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10.1371/journal.pone.0138381

The Role of ARF6 in Biliary Atresia
Cited by: 51
Author(s): Mylarappa Ningappa, Juhoon So, Joseph T. Glessner, Chethan Ashokkumar, Sarangarajan Ranganathan, Jin‐Young Min, Brandon W. Higgs, Qing Sun, Kimberly Haberman, Lori Schmitt, Sílvia Vilarinho, Pramod K. Mistry, Gerard Vockley, Anil Dhawan, George K. Gittes, Hákon Hákonarson, Ronald Jaffe, Shankar Subramaniam, Donghun Shin, Rakesh Sindhi
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.11752

A new view of transcriptome complexity and regulation through the lens of local splicing variations
Cited by: 338
Author(s): Jorge Vaquero-Garcia, Alejandro Barrera, Matthew R. Gazzara, Juan González-Vallinas, Nicholas F. Lahens, John B. Hogenesch, Kristen W. Lynch, Yoseph Barash
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.celrep.2015.10.030

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis
Cited by: 33
Author(s): Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung Han Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder‐Münster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, Craig L. Peterson
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.19942

Genome-wide identification of neuronal activity-regulated genes in Drosophila
Cited by: 67
Author(s): Chen Xiao, Reazur Rahman, Fang Guo, Michael Rosbash
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/baw162

viruSITE—integrated database for viral genomics
Cited by: 47
Author(s): Matej Stano, Gábor Beke, Ľuboš Klučár
Software Mentions: 2
Published: almost 10 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: almost 9 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: almost 9 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 10 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 10 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: over 10 years ago

10.1371/journal.pone.0120296

Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAs
Cited by: 3
Author(s): Sang Woo Kim, Elane Fishilevich, Gustavo Arango-Argoty, Yuefeng Lin, Guodong Liu, Zhihua Li, A. Paula Monaghan, Mark Nichols, Bino John
Software Mentions: 2
Published: over 10 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: almost 11 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 11 years ago

10.1111/cmi.12890

Systematic gene overexpression inCandida albicansidentifies a regulator of early adaptation to the mammalian gut
Cited by: 35
Author(s): Sadri Znaidi, Lasse van Wijlick, Arturo Hernández‐Cervantes, Natacha Sertour, Jean‐Luc Desseyn, Frédéric Vincent, Ralitsa Atanassova, Valérie Gouyer, Carol A. Munro, Sophie Bachellier‐Bassi, Frédéric Dalle, Thierry Jouault, Marie‐Elisabeth Bougnoux, Christophe d’Enfert
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.09571

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Cited by: 95
Author(s): J. Ż̷ylicz, Sabine Dietmann, Ufuk Günesdogan, Jim Hackett, Delphine Cougot, Caroline Lee, M. Azim Surani
Software Mentions: 2
Published: about 10 years ago

10.1093/database/bat034

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
Cited by: 120
Author(s): Deeksha Bhartiya, Koustav Pal, Sourav Ghosh, Shruti Kapoor, Saakshi Jalali, Bharat Panwar, Sakshi Jain, Satish Sati, Shantanu Sengupta, Chetana Sachidanandan, Gajendra P. S. Raghava, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 2
Published: almost 13 years ago

10.7554/eLife.01257

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
Cited by: 262
Author(s): Liana F. Lareau, Dustin H Hite, Gregory J. Hogan, Patrick O. Brown
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.00994

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity
Cited by: 145
Author(s): Alyson Ashe, Tony Bélicard, Jérémie Le Pen, Peter Sarkies, Lise Frézal, Nicolas J Lehrbach, Marie‐Anne Félix, Eric A. Miska
Software Mentions: 2
Published: about 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: almost 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: almost 12 years ago

10.1371/journal.pone.0220378

Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells
Cited by: 12
Author(s): Pia Bagamasbad, Jose Ezekiel C. Espina, Joseph R. Knoedler, Arasakumar Subramani, Ariel J. Harden, Robert J. Denver
Software Mentions: 2
Published: over 6 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 12 years ago

10.1371/journal.pone.0165176

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family
Cited by: 44
Author(s): Saura R. Silva, Yani C. A. Diaz, Helen Alves Penha, Daniel Guariz Pinheiro, Camila Cesário Fernandes, Vitor F. O. Miranda, Todd P. Michael, Alessandro M. Varani
Software Mentions: 2
Published: about 9 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: almost 7 years ago

10.1186/s13148-018-0470-7

Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma
Cited by: 15
Author(s): Yu Cao, Katherine Green, Steve Quattlebaum, Ben Milam, Ling Lu, Dexiang Gao, Hui He, Ningning Li, Liwei Gao, F. De Havilland Hall, Matthew Whinery, Elyse Handley, Yi Ma, Tao Xu, Feng Jin, Jing Xiao, Minjie Wei, Derek E. Smith, Sophia Bornstein, Neil D. Gross, Dohun Pyeon, John I. Song, Shi Lu
Software Mentions: 2
Published: over 7 years ago

10.3390/genes12081249

Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector
Cited by: 7
Author(s): Takehito Sugasawa, Takuro Nakano, Shin‐ichiro Fujita, Yuki Matsumoto, Genki Ishihara, Kai Aoki, Koki Yanazawa, S. Ono, Shinsuke Tamai, Lev Manevich, Hiroshi Ueda, Noriyo Ishibashi, Kenshirou Tamai, Yasuharu Kanki, Yasuko Yoshida, Koichi Watanabe, Tohru Takemasa, Yasushi Kawakami, Kazuhiro Takekoshi
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms17111848

IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells
Cited by: 10
Author(s): Giuseppe Fiume, Annarita Scialdone, Francesca Rizzo, Maria Rosaria De Filippo, Carmelo Laudanna, Fabio Albano, Gaetanina Golino, Eleonora Vecchio, Marilena Pontoriero, Selena Mimmi, Simona Ceglia, Antonio Pisano, Enrico Iaccino, Camillo Palmieri, Sergio Paduano, Giuseppe Viglietto, Alessandro Weisz, Giuseppe Scala, Ileana Quinto
Software Mentions: 2
Published: about 9 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 14 years ago

10.1371/journal.pone.0117415

A Non-Parametric Peak Calling Algorithm for DamID-Seq
Cited by: 5
Author(s): Renhua Li, Leonie U. Hempel, Tingbo Jiang
Software Mentions: 2
Published: over 10 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: almost 9 years ago

10.1038/s41421-018-0039-9

DNA methylation reprogramming of functional elements during mammalian embryonic development
Cited by: 43
Author(s): Congru Li, Yong Fan, Guoqiang Li, Xiaocui Xu, Jialei Duan, Rong Li, Xiangjin Kang, Xin Ma, Xuepeng Chen, Youqi Ke, Jie Yan, Ying Lian, Ping Liu, Yue Zhao, Haiquan Zhao, Yaoyong Chen, Yang Yu, Jiang Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0131908

Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish
Cited by: 12
Author(s): Christoph Seiler, Nichole Gebhart, Yong Zhang, Susan A. Shinton, Yuesheng Li, Nicola L. Ross, Xingjun Liu, Qin Li, Alison N. Bilbee, Gaurav K. Varshney, Shawn M. Burgess, Jorune Balciuniene, Darius Balciunas, Richard R. Hardy, Dietmar J. Kappes, David L. Wiest, Jennifer Rhodes
Software Mentions: 2
Published: over 10 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: almost 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: almost 16 years ago

10.3390/genes12020221

Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification
Cited by: 7
Author(s): Michele Reni, Giulio Puleri, Valeria Errichiello, L Manzo, Laura Luzzi, Saverio Potenza, Claudia Strafella, Cristina Peconi, Fabio Nicastro, Valerio Caputo, Emiliano Giardina
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms19061722

Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing
Cited by: 30
Author(s): Yi Liu, Mengxun Li, Xiaochen Bo, Tao Li, Ligeng Ma, Tenjiao Zhai, Tao Huang
Software Mentions: 2
Published: over 7 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: over 9 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: almost 16 years ago

10.1371/journal.pone.0203843

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin
Cited by: 11
Author(s): Shraddha Shrestha, Dong-Ha Oh, J. Keller McKowen, Maheshi Dassanayake, Craig M. Hart
Software Mentions: 2
Published: about 7 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: almost 16 years ago

10.1038/s41419-018-0777-5

An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a
Cited by: 7
Author(s): Jason T. Serviss, Nathanael Andrews, Jimmy Van den Eynden, Felix Clemens Richter, Miranda Houtman, Mattias Vesterlund, Laura Schwarzmueller, Per Johnsson, Erik Larsson, Dan Grandér, Katja Pokrovskaja Tamm
Software Mentions: 2
Published: over 7 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: almost 18 years ago

10.3390/ijms21061908

Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging
Cited by: 13
Author(s): Hongxia Zhang, Kunlin Jin
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0067885

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting
Cited by: 50
Author(s): Hyunsung John Kim, Nader Pourmand
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0011109

Large-Scale Expression Analysis Reveals Distinct MicroRNA Profiles at Different Stages of Human Neurodevelopment
Cited by: 72
Author(s): Brandon Smith, Julie A. Treadwell, Dongling Zhang, Dao Ly, Iain W. McKinnell, P. Roy Walker, Marianna Sikorska
Software Mentions: 2
Published: over 15 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 14 years ago

10.1038/s41419-019-2201-1

Epigenetic priming by Dot1l in lymphatic endothelial progenitors ensures normal lymphatic development and function
Cited by: 11
Author(s): Hyunjin Yoo, Young Jae Lee, Chanhyeok Park, Dabin Son, Dong Yoon Choi, Ji Hyun Park, Hee-Jin Choi, Hyun Woo La, Yun Jung Choi, Eun Hye Moon, Dieter Saur, Hyung Min Chung, Hyuk Song, Jeong Tae, Hoon Jang, Dong Ryul Lee, Chankyu Park, Ok Hee Lee, Ssang-Goo Cho, Seok Ho Hong, Gu Kong, Jin‐Hoi Kim, Yun‐Sang Choi, Kwonho Hong
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12091388

A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review
Cited by: 2
Author(s): Ji Yoon Han, Joonhong Park
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21165831

BrassicaEDB: A Gene Expression Database for Brassica Crops
Cited by: 37
Author(s): Haoyu Chao, Li Tian, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lü
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-04017-8

Tissue-specific expression of p73 and p63 isoforms in human tissues
Cited by: 10
Author(s): Clayton B. Marshall, J. Scott Beeler, Brian D. Lehmann, Paula I. González-Ericsson, Violeta Sánchez, Melinda E. Sanders, Kelli L. Boyd, Jennifer A. Pietenpol
Software Mentions: 2
Published: over 4 years ago

10.18632/genesandcancer.113

Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development
Cited by: 12
Author(s): Meng Chen, Nathaniel Rothman, Yuanqing Ye, Jian Gu, Paul Scheet, Maosheng Huang, David W. Chang, Colin P.N. Dinney, Debra T. Silverman, Jonine D. Figueroa, Stephen J. Chanock, Xifeng Wu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0225801

Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP
Cited by: 7
Author(s): Tõnis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, Ants Kurg
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21249701

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1)
Cited by: 4
Author(s): Peter Q. Nguyen, Kyle Hess, Larissa Smulders, Dat Le, Carolina Briseno, Christina M Chavez, Nikolas Nikolaidis
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22020602

Transposable Elements and Teleost Migratory Behaviour
Cited by: 8
Author(s): Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca, Samuele Greco, Marco Gerdol, Maria Assunta Biscotti
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0041709

Brain Transcriptional Responses to High-Fat Diet in Acads-Deficient Mice Reveal Energy Sensing Pathways
Cited by: 9
Author(s): Claudia Krüger, K. Ganesh Kumar, Randall L. Mynatt, Júlia Vólaufová, Brenda Richards
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0171661

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer
Cited by: 88
Author(s): Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0123261

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets
Cited by: 3
Author(s): Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig
Software Mentions: 2
Published: over 10 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: almost 12 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: almost 5 years ago

10.3390/ijms22168646

PPARγ-Induced Global H3K27 Acetylation Maintains Osteo/Cementogenic Abilities of Periodontal Ligament Fibroblasts
Cited by: 7
Author(s): Hang Yuan, Shigeki Suzuki, Shizu Hirata-Tsuchiya, Akiko Satô, Eiji Nemoto, Masahiro Saito, Hideki Shiba, Satoru Yamada
Software Mentions: 2
Published: over 4 years ago

10.2196/jmir.9644

Online Information Infrastructure Increases Inter-Rater Reliability of Medical Coders: A Quasi-Experimental Study (Preprint)
Cited by: 6
Author(s): Julian Varghese, Sarah Sandmann, Martin Dugas
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0007479

Probe-Level Analysis of Expression Microarrays Characterizes Isoform-Specific Degradation during Mouse Oocyte Maturation
Cited by: 29
Author(s): Jesse Salisbury, Keith W. Hutchison, Karen Wigglesworth, John J. Eppig, Joel H. Graber
Software Mentions: 2
Published: about 16 years ago

10.2196/10227

What People “Like”: Analysis of Social Media Strategies Used by Food Industry Brands, Lifestyle Brands, and Health Promotion Organizations on Facebook and Instagram
Cited by: 106
Author(s): Karen Klassen, Emily S. Borleis, Louis Brennan, Mike Reid, Tracy A. McCaffrey, Megan S C Lim
Software Mentions: 2
Published: over 7 years ago

10.3390/genes12060870

Age Prediction of Human Based on DNA Methylation by Blood Tissues
Cited by: 5
Author(s): Jiansheng Zhang, Hongli Fu, Yan Xu
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0019470

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Cited by: 110
Author(s): Anja Nitzsche, Maciej Paszkowski‐Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, Ingrid de Vries, Li Ding, Norbert Huebner, Matthias Mann, Hendrik G. Stunnenberg, Frank Buchholz
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0054359

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data
Cited by: 37
Author(s): Анна Герасимова, Lukas Chávez, Bin Li, Grégory Seumois, Jason A. Greenbaum, Anjana Rao, Pandurangan Vijayanand, Bjoern Peters
Software Mentions: 2
Published: almost 13 years ago

10.1093/database/bat067

BBGRE: brain and body genetic resource exchange
Cited by: 3
Author(s): Joo Wook Ahn, Abhishek Dixit, Caroline Johnston, Caroline Mackie Ogilvie, David A. Collier, Sarah Curran, Richard Dobson
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0010563

Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers
Cited by: 270
Author(s): Jian-You Liao, Liming Ma, Yanhua Guo, Yuchan Zhang, Hui Zhou, Pengfei Shao, Yue‐Qin Chen, Liang‐Hu Qu
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0029758

Twist1 Directly Regulates Genes That Promote Cell Proliferation and Migration in Developing Heart Valves
Cited by: 40
Author(s): Mary P. Lee, Katherine E. Yutzey
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0000412

The Extrachromosomal EAST Protein of Drosophila Can Associate with Polytene Chromosomes and Regulate Gene Expression
Cited by: 6
Author(s): Martin Wasser, William Chia
Software Mentions: 2
Published: over 18 years ago

10.1093/database/baz009

The radish genome database (RadishGD): an integrated information resource for radish genomics
Cited by: 11
Author(s): Hee‐Ju Yu, Seung-Hoon Baek, Young-Joon Lee, Ara Cho, Jeong‐Hwan Mun
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0031621

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Cited by: 80
Author(s): Satish Sati, Vinay Singh Tanwar, Kalle Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, Sujatha Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
Software Mentions: 2
Published: over 13 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: almost 6 years ago

10.1371/journal.pone.0164632

A Novel Class of Small Molecule Agonists with Preference for Human over Mouse TLR4 Activation
Cited by: 16
Author(s): Jason D. Marshall, Darren Heeke, Eileen Rao, Sean K. Maynard, David C. Hornigold, Christopher McCrae, Neil Fraser, Andrey Tovchigrechko, Li Yu, Nicola Williams, Sarah King, Martin Cooper, Adeline M. Hajjar, Jennifer Woo
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.53447

Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity
Cited by: 25
Author(s): Nicholas Sciascia, Wei Wu, Dali Zong, Yilun Sun, Nancy Wong, Sam John, Darawalee Wangsa, Thomas Ried, Samuel F. Bunting, Yves Pommier, André Nussenzweig
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.17061

Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling
Cited by: 121
Author(s): Krzysztof Brzezinka, Simone Altmann, Hjördis Czesnick, Philippe Naveilhan, Michał Górka, Eileen Benke, Tina Kabelitz, Felix Jähne, Alexander Graf, Christian Kappel, Isabel Bäurle
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.23670

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids
Cited by: 101
Author(s): Sebastián Cánovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano‐Úbeda, Francisco Alberto García–Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey, Pilar Coy
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.41444

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci
Cited by: 35
Author(s): Anand Kumar Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Marija Petrić, Luisa Orsini, Daniel Hebenstreit
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.56697

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
Cited by: 5
Author(s): Jan Hendrik van Weerd, Rajiv A Mohan, Karel van Duijvenboden, Ingeborg B. Hooijkaas, Vincent Wakker, Bastiaan J. Boukens, Phil Barnett, Vincent M. Christoffels
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0255085

Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive
Cited by: 0
Author(s): J. L. Webb, Simon M. Moe, Andrew Bolstad, Elizabeth McNeill
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0228362

Jmjd1c is dispensable for healthy adult hematopoiesis and Jak2V617F-driven myeloproliferative disease initiation in mice
Cited by: 4
Author(s): Hans Felix Staehle, Johannes Heinemann, Albert Gruender, Anne Marie Omlor, Heike L. Pahl, Jonas S. Jutzi
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/bax074

Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo
Cited by: 76
Author(s): Michael Stadler, Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: almost 8 years ago

10.3390/cells1041029

A Novel Type III Endosome Transmembrane Protein, TEMP
Cited by: 1
Author(s): Rajith Aturaliya, Markus C. Kerr, Rohan D. Teasdale
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0214816

SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
Cited by: 21
Author(s): Kerstin Neininger, Tobias Marschall, Volkhard Helms
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.11155

Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway
Cited by: 112
Author(s): Zhiyun Ge, Bao Lin Quek, Karen Beemon, J. Robert Hogg
Software Mentions: 2
Published: almost 10 years ago

10.3390/cancers13133180

Immunity Depletion, Telomere Imbalance, and Cancer-Associated Metabolism Pathway Aberrations in Intestinal Mucosa upon Short-Term Caloric Restriction
Cited by: 0
Author(s): Evan Maestri, Kalina Duszka, Vladimir A. Kuznetsov
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0099069

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry
Cited by: 33
Author(s): Osama Alsmadi, Sumi Elsa John, Gaurav Thareja, Prashantha Hebbar, Dinu Antony, Kazem Behbehani, Thangavel Alphonse Thanaraj
Software Mentions: 2
Published: over 11 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 9 years ago

10.1371/journal.pone.0067222

Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p
Cited by: 10
Author(s): Pontus Eriksson, Mattias Aine, Gottfrid Sjödahl, Johan Staaf, David Lindgren, Mattias Höglund
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0161414

Neuronal Calcium Sensor 1 Has Two Variants with Distinct Calcium Binding Characteristics
Cited by: 8
Author(s): Baisheng Wang, Göran Ramin Boeckel, Larry Huynh, Lien D. Nguyen, Wenxiang Cao, Enrique M. De La Cruz, Edward Kaftan, Barbara E. Ehrlich
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.02224

The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways
Cited by: 200
Author(s): Qingqing Zhu, Lu Song, Guangdun Peng, Na Sun, Jun Chen, Ting Zhang, Nengyin Sheng, Wei Tang, Qian Cheng, Yong Qiao, Ke Tang, Jing–Dong Jackie Han, Jinsong Li, Naihe Jing
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.00426

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice
Cited by: 67
Author(s): Kazuhiro Shimomura, Vivek Kumar, Nobuya Koike, Tae Kyung Kim, Jason Chong, Ethan D. Buhr, Andrew R. Whiteley, Sharon S. Low, Chiaki Omura, Deborah Fenner, Joseph R. Owens, Marc Richards, Seung Hee Yoo, Hee Kyung Hong, Martha Hotz Vitaterna, Joseph Bass, Mathew T. Pletcher, Tim Wiltshire, John B. Hogenesch, Phillip L. Lowrey, Joseph S. Takahashi
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.28590

Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors
Cited by: 10
Author(s): Silvia Peluso, Adam Douglas, Alison Hill, Carlo DeAngelis, Benjamin L. Moore, Graeme R. Grimes, Giulia Petrovich, Abdelkader Essafi, Robert E. Hill
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0026837

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma
Cited by: 95
Author(s): Volkhard Seitz, Peter Butzhammer, Burkhard Hirsch, Jochen Hecht, Ines Gütgemann, Anke Ehlers, Dido Lenze, Elisabeth Oker, Anke Sommerfeld, Edda von der Wall, Christoph König, Christian Zinser, Rainer Spang, Michael Hummel
Software Mentions: 2
Published: about 14 years ago

10.1186/s13073-018-0562-1

Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Cited by: 36
Author(s): Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael W. Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, H Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R. Schweiger
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0131296

BGD: A Database of Bat Genomes
Cited by: 3
Author(s): Jian‐an Fang, Xuan Wang, Shuo Mu, Shuyi Zhang, Dong Dong
Software Mentions: 2
Published: over 10 years ago

10.1186/s13148-017-0386-7

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel
Cited by: 44
Author(s): Luca Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini
Software Mentions: 2
Published: about 8 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: almost 20 years ago

10.7554/eLife.01503

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation
Cited by: 354
Author(s): Ji-Eun Lee, Chaochen Wang, Shiliyang Xu, Young Wook Cho, Lifeng Wang, Xuesong Feng, Anne Baldridge, Vittorio Sartorelli, Lenan Zhuang, Weiqun Peng, Kai Ge
Software Mentions: 2
Published: almost 12 years ago

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