Ross M. Fraser, Camilla Drake, Véronique Vitart, Caroline Hayward, Colin A. Semple, James F. Wilson
Software Mentions: 2
Published: about 11 years ago

10.1186/gb-2013-14-6-r59

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Cited by: 251
Author(s): Emanuela Sani, Paweł Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann
Software Mentions: 2
Published: over 13 years ago

10.1002/humu.22842

Facilitating Collaboration in Rare Genetic Disorders Through Effective Matchmaking in DECIPHER
Cited by: 35
Author(s): Eleni A. Chatzimichali, Simon Brent, Benjamin Hutton, Daniel Perrett, Caroline F. Wright, A. Paul Bevan, Matthew E. Hurles, Helen V. Firth, Ganesh Swaminathan
Software Mentions: 2
Published: about 11 years ago

10.15252/embj.201488740

<scp>TDP</scp>‐1, the <scp>C</scp>aenorhabditis elegans ortholog of <scp>TDP</scp>‐43, limits the accumulation of double‐stranded <scp>RNA</scp>
Cited by: 58
Author(s): Tassa Saldi, Peter E.A. Ash, Gavin Wilson, Patrick Gonzales, Alfonso Garrido-Lecca, Christine M. Roberts, Vishantie Dostal, Tania F. Gendron, Lincoln Stein, Thomas Blumenthal, Leonard Petrucelli, Christopher D. Link
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-017-4220-6

An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes
Cited by: 22
Author(s): Nora Hohmann, Marcus A. Koch
Software Mentions: 2
Published: almost 9 years ago

10.15252/embj.2020105220

IL‐2/IL‐7‐inducible factors pioneer the path to T cell differentiation in advance of lineage‐defining factors
Cited by: 20
Author(s): Sarah L Bevington, Peter Keane, Jake K Soley, Saskia Tauch, Dominika W Gajdasik, Rémi Fiancette, Veronika Matei-Rascu, Claire Willis, David R. Withers, Peter N. Cockerill
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2148-7-199

Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies
Cited by: 37
Author(s): Aurora Ruiz‐Herrera, Terence J. Robinson
Software Mentions: 2
Published: over 19 years ago

10.1002/humu.22471

A 129-kb Deletion on Chromosome 12 Confers Substantial Protection Against Rheumatoid Arthritis, Implicating the GeneSLC2A3
Cited by: 21
Author(s): Colin Veal, Katherine Reekie, Johnny C. Lorentzen, Peter K. Gregersen, Leonid Padyukov, Anthony J. Brookes
Software Mentions: 2
Published: almost 13 years ago

10.1002/humu.22594

Genetic Variations and Diseases in UniProtKB/Swiss‐Prot: The Ins and Outs of Expert Manual Curation
Cited by: 49
Author(s): Maria Livia Famiglietti, Anne Estreicher, Arnaud Gos, Jerven Bolleman, Sébastien Géhant, Lionel Breuza, Alan Bridge, Sylvain Poux, Nicole Redaschi, Lydie Bougueleret, Ioannis Xénarios
Software Mentions: 2
Published: about 12 years ago

10.1186/gb-2014-15-1-r8

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Cited by: 153
Author(s): Shaun Webb, Ralph D. Hector, Grzegorz Kudla, Sander Granneman
Software Mentions: 2
Published: over 12 years ago

10.1186/gb-2014-15-1-r1

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Cited by: 1,195
Author(s): Peng Cui, Shoudong Zhang, Feng Ding, Shahjahan Ali, Liming Xiong
Software Mentions: 2
Published: over 12 years ago

10.1186/1476-4598-8-42

The novel RASSF6 and RASSF10 candidate tumour suppressor genes are frequently epigenetically inactivated in childhood leukaemias
Cited by: 105
Author(s): Luke B. Hesson, Thomas L. Dunwell, Wendy N. Cooper, Daniel Catchpoole, A.T. Brini, Raffaella Chiaramonte, Mike Griffiths, Andrew D. Chalmers, Eamonn R. Maher, Farida Latif
Software Mentions: 2
Published: about 17 years ago

10.1242/dev.115808

Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells
Cited by: 22
Author(s): Emmanouil Metzakopian, Kamal Bouhali, Matías Alvarez-Saavedra, Jeffrey A. Whitsett, David J. Picketts, Siew‐Lan Ang
Software Mentions: 2
Published: over 11 years ago

10.1242/dev.152504

Long noncoding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells
Cited by: 59
Author(s): M.J. Barter, Rodolfo Gómez, Sam Hyatt, Kathleen Cheung, Andrew Skelton, Yaobo Xu, Ian M. Clark, David A. Young
Software Mentions: 2
Published: over 9 years ago

10.1093/database/baz048

YeasTSS: an integrative web database of yeast transcription start sites
Cited by: 31
Author(s): Jonathan McMillan, Zheng Lü, Juan Luis Rodríguez Rodríguez, Tae-Hyuk Ahn, Lin Zhang
Software Mentions: 2
Published: over 7 years ago

10.1093/humrep/deab099

Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders
Cited by: 28
Author(s): Manon S Oud, Brendan J Houston, Ludmila Voložonoka, Francesco K. Mastrorosa, Giles Holt, Bilal Alobaidi, P F deVries, Galuh D.N. Astuti, Liliana Ramos, Robert I McLachlan, Moira K O'Bryan, Joris A. Veltman, H Chemes, Harsh Sheth
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-014-0469-0

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
Cited by: 137
Author(s): Adam Blattler, Lijing Yao, Heather Witt, Yu Guo, Charles M. Nicolet, Benjamin P. Berman, Peggy J. Farnham
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0017125

Ontogenetic De Novo Copy Number Variations (CNVs) as a Source of Genetic Individuality: Studies on Two Families with MZD Twins for Schizophrenia
Cited by: 66
Author(s): Sujit Maiti, Kiran Kumar, Christina A Castellani, Richard O’Reilly, Shiva M. Singh
Software Mentions: 2
Published: over 15 years ago

10.1186/s13059-014-0578-9

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds
Cited by: 51
Author(s): Carolina Frankl-Vilches, Heiner Kuhl, Martin Werber, Sven Klages, Martin Kerick, Antje Bakker, Edivaldo Herculano Corrêa de Oliveira, Christina Reusch, Floriana Capuano, Jakob Vowinckel, Stefan Leitner, Markus Ralser, Bernd Timmermann, Manfred Gahr
Software Mentions: 2
Published: over 11 years ago

10.1093/database/baaa044

MaizeCUBIC: a comprehensive variation database for a maize synthetic population
Cited by: 4
Author(s): Jingyun Luo, Chengcheng Wei, Haijun Liu, Shikun Cheng, Yingjie Xiao, Xiaqing Wang, Jianbing Yan, Jianxiao Liu
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj-cs.433

Multi-level aspect based sentiment classification of Twitter data: using hybrid approach in deep learning
Cited by: 6
Author(s): Sadaf Hussain Janjua, Ghazanfar Farooq Siddiqui, Muddassar Azam Sindhu, Umer Rashid
Software Mentions: 2
Published: over 5 years ago

10.1093/molbev/msz060

Emergence of a Thrombospondin Superfamily at the Origin of Metazoans
Cited by: 5
Author(s): Deborah K. Shoemark, Berenice Ziegler, Hiroshi Watanabe, Jennifer Strompen, Richard P. Tucker, Suat Özbek, Josephine C. Adams
Software Mentions: 2
Published: over 7 years ago

10.1093/molbev/msaa296

dbCNS: A New Database for Conserved Noncoding Sequences
Cited by: 3
Author(s): Jun Inoue, Naruya Saitou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-015-0727-9

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Cited by: 107
Author(s): Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas Albert, Joakim Lundeberg, Rickard Sandberg
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-015-0736-8

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Cited by: 83
Author(s): Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Tomohiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E.J. Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: over 16 years ago

10.1186/s13059-015-0835-6

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Cited by: 30
Author(s): Young Chae Kim, Sangwon Byun, Yang Zhang, Sunmi Seok, Byron Kemper, Jian Ma, Jongsook Kim Kemper
Software Mentions: 2
Published: almost 11 years ago

10.1093/molbev/msab050

The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects
Cited by: 46
Author(s): Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: almost 17 years ago

10.1093/database/bax059

BioSearch: a semantic search engine for Bio2RDF
Cited by: 19
Author(s): Wei Hu, Honglei Qiu, Junhui Huang, Michel Dumontier
Software Mentions: 2
Published: over 9 years ago

10.1093/bioinformatics/btt330

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Cited by: 9
Author(s): Colin Veal, Hang Xu, Katherine Reekie, Robert C. Free, Robert J. Hardwick, David G. McVey, Anthony J. Brookes, Edward J. Hollox, Chris J. Talbot
Software Mentions: 2
Published: about 13 years ago

10.1186/s12920-015-0087-z

Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
Cited by: 19
Author(s): Zhaohui Luo, Ye Li, Xiaofang Liu, Mingyao Luo, Liqun Xu, Yue‐Bei Luo, Bo Xiao, Huan Yang
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-016-1142-6

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Cited by: 145
Author(s): Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Saixia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael Feolo, Nataliya Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy L. Heard‐Costa, Han Chen, Poching Liu, Thomas J. Wang, Kimberly A. Woodhouse, Kahraman Tanrıverdi, Jane E. Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D. Johnson, Christopher J. O’Donnell, Daniel Levy, Peter J. Munson
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-216

The Xenopusalcohol dehydrogenase gene family: characterization and comparative analysis incorporating amphibian and reptilian genomes
Cited by: 5
Author(s): Emma Borràs, Ricard Albalat, Gregg Duester, Xavier Parés, Jaume Farrés
Software Mentions: 2
Published: over 12 years ago

10.1093/database/baz056

LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species
Cited by: 6
Author(s): Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Tingan Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu
Software Mentions: 2
Published: over 7 years ago

10.3390/genes11121486

citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement
Cited by: 8
Author(s): Naveen Duhan, Manish Meshram, Cristian D Loaiza, Rakesh Kaundal
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0031092

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing
Cited by: 208
Author(s): Andreas Dötsch, Denitsa Eckweiler, Monika Schniederjans, Ariane Zimmermann, Vanessa Jensen, Maren Scharfe, Robert Geffers, Susanne Häußler
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0063925

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci
Cited by: 42
Author(s): Suhn Kyong Rhie, Simon Coetzee, Houtan Noushmehr, Chunli Yan, Jae Mun Kim, Christopher A. Haiman
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0202369

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates
Cited by: 13
Author(s): Xiaoyong Pan, Anne Wenzel, Lars Juhl Jensen, Jan Gorodkin
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0012315

A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina
Cited by: 15
Author(s): Lev Prasov, Nadean L. Brown, Thomas Gläser
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0209096

Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1
Cited by: 8
Author(s): Varalee Yodsurang, Yaqi Tang, Yusuke Takahashi, Chizu Tanikawa, Yoichiro Kamatani, Atsushi Takahashi, Yukihide Momozawa, Nobuo Fuse, Junichi Sugawara, Atsushi Shimizu, Akimune Fukushima, Asahi Hishida, Norihiro Furusyo, Mariko Naito, Kenji Wakai, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Shoichiro Tsugane, Makoto Hirata, Yoshinori Murakami, Michiaki Kubo, Koichi Matsuda
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0086822

DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women
Cited by: 80
Author(s): Claire Guillemin, Nadine Provençal, Matthew Suderman, Sylvana M. Côté, Frank Vitaro, Michael Hallett, Richard E. Tremblay, Moshe Szyf
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0074132

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates
Cited by: 25
Author(s): Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0006146

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery
Cited by: 647
Author(s): Jennifer L. Kao, Keyan Salari, Melanie Bocanegra, Yoon‐La Choi, Luc Girard, Jeet Gandhi, Kevin Kwei, Tina Hernandez‐Boussard, Pei Wang, Adi F. Gazdar, John D. Minna, Jonathan R. Pollack
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0012362

Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Cited by: 65
Author(s): Jiří Zavadil, Huihui Ye, Zhaojian Liu, Jingjing Wu, Peng Lee, Eva Hernando, Patricia Soteropoulos, Gokce Toruner, Jian Jun Wei
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0053452

From QTL to QTN: Candidate Gene Set Approach and a Case Study in Porcine IGF1-FoxO Pathway
Cited by: 9
Author(s): Minghui Wang, Qishan Wang, Yuchun Pan
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0099844

OccuPeak: ChIP-Seq Peak Calling Based on Internal Background Modelling
Cited by: 10
Author(s): Bouke A. de Boer, Karel van Duijvenboden, Malou van den Boogaard, Vincent M. Christoffels, Phil Barnett, Jan M. Ruijter
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0238179

Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L
Cited by: 12
Author(s): Xin-Tong Zhou, Longfei Jia, Mouzheng Duan, Xue Chen, Cailin Qiao, Jinqi Ma, Chao Zhang, Fuyu Jing, Shengsen Zhang, Bo Yang, Liyuan Zhang, Jiana Li
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0173723

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability
Cited by: 28
Author(s): Anna C. Salzberg, Abigail Harris-Becker, Evgenya Y. Popova, Nikki Keasey, Thomas P. Loughran, David F. Claxton, Sergei A. Grigoryev
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0006589

Integrated Expression Profiling and ChIP-seq Analyses of the Growth Inhibition Response Program of the Androgen Receptor
Cited by: 73
Author(s): Biaoyang Lin, Jun Wang, Hong Xu, Xiaowei Yan, Daehee Hwang, Ji Hoon Cho, Danielle Yi, Angelita G. Utleg, Xuefeng Fang, Dustin E. Schones, Keji Zhao, Gilbert S. Omenn, Leroy Hood
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0098585

Drosophila Polypyrimidine Tract-Binding Protein (DmPTB) Regulates Dorso-Ventral Patterning Genes in Embryos
Cited by: 7
Author(s): Joseph Heimiller, Vinod Sridharan, James S Huntley, Cedric S. Wesley, Ravinder Singh
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0198463

Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens
Cited by: 0
Author(s): Bansari Patel, Andres M. Lebensohn, Ganesh V. Pusapati, Jan E. Carette, Julia Salzman, Rajat Rohatgi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0150719

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads
Cited by: 49
Author(s): Chong Chu, Rasmus Nielsen, Yufeng Wu
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0190664

Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma
Cited by: 9
Author(s): DeAnalisa C. Jones, Adriana Scanteianu, Matthew DiStefano, Mehdi Bouhaddou, Marc R. Birtwistle
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0161997

Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation
Cited by: 16
Author(s): Daria Shlyueva, Antonio C. A. Meireles-Filho, Michaela Pagani, Alexander Stark
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0176031

Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures
Cited by: 63
Author(s): Moon Young Lee, Se Eun Ha, Chanjae Park, Paul J. Park, Robert Fuchs, Lai Wei, Brian G. Jorgensen, Doug Redelman, Sean M. Ward, Kenton M. Sanders, Seungil Ro
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0162504

Characterization of the Mouse and Human Monoacylglycerol O-Acyltransferase 1 (Mogat1) Promoter in Human Kidney Proximal Tubule and Rat Liver Cells
Cited by: 11
Author(s): Shireesha Sankella, Abhimanyu Garg, Anil K. Agarwal
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0146107

Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii
Cited by: 20
Author(s): Stephen A. Bell, Chien-Hua Shen, A. Brown, Arthur G. Hunt
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0147990

Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes
Cited by: 38
Author(s): Inês G. Mollet, Dinesh S. Patel, Fatima S Govani, Adam Giess, Koralia Paschalaki, Manikandan Periyasamy, Elaine C. Lidington, Justin C. Mason, Michael D. Jones, Laurence Gamé, Simak Ali, Claire L. Shovlin
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0097524

GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap
Cited by: 6
Author(s): Eric P. Xing, Ross E. Curtis, Georg P. Schoenherr, Seunghak Lee, Jun Yin, Kriti Puniyani, Wei Wu, Peter Kinnaird
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0020509

Deep Sequencing Reveals Novel MicroRNAs and Regulation of MicroRNA Expression during Cell Senescence
Cited by: 71
Author(s): Joseph M. Dhahbi, Hani Atamna, Dario Boffelli, Wendy Magis, Stephen R. Spindler, David I. K. Martin
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0098635

Gene Expression Profiling Analysis of Bisphenol A-Induced Perturbation in Biological Processes in ER-Negative HEK293 Cells
Cited by: 20
Author(s): Rong Yin, Liang Gu, Min Li, Cizhong Jiang, Tongcheng Cao, Xiaobai Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0150768

High Throughput Sequencing Identifies Misregulated Genes in the Drosophila Polypyrimidine Tract-Binding Protein (hephaestus) Mutant Defective in Spermatogenesis
Cited by: 4
Author(s): Vinod Sridharan, Joseph Heimiller, Mark D. Robida, Ravinder Singh
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0128916

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples
Cited by: 41
Author(s): Jonathan Scolnick, Michelle Dimon, I‐Ching Wang, Stephanie C. Huelga, Douglas A. Amorese
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0250669

Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states
Cited by: 1
Author(s): Shaoyi Ji, Zihui Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes
Software Mentions: 2
Published: over 5 years ago

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