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10.1186/s12864-021-07934-2

CAMPAREE: a robust and configurable RNA expression simulator
Cited by: 1
Author(s): Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-017-00176-x

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
Cited by: 28
Author(s): Feinan Wu, Jie Yao
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42686-w

Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls
Cited by: 12
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-14-648

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
Cited by: 80
Author(s): Jeroen Crappé, Wim Van Criekinge, Geert Trooskens, Eisuke Hayakawa, Walter Luyten, Geert Baggerman, Gerben Menschaert
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-021-07512-6

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
Cited by: 15
Author(s): Aleksandra Bliznina, Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Charlotte West, Tanmay Rustagi, Hsiao-Chiao Chien, Saurabh Kumar, Julien Pichon, Charles Plessy, Nicholas M. Luscombe
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-020-6697-7

iMarmot: an integrative platform for comparative and functional genomics of marmots
Cited by: 3
Author(s): Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Zhao Song, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan, Enqi Liu
Software Mentions: 3
Published: over 4 years ago

10.1038/srep22851

An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder
Cited by: 17
Author(s): Leandro Lima, Ana Cecília Feio-dos-Santos, Síntia Belangero, Ary Gadelha, Rodrigo A. Bressan, Giovanni Abrahão Salum, Pedro Mário Pan, Tais Moriyama, Ana Soledade Graeff‐Martins, Ana Carina Tamanaha, Pedro Gomes de Alvarenga, Fernanda Valle Krieger, Bacy Fleitlich-Bilyk, Andrea Parolin Jackowski, Elisa Brietzke, João Ricardo Sato, Guilherme Polanczyk, Jair de Jesus Mari, Gisele Gus Manfro, Maria Conceição do Rosário, Eurípedes Constantino Miguel, Renato Puga, Ana Carolina Tahira, Viviane Neri Souza, Thais Chile, Gisele Rodrigues Gouveia, Sérgio Nery Simões, Xiao Chang, Renata Pellegrino, Lifeng Tian, Joseph T. Glessner, Ronaldo Fumio Hashimoto, Luís Augusto Rohde, Patrick Sleiman, Hákon Hákonarson, Helena Brentani
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1005154

Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
Cited by: 49
Author(s): Tasuku Ito, Yoshiaki Tarutani, Taiko Kim To, Mohamed Kassam, Evelyne Duvernois-Berthet, Sandra Cortijo, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Vincent Colot, Tetsuji Kakutani
Software Mentions: 3
Published: over 9 years ago

10.1038/srep12062

Differential and coherent processing patterns from small RNAs
Cited by: 21
Author(s): Sachin Pundhir, Jan Gorodkin
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1007156

Regulation of circadian clock transcriptional output by CLOCK:BMAL1
Cited by: 112
Author(s): Alexandra J. Trott, Jérôme S. Menet
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: about 11 years ago

10.1038/srep19615

Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells
Cited by: 67
Author(s): Renaud Massart, Sergiy Dymov, Magali Millecamps, Matthew Suderman, Stéphanie Grégoire, Kevin Koenigs, Sebastian Alvarado, Maral Tajerian, Laura S. Stone, Moshe Szyf
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep28396

Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Cited by: 42
Author(s): Eva D’haene, Eva Jacobs, Pieter-Jan Volders, Tim De Meyer, Björn Menten, Sarah Vergult
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1005652

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals
Cited by: 69
Author(s): Gung Wei Chirn, Reazur Rahman, Yuliya A. Sytnikova, Jessica Matts, Mei Zeng, Daniel Gerlach, Michael Yu, Bonnie Berger, Mayumi Naramura, Benjamin T. Kile, Nelson C. Lau
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2148-9-252

Positive selection for the male functionality of a co-retroposed gene in the hominoids
Cited by: 13
Author(s): Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, Liping Wei
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2164-13-147

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions
Cited by: 40
Author(s): Sergio Ruiz‐Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero‐Conde, Gonzalo Goméz-López, James A. Fagin, Alfonso Valencia, David G. Pisano, Pilar Santisteban
Software Mentions: 3
Published: over 12 years ago

10.1530/REP-18-0270

Dynamic changes in gene expression and signalling during trophoblast development in the horse
Cited by: 10
Author(s): Jordan E. Read, Victoria Cabrera-Sharp, Victoria Offord, Samantha Mirczuk, Steve Allen, Robert C. Fowkes, Amanda M. de Mestre
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1004613

Targeted H3R26 Deimination Specifically Facilitates Estrogen Receptor Binding by Modifying Nucleosome Structure
Cited by: 43
Author(s): Michael J. Guertin, Xuesen Zhang, Lynne J. Anguish, Sohyoung Kim, Lyuba Varticovski, John T. Lis, Gordon L. Hager, Scott A. Coonrod
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1006260

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis
Cited by: 73
Author(s): Martha C. Castaño-Betancourt, Dan S. Evans, Yolande F M Ramos, Cindy G. Boer, Sarah Metrustry, Youfang Liu, Wouter den Hollander, Jeroen van Rooij, Virginia B. Kraus, Michelle S. Yau, Braxton D. Mitchell, Kenneth Muir, Albert Hofman, Michael Doherty, Sally Doherty, Weiya Zhang, Robert Kraaij, Fernando Rivadeneira, Elizabeth Barrett‐Connor, Rose A. Maciewicz, N K Arden, Rob G H H Nelissen, Margreet Kloppenburg, Joanne M. Jordan, Michael C. Nevitt, P. Eline Slagboom, Deborah Hart, Floris P. J. G. Lafeber, Unnur Styrkársdóttir, Eleftheria Zeggini, Εvangelos Εvangelou, Tim D. Spector, André G. Uitterlinden, Nancy E Lane, Ingrid Meulenbelt, Ana M. Valdes, Joyce B. J. van Meurs
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.ppat.1007875

Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells
Cited by: 20
Author(s): William J. Neidermyer, Sean P. J. Whelan
Software Mentions: 3
Published: over 5 years ago

10.1186/s13015-018-0133-4

Coordinate systems for supergenomes
Cited by: 10
Author(s): Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1009634

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin
Cited by: 5
Author(s): Salini Konikkat, Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, C. Joel McManus
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1007948

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Cited by: 19
Author(s): Rocı́o Canals, Roy R. Chaudhuri, Rebecca E. Steiner, Siân V. Owen, Natalia Quinones-Olvera, Michael A. Gordon, Michael Baym, Michael Ibba, Jay C. D. Hinton
Software Mentions: 3
Published: about 5 years ago

10.1038/sdata.2018.240

Meta-mining of copy number profiles of high-risk neuroblastoma tumors
Cited by: 26
Author(s): Pauline Depuydt, Jan Koster, Valentina Boeva, Toby Dylan Hocking, Frank Speleman, Gudrun Schleiermacher, Katleen De Preter
Software Mentions: 3
Published: about 6 years ago

10.1186/s40537-015-0018-z

SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information
Cited by: 23
Author(s): Syed Sameed Husain, Alexandr A. Kalinin, Anh Truong, Ivo D. Dinov
Software Mentions: 3
Published: over 9 years ago

10.1038/s41438-020-00347-4

Major-effect candidate genes identified in cultivated strawberry (Fragaria × ananassa Duch.) for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis, key polyphenolic compounds
Cited by: 17
Author(s): Jahn Davik, Kjersti Aaby, Matteo Buti, Muath Alsheikh, Nada Šurbanovski, Stefan Martens, D. Røen, Daniel J. Sargent
Software Mentions: 3
Published: over 4 years ago

10.1016/j.jbc.2021.100784

Generation of an isoform-level transcriptome atlas of macrophage activation
Cited by: 14
Author(s): Apple Cortez Vollmers, Honey Mekonen, Sophia Campos, Susan Carpenter, Christopher Vollmers
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1004290

Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Cited by: 55
Author(s): Roberta L. Hannibal, Edward B. Chuong, Juan Carlos Rivera-Mulia, David M. Gilbert, Anton Valouev, Julie C. Baker
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1009008

Male-biased aganglionic megacolon in the TashT mouse model of Hirschsprung disease involves upregulation of p53 protein activity and Ddx3y gene expression
Cited by: 6
Author(s): Tatiana Cardinal, Karl-F. Bergeron, Rodolphe Soret, Ouliana Souchkova, Christophe Fauré, Amélina Guillon, Nicolas Pilon
Software Mentions: 3
Published: about 4 years ago

10.1111/jcmm.15568

A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air‐liquid interface
Cited by: 10
Author(s): Jenny L. Kerschner, Alekh Paranjapye, Shiyi Yin, Dannielle L. Skander, Gürkan Bebek, Shih Hsing Leir, Ann Harris
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giz073

A large interactive visual database of copy number variants discovered in taurine cattle
Cited by: 21
Author(s): Arun Kommadath, Jason R. Grant, Kirill Krivushin, Adrien M. Butty, C.F. Baes, Tara R. Carthy, D.P. Berry, Paul Stothard
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa001

A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)
Cited by: 8
Author(s): Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, Anna K. Hundsdoerfer
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1002728

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Cited by: 66
Author(s): Julia Heisig, D. F. Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Wei Chia-Lin, Manfred Gessler
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1006581

Differences in the rare variant spectrum among human populations
Cited by: 90
Author(s): Iain Mathieson, David Reich
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-7-42

Gene expression profiling of Naïve sheep genetically resistant and susceptible to gastrointestinal nematodes
Cited by: 87
Author(s): Orla M. Keane, Amonida Zadissa, Theresa Wilson, D. L. Hyndman, G. J. Greer, David Baird, Alan McCulloch, A. M. Crawford, John C. McEwan
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-021-02409-9

Evolution of mouse circadian enhancers from transposable elements
Cited by: 29
Author(s): Julius Judd, Hayley Sanderson, Cédric Feschotte
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: about 10 years ago

10.3390/cells10092375

Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis
Cited by: 10
Author(s): Nicolas Buisine, Alexis Grimaldi, Vincent Jonchère, Muriel Rigolet, Corinne Blugeon, Juliette Hamroune, Laurent M. Sachs
Software Mentions: 3
Published: about 3 years ago

10.1093/gbe/evaa228

Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Cited by: 5
Author(s): Alex Dornburg, Zheng Wang, Junrui Wang, Elizabeth S. Mo, Francesc López-Giráldez, Jeffrey P. Townsend
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1004566

Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation
Cited by: 174
Author(s): Relja Popovic, Eva Martínez-García, Ευγενία Γιαννοπούλου, Quanwei Zhang, Qingyang Zhang, Teresa Ezponda, Mrinal Y. Shah, Yupeng Zheng, Christine M. Will, Eliza C. Small, Youjia Hua, Marinka Bulic, Yanwen Jiang, Matteo Carrara, Raffaele Calogero, William L. Kath, Neil L. Kelleher, Ji Ping Wang, Olivier Elemento, Jonathan D. Licht
Software Mentions: 3
Published: about 10 years ago

10.1186/s13059-020-02201-1

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Cited by: 28
Author(s): Yue Feng, Yao Wang, Xiangnan Wang, Xiaohong He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie, Hanhui Ma
Software Mentions: 3
Published: almost 4 years ago

10.1074/mcp.O115.048777

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*
Cited by: 28
Author(s): Jun Fan, Shyamasree Saha, Gary Barker, Kate J Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pcbi.1007274

A benchmark of computational CRISPR-Cas9 guide design methods
Cited by: 23
Author(s): Jacob Bradford, Dimitri Perrin
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-020-02186-x

Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Cited by: 17
Author(s): Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qianqian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang, Yue‐Qin Chen
Software Mentions: 3
Published: about 4 years ago

10.1186/s12943-020-01293-4

Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine
Cited by: 154
Author(s): Simeng Wen, Yulei Wei, Chong Zen, Wei Xiong, Yuanjie Niu, Yu Zhao
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12885-017-3252-2

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns
Cited by: 47
Author(s): Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar Gulzar, Devin Absher, Sara J. Cooper, James D. Brooks, R Myers
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-4869-5

Limitations of alignment-free tools in total RNA-seq quantification
Cited by: 61
Author(s): Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz, Claus O. Wilke
Software Mentions: 3
Published: over 6 years ago

10.1186/gb-2013-14-7-r72

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Cited by: 18
Author(s): Robin P. Smith, Samantha J. Riesenfeld, Alisha K. Holloway, Qiang Li, Karl K. Murphy, Natalie M. Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S. Pollard, Nadav Ahituv
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-016-0924-1

JBrowse: a dynamic web platform for genome visualization and analysis
Cited by: 595
Author(s): Robert Buels, Eric Yao, Colin Diesh, Richard D. Hayes, Monica Muñoz-Torres, Gregg Helt, David Goodstein, Christine G. Elsik, Suzanna Lewis, Lincoln Stein, Ian Holmes
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-019-0699-9

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing
Cited by: 14
Author(s): Xiaojian Shao, Marie Hudson, Inés Colmegna, Celia Greenwood, Marvin J. Fritzler, Philip Awadalla, Tomi Pastinen, Sasha Bernatsky
Software Mentions: 3
Published: over 5 years ago

10.1186/gb-2014-15-1-r3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Cited by: 76
Author(s): Ian M. Silverman, Liancheng Fan, A Vinogradov Alexander, Loyal A. Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory
Software Mentions: 3
Published: almost 11 years ago

10.1186/gb-2012-13-8-r75

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Cited by: 220
Author(s): Alayne Brunner, Andrew H. Beck, Badreddin Edris, Robert T. Sweeney, Shirley Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W. Foley, Daniela Witten, Craig P. Giacomini, Ryan A. Flynn, Jonathan R. Pollack, Robert Tibshirani, Howard Y. Chang, Matt van de Rijn, Robert B. West
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-021-07421-8

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Cited by: 4
Author(s): Junling Dou, F.S. Schenkel, Lirong Hu, Adnan Khan, Muhammad Zahoor Khan, Ying Yu, Yajing Wang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1005720

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
Cited by: 16
Author(s): Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: over 8 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: about 15 years ago

10.1186/s12885-021-07900-x

Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer
Cited by: 7
Author(s): Yan Liu, Huanhuan Chen, Li Tang, Pan Jiang, Feng Yan
Software Mentions: 3
Published: over 3 years ago

10.1186/s13100-021-00233-3

RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Cited by: 17
Author(s): Erica M. Briggs, Wilson McKerrow, Paolo Mita, Jef D. Boeke, Susan K. Logan, David Fenyö
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms7100420

Reduced Virulence of an Introduced Forest Pathogen over 50 Years
Cited by: 6
Author(s): Rosie E. Bradshaw, Shannon Ormond, Pierre‐Yves Dupont, Pranav Chettri, I. Kutay Ozturk, Rebecca McDougal, L. S. Bulman, Murray P. Cox
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2007-8-12-r269

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
Cited by: 90
Author(s): Samuel S. Gross, B. Chuong, Marina Sirota, Serafim Batzoglou
Software Mentions: 3
Published: almost 18 years ago

10.3389/fgene.2018.00132

Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs
Cited by: 10
Author(s): Luis DaSilva, Felipe Beckedorff, Ana C. Ayupe, Murilo Sena Amaral, Vinícius C. Mesel, Alexandre Videira, Eduardo M. Reis, João Carlos Setúbal, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.597943

The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep
Cited by: 14
Author(s): Nicole Groß, Todd D. Taylor, Thomas D. Crenshaw, Hasan Khatib
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2019.01409

LncRNA LUCRC Regulates Colorectal Cancer Cell Growth and Tumorigenesis by Targeting Endoplasmic Reticulum Stress Response
Cited by: 13
Author(s): G.H. Tang, Xue Chen, Jian Ding, Jie Du, Xun Lin, Lu Xia, Jiabian Lian, Yang Feng, Xiu‐Sheng He, Wen Li
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2019.00508

F8 Inversions at Xq28 Causing Hemophilia A Are Associated With Specific Methylation Changes: Implication for Molecular Epigenetic Diagnosis
Cited by: 14
Author(s): Muhammad Ahmer Jamil, Amit Sharma, Nicole Nuesgen, Behnaz Pezeshkpoor, André Heimbach, A. Pavlova, Johannes Oldenburg, Osman El‐Maarri
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00003

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Cited by: 13
Author(s): Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil K. Raghav
Software Mentions: 3
Published: almost 5 years ago

10.1186/gb-2009-10-4-r38

Transcriptional features of genomic regulatory blocks
Cited by: 100
Author(s): Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O. Daub, Yoshihide Hayashizaki, Boris Lenhard
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 9 years ago

10.1097/MD.0000000000012679

Comprehensive assessment gene signatures for clear cell renal cell carcinoma prognosis
Cited by: 11
Author(s): Po-Ya Chang, Zhitong Bing, Jinhui Tian, Jingyun Zhang, Xiuxia Li, Long Ge, Juan Ling, Kun Yang, Yumin Li
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2019.00007

A New Panel-Based Next-Generation Sequencing Method for ADME Genes Reveals Novel Associations of Common and Rare Variants With Expression in a Human Liver Cohort
Cited by: 35
Author(s): Kathrin Klein, Roman Tremmel, Stefan Winter, Sarah Fehr, Florian Battke, Tim Scheurenbrand, Elke Schaeffeler, Saskia Biskup, Matthias Schwab, Ulrich M. Zanger
Software Mentions: 3
Published: almost 6 years ago

10.3389/fendo.2015.00021

Promoter Methylation Status of Ras-Association Domain Family Member in Pheochromocytoma
Cited by: 17
Author(s): Antje Richter, Tobias Zimmermann, Tanja Haag, Sara K. Walesch, Reinhard Dammann
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12915-015-0159-8

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline
Cited by: 58
Author(s): Ho-Su Sin, Andrey V. Kartashov, Kazuteru Hasegawa, Artem Barski, Satoshi H. Namekawa
Software Mentions: 3
Published: over 9 years ago

10.1007/s00335-015-9599-2

A mouse informatics platform for phenotypic and translational discovery
Cited by: 28
Author(s): Natalie Ring, Terrence F. Meehan, Judith A. Blake, James M. Brown, Chao-Kung Chen, Nathalie Conte, Armida Di Fenza, Tanja Fiegel, Neil R. Horner, Julius O. B. Jacobsen, Natasha A. Karp, Thomas N. Lawson, Justin C. Mason, Peter Matthews, Hugh W. Morgan, Mike Relac, Luís Santos, Damian Smedley, Duncan Sneddon, Alice Pengelly, Ilinca Tudose, Jonathan Warren, Henrik Westerberg, Gagarine Yaikhom, Helen Parkinson, Ann‐Marie Mallon
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.8592

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Cited by: 2
Author(s): Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Software Mentions: 3
Published: over 4 years ago

10.1186/1476-511X-13-25

Leptin gene promoter DNA methylation in WNIN obese mutant rats
Cited by: 9
Author(s): Rajender Rao Kalashikam, Padmavathi J. N. Inagadapa, Anju Elizabeth Thomas, Sugeetha Jeyapal, Nappan Veettil Giridharan, Manchala Raghunath
Software Mentions: 3
Published: almost 11 years ago

10.12688/wellcomeopenres.15355.2

GeneDB and Wikidata
Cited by: 2
Author(s): Magnus Manske, Ulrike Böhme, Christoph Püthe, Matthew Berriman
Software Mentions: 3
Published: about 5 years ago

10.3390/v13040544

Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis
Cited by: 4
Author(s): Liana V. Basova, Alexander Lindsey, Anne Marie McGovern, Ronald J. Ellis, Maria Cecília Garibaldi Marcondes
Software Mentions: 3
Published: over 3 years ago

10.3390/v12070783

Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice
Cited by: 9
Author(s): Rita Rebollo, Mariana Galvão Ferrarini, Liane Gagnier, Ying Zhang, Ardian Ferraj, Christine R. Beck, Matthew C. Lorincz, Dixie L. Mager
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.3640

Expression differences in<i>Aphidius ervi</i>(Hymenoptera: Braconidae) females reared on different aphid host species
Cited by: 11
Author(s): Gabriel I. Ballesteros, Juergen Gadau, Fabrice Legeai, Angélica González-González, Blas Lavandero, Jean Simon, Christian C. Figueroa
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2009-10-4-r39

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Cited by: 64
Author(s): Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J. Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O. Daub, Alistair R.R. Forrest
Software Mentions: 3
Published: almost 16 years ago

10.1093/gigascience/giy095

Draft genome assembly of the invasive cane toad, Rhinella marina
Cited by: 56
Author(s): Richard J. Edwards, Daniel Enosi Tuipulotu, Timothy G. Amos, Denis O’Meally, Mark F. Richardson, Tonia Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R. Wilkins, Fernando Sequeira, Lee A. Rollins, Edward C. Holmes, Richard Shine
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-78555-0

Evolutionary divergence of novel open reading frames in cichlids speciation
Cited by: 5
Author(s): Shraddha Puntambekar, Rachel Newhouse, Jaime San-Miguel, Ruchi Chauhan, Grégoire Vernaz, Thomas W. Willis, Matthew T. Wayland, Yagnesh Umrania, Eric A. Miska, Sudhakaran Prabakaran
Software Mentions: 3
Published: almost 4 years ago

10.3389/fcell.2021.682593

Epigenetic Reprogramming Mediated by Maternal Diet Rich in Omega-3 Fatty Acids Protects From Breast Cancer Development in F1 Offspring
Cited by: 13
Author(s): Ata Abbas, Theodore R. Witte, William L. Patterson, Johannes F. Fahrmann, Kai Guo, Junguk Hur, W. Elaine Hardman, Philippe Georgel
Software Mentions: 2
Published: over 3 years ago

10.3390/life11040340

Cross-Validation of Next-Generation Sequencing Technologies for Diagnosis of Chromosomal Mosaicism and Segmental Aneuploidies in Preimplantation Embryos Model
Cited by: 6
Author(s): Anıl Biricik, Ettore Cotroneo, Maria Giulia Minasi, Pierfrancesco Greco, Sara Bono, Matteo Surdo, Federica Lecciso, Mariateresa Sessa, Francesco Fiorentino, Francesca Spinella, Ermanno Greco
Software Mentions: 2
Published: over 3 years ago

10.3389/fcvm.2020.00135

Studies in Zebrafish Demonstrate That CNNM2 and NT5C2 Are Most Likely the Causal Genes at the Blood Pressure-Associated Locus on Human Chromosome 10q24.32
Cited by: 10
Author(s): Krishan Kumar Vishnolia, Celine Hoene, Karim Tarhbalouti, Julian Revenstorff, Zouhair Aherrahrou, Jeanette Erdmann
Software Mentions: 2
Published: about 4 years ago

10.1093/femsec/fiy217

Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in<i>Pasteuria penetrans</i>
Cited by: 6
Author(s): Arohi Srivastava, Sharad Mohan, Tim H. Mauchline, Keith Davies
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-14-84

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury
Cited by: 34
Author(s): Li‐Wei Chang, Andreu Viader, Nobish Varghese, Jacqueline E. Payton, Jeffrey Milbrandt, Rakesh Nagarajan
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12915-019-0702-0

Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants
Cited by: 18
Author(s): Isidro Álvarez‐Escribano, Christoph Sasse, Jin Woo Bok, Hyunsoo Na, Mojgan Amirebrahimi, Anna Lipzen, Wendy Schackwitz, Joel Martin, Kerrie Barry, Gabriel Gutiérrez, Sara Cea-Sánchez, Ana T. Marcos, Igor V. Grigoriev, Nancy P. Keller, Gerhard H. Braus, David Cánovas
Software Mentions: 2
Published: about 5 years ago

10.12688/f1000research.2-288.v1

JSim, an open-source modeling system for data analysis
Cited by: 35
Author(s): Erik Butterworth, Bartholomew E. Jardine, Gary M. Raymond, Maxwell Lewis Neal, James B. Bassingthwaighte
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-13-394

Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
Cited by: 23
Author(s): Radhika Das, Nathan Anderson, Mary Ellen Koran, Jennifer R. Weidman, Tarjei S. Mikkelsen, Michael Kamal, Susan K. Murphy, Kerstin Linblad-Toh, John M. Greally, Randy L. Jirtle
Software Mentions: 2
Published: over 12 years ago

10.1111/eva.12717

Genomic clustering of fitness-affecting mutations favors the evolution of chromosomal instability
Cited by: 3
Author(s): Yevgeniy Raynes, Daniel Weinreich
Software Mentions: 2
Published: about 6 years ago

10.1096/fj.14-255729

Autocrine androgen action is essential for Leydig cell maturation and function, and protects against late‐onset Leydig cell apoptosis in both mice and men
Cited by: 72
Author(s): Laura O’Hara, Kerry J. McInnes, Ioannis Simitsidellis, Stephanie Morgan, Nina Atanassova, Jolanta Słowikowska-Hilczer, Krzysztof Kula, Maria Szarras‐Czapnik, Louise Milne, Rod T Mitchell, Lee B. Smith
Software Mentions: 2
Published: about 10 years ago

10.3389/fcell.2021.650344

Genetic Screening Revealed Latent Keratoconus in Asymptomatic Individuals
Cited by: 6
Author(s): Shihao Chen, Xing-Yong Li, Jiajia Jin, Ren‐Juan Shen, Jian-Yang Mao, Feifei Cheng, Zhen‐Ji Chen, Emmanouela Linardaki, Stavroula Voulgaraki, Ioannis M. Aslanides, Zi‐Bing Jin
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-017-3650-5

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation
Cited by: 75
Author(s): Philip Kelleher, Francesca Bottacini, Jennifer Mahony, Kieran N. Kilcawley, Douwe van Sinderen
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-16-S8-S8

Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)
Cited by: 3
Author(s): Samuel K. Handelman, Michał Seweryn, Ryan M. Smith, Katherine E. Hartmann, Daqing Wang, Maciej Pietrzak, Andrew D. Johnson, Andrzej Kloczkowski, Wolfgang Sadée
Software Mentions: 2
Published: over 9 years ago

10.1186/1756-8935-6-13

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes
Cited by: 65
Author(s): Adam Blattler, Lijing Yao, Yao Wang, Zhenqing Ye, Victor X. Jin, Peggy J. Farnham
Software Mentions: 2
Published: over 11 years ago

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