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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 5 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 8 years ago

10.1371/journal.ppat.1005166

Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Cited by: 12
Author(s): Seth B. Garren, Yuvabharath Kondaveeti, Michael O. Duff, Gordon G. Carmichael
Software Mentions: 3
Published: about 10 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 13 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 4 years ago

10.1186/s13059-014-0414-2

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: almost 6 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 5 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 6 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 14 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 12 years ago

10.15252/embj.201797038

Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Cited by: 88
Author(s): Massimiliano Manzo, Joël Wirz, Christina M. Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki, Tuncay Baubec
Software Mentions: 3
Published: about 8 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 8 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 17 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 14 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 10 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 7 years ago

10.7717/peerj.4106

Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95
Cited by: 6
Author(s): Daniel F. Frank, Galen W. Miller, Richard E. Connon, Juergen Geist, Pamela J. Lein
Software Mentions: 3
Published: almost 8 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 10 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 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 19 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 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 12 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 6 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 4 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 5 years ago

10.7717/peerj.3640

Expression differences inAphidius ervi(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: about 8 years ago

10.26508/lsa.202000663

Splicing of enhancer-associated lincRNAs contributes to enhancer activity
Cited by: 22
Author(s): Jennifer Y. Tan, Adriano Biasini, Robert S. Young, Ana C. Marques
Software Mentions: 3
Published: over 5 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 6 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 13 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 17 years ago

10.1186/1745-6150-2-34

Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach
Cited by: 5
Author(s): Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli
Software Mentions: 3
Published: almost 18 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 6 years ago

10.1038/s41598-021-89798-w

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities
Cited by: 3
Author(s): Anil Prakash, Moinak Banerjee
Software Mentions: 3
Published: over 4 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 6 years ago

10.3389/fgene.2019.01348

Long Noncoding RNA RAET1K Enhances CCNE1 Expression and Cell Cycle Arrest of Lung Adenocarcinoma Cell by Sponging miRNA-135a-5p
Cited by: 12
Author(s): Chang Zheng, Xuelian Li, Yong Ren, Zhihua Yin, Baosen Zhou
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.02016

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells
Cited by: 10
Author(s): Stephanie D. Byrum, Charity L. Washam, John M. Patterson, Kanan K. Vyas, Kathleen M. Gilbert, Sarah J. Blossom
Software Mentions: 3
Published: about 6 years ago

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: about 5 years ago

10.1093/database/bax009

HopBase: a unified resource for Humulus genomics
Cited by: 27
Author(s): Steven T. Hill, Ramcharan Sudarsanam, Jimmy C. Henning, David A. Hendrix
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.cell.2019.04.038

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins
Cited by: 78
Author(s): Lea H. Gregersen, Richard Mitter, Alejandro P. Ugalde, Takayuki Nojima, Nick J. Proudfoot, Reuven Agami, Aengus Stewart, Jesper Q. Svejstrup
Software Mentions: 3
Published: over 6 years ago

10.1038/cr.2017.134

Derivation of hypermethylated pluripotent embryonic stem cells with high potency
Cited by: 39
Author(s): Siqin Bao, Walfred W.C. Tang, Baojiang Wu, Shinseog Kim, Jingyun Li, Lin Li, Toshihiro Kobayashi, Caroline Lee, Yanglin Chen, Mengyi Wei, Shudong Li, Sabine Dietmann, Fuchou Tang, Xihe Li, M. Azim Surani
Software Mentions: 3
Published: about 8 years ago

10.1534/g3.115.019828

Enrichment of H3K9me2 on Unsynapsed Chromatin inCaenorhabditis elegansDoes Not Targetde NovoSites
Cited by: 14
Author(s): Yiqing Guo, Bing Yang, Yini Li, Xia Xu, Eleanor M. Maine
Software Mentions: 3
Published: about 10 years ago

10.3389/fmicb.2020.596626

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
Cited by: 3
Author(s): Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard Ø. Palsson, M. N. Parenteau
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-020-00876-8

Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets
Cited by: 34
Author(s): Julia Krushkal, Thomas Silvers, William C. Reinhold, Dmitriy Sonkin, Suleyman Vural, John W. Connelly, Sudhir Varma, Paul S. Meltzer, Mark W. Kunkel, Annamaria Rapisarda, David M. Evans, Yves Pommier, Beverly A. Teicher
Software Mentions: 3
Published: over 5 years ago

10.1016/j.dib.2015.10.033

Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model
Cited by: 6
Author(s): Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Distèche, Xinxian Deng
Software Mentions: 3
Published: almost 10 years ago

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: over 4 years ago

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-97350-z

Genetic predisposition to tinnitus in the UK Biobank population
Cited by: 1
Author(s): Madeleine E Urbanek, Jian Zuo
Software Mentions: 3
Published: about 4 years ago

10.1093/g3journal/jkab163

Nuku, a family of primate retrocopies derived from KU70
Cited by: 0
Author(s): Paul A. Rowley, Aisha Ellahi, Kyudong Han, Jagdish Suresh Patel, James T. Van Leuven, Sara L. Sawyer
Software Mentions: 3
Published: over 4 years ago

10.1038/celldisc.2015.8

The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells
Cited by: 26
Author(s): Robert Liefke, Yang Shi
Software Mentions: 3
Published: over 10 years ago

10.1038/s41398-021-01360-4

Genome wide association study identifies four loci for early onset schizophrenia
Cited by: 12
Author(s): Shuxia Guo, Jiewei Liu, Wenqiang Li, Yongfeng Yang, Luxian Lv, Xiao Xiao, Ming Li, Fanglin Guan, Xiong‐Jian Luo
Software Mentions: 3
Published: over 4 years ago

10.3390/genes9090424

Human Age Prediction Based on DNA Methylation Using a Gradient Boosting Regressor
Cited by: 41
Author(s): Xingyan Li, Weidong Li, Yan Xu
Software Mentions: 3
Published: about 7 years ago

10.3389/fnhum.2018.00249

Measuring Mindfulness: A Psychophysiological Approach
Cited by: 14
Author(s): Vladimir Bostanov, Lilian Ohlrogge, Rita Britz, Martin Hautzinger, Boris Kotchoubey
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2018.00603

Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment
Cited by: 20
Author(s): Cory H. White, Nadejda Beliakova-Bethell, Steven M. Lada, Michael S. Breen, Tara Hurst, Celsa A. Spina, Douglas D. Richman, John Frater, Gkikas Magiorkinis, Christopher H. Woelk
Software Mentions: 3
Published: over 7 years ago

10.3389/fnmol.2017.00283

RNA-Sequencing Analysis Reveals a Regulatory Role for Transcription Factor Fezf2 in the Mature Motor Cortex
Cited by: 6
Author(s): Alison J Clare, Hollie E. Wicky, Ruth M. Empson, Stephanie M. Hughes
Software Mentions: 3
Published: about 8 years ago

10.1161/CIRCRESAHA.120.316770

Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics
Cited by: 239
Author(s): Marie A.C. Depuydt, K.H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, Saskia C.A. de Jager, Folkert W. Asselbergs, Gert J. de Borst, Einari Aavik, Tapio Lönnberg, Esther Lutgens, Christopher K. Glass, Hester M. den Ruijter, Minna U. Kaikkonen, Ilze Bot, Bram Slütter, Sander W. van der Laan, Seppo Ylä‐Herttuala, Michal Mokrý, Johan Kuiper, Menno P.J. de Winther, Gérard Pasterkamp
Software Mentions: 3
Published: about 5 years ago

10.3390/cells8060623

Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates
Cited by: 10
Author(s): Pavel Dvořák, Sarah Leupen, Pavel Souček
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2019.00667

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation
Cited by: 11
Author(s): Satyajeet P. Khare, Ankitha Shetty, Rahul Biradar, Indumathi Patta, Zhi Chen, Ameya Sathe, Puli Chandramouli Reddy, Riitta Lahesmaa, Sanjeev Galande
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2020.108533

USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells
Cited by: 10
Author(s): Paul van den Berk, Cesare Lancini, Michela Serresi, María Pilar Sánchez-Bailón, Danielle Hulsman, Colin C. Pritchard, Ji‐Ying Song, Matthias Jürgen Schmitt, Ellen Tanger, Oliver Popp, Philipp Mertins, Ivo J. Huijbers, Heinz Jacobs, Maarten van Lohuizen, Gaetano Gargiulo, Elisabetta Citterio
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2019.00660

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis
Cited by: 47
Author(s): Néstor Vázquez Bernat, Martin Corcoran, Uta Hardt, Mateusz Kaduk, Ganesh E. Phad, Marcel Martin, Gunilla B. Karlsson Hedestam
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: about 4 years ago

10.1016/j.stemcr.2020.01.004

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media
Cited by: 13
Author(s): Baojiang Wu, Lin Li, Bojiang Li, Junpeng Gao, Yanglin Chen, Mengyi Wei, Zhiqing Yang, Baojing Zhang, Shudong Li, Kexin Li, Changshan Wang, M. Azim Surani, Xihe Li, Fuchou Tang, Siqin Bao
Software Mentions: 3
Published: almost 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 5 years ago

10.3390/cells9061435

Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats
Cited by: 13
Author(s): Yu‐Chin Lien, Paul Zhiping Wang, Xueqing Maggie Lu, Rebecca A. Simmons
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers12030764

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability
Cited by: 41
Author(s): Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
Software Mentions: 3
Published: over 5 years ago

10.1186/1751-0473-6-2

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
Cited by: 55
Author(s): Guiyin Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
Software Mentions: 3
Published: almost 15 years ago

10.3390/cancers11030284

Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature
Cited by: 15
Author(s): Bartosz Wojtaś, Bartłomiej Gielniewski, Kamil Wojnicki, Marta Maleszewska, Shamba S. Mondal, Paweł Nauman, Wiesława Grajkowska, Rainer Glaß, Ulrich Schüller, Christel Herold‐Mende, Bożena Kamińska
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-019-0488-1

Systematic discovery of conservation states for single-nucleotide annotation of the human genome
Cited by: 16
Author(s): Adriana Arneson, Jason Ernst
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-017-0344-4

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals
Cited by: 27
Author(s): Donia Macartney-Coxson, Miles C. Benton, R. A. J. Blick, Richard S. Stubbs, R. D. Hagan, Michael A. Langston
Software Mentions: 3
Published: over 8 years ago

10.3389/fimmu.2021.636061

Human β-Defensin 2 Mutations Are Associated With Asthma and Atopy in Children and Its Application Prevents Atopic Asthma in a Mouse Model
Cited by: 10
Author(s): Natascha Borchers, Elisangela Santos-Valente, Antoaneta A. Toncheva, Jan Wehkamp, André Franke, Vincent D. Gaertner, Peter Nordkild, Jon Genuneit, Benjamin Anderschou Holbech Jensen, Michael Kabesch
Software Mentions: 3
Published: over 4 years ago

10.3389/fphys.2020.587358

Transcriptional Programs Driving Shear Stress-Induced Differentiation of Kidney Proximal Tubule Cells in Culture
Cited by: 18
Author(s): Hyun Jung Park, Zhenjiang Fan, Yinge Bai, Qidong Ren, Youssef Rbaibi, Kimberly R. Long, Megan L. Gliozzi, Natalie Rittenhouse, Joseph Locker, Amanda C. Poholek, Ora A. Weisz
Software Mentions: 3
Published: about 5 years ago

10.1016/j.celrep.2018.07.104

Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3′ End RNA-Seq
Cited by: 9
Author(s): Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.01333

AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States
Cited by: 34
Author(s): Lingling Da, Yue Liu, Jiaotong Yang, Tian Tian, Jiajie She, Xuelian Ma, Wenying Xu, Zhen Su
Software Mentions: 3
Published: about 6 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 6 years ago

10.1186/1756-8722-6-25

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia
Cited by: 12
Author(s): Maoxiang Qian, Ji Wen, Xuehua Zhu, Xiaohong Jia, Xian‐Wen Yang, Yanzhi Du, Kankan Wang, Ji Zhang
Software Mentions: 3
Published: over 12 years ago

10.3390/cancers13133176

Epigenetic Upregulation of MAGE-A Isoforms Promotes Breast Cancer Cell Aggressiveness
Cited by: 4
Author(s): Chaeun Oh, Hwa Ryeon Kim, Seungmin Oh, Je Yeong Ko, Yesol Kim, Keunsoo Kang, Young Yang, Jongmin Kim, Jae Seok Roe, Kyung Hyun Yoo
Software Mentions: 3
Published: over 4 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 4 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41419-019-1892-7

Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein
Cited by: 7
Author(s): Jung S. Byun, Samson Park, Dae Ik Yi, Jee-Hye Shin, Sara Gil Hernandez, Stephen M. Hewitt, Marc C. Nicklaus, Megan L. Peach, Laura Guasch, Binwu Tang, Lalage M. Wakefield, Tingfen Yan, Ambar Caban, Alana Jones, Mohamed Kabbout, Nasreen A. Vohra, Anna María Nápoles, Sandeep K. Singhal, Ryan Yancey, Adriana De Siervi, Kevin Gardner
Software Mentions: 3
Published: about 6 years ago

10.2196/resprot.9639

A Web-Based Telemanagement System for Patients With Complex Inflammatory Bowel Disease: Protocol for a Randomized Controlled Clinical Trial
Cited by: 9
Author(s): Mariam Aguas, Javier del Hoyo, Raquel Faubel, Diana Muñoz, Dana A. Dominguez, Guillermo Bastida, Belén Navarro, Alejandra Barrios, Bernardo Valdivieso, Marisa Correcher, Pilar Nos
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphar.2019.00050

Semantic Queries Expedite MedDRA Terms Selection Thanks to a Dedicated User Interface: A Pilot Study on Five Medical Conditions
Cited by: 3
Author(s): Julien Souvignet, Gunnar Declerck, Béatrice Trombert-Paviot, Hadyl Asfari, Marie-Christine Jaulent, Cédric Bousquet
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2020.00538

5-Azacytidine Potentiates Anti-tumor Immunity in a Model of Pancreatic Ductal Adenocarcinoma
Cited by: 11
Author(s): Nancy D. Ebelt, Edith Zuniga, B. Lamar Johnson, Don J. Diamond, Edwin R. Manuel
Software Mentions: 3
Published: over 5 years ago

10.1534/g3.117.043752

Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression
Cited by: 23
Author(s): Biao Zeng, Luke R. Lloyd‐Jones, Alexander Holloway, Urko M. Marigorta, Andres Metspalu, Grant W. Montgomery, Tõnu Esko, Kenneth L. Brigham, Arshed A Quyyumi, Youssef Idaghdour, Jian Yang, Peter M. Visscher, Joseph E. Powell, Greg Gibson
Software Mentions: 3
Published: over 8 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.54782

Epigenetic regulation of Wnt7b expression by the cis-acting long noncoding RNA Lnc-Rewind in muscle stem cells
Cited by: 17
Author(s): Andrea Cipriano, Martina Macino, Giulia Buonaiuto, Tiziana Santini, Beatrice Biferali, Giovanna Peruzzi, Alessio Colantoni, Chiara Mozzetta, Monica Ballarino
Software Mentions: 2
Published: almost 5 years ago

10.1534/g3.112.003194

Microarray-Based Capture of Novel Expressed Cell Type–Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Cited by: 0
Author(s): Xiaojing Hong, Harshavardhan Doddapaneni, Josep M. Comeron, Matthew J. Rodesch, Heather A. Halvensleben, Chung Yi Nien, F. Bolei, Raghu Metpally, Todd Richmond, Thomas Albert, J. Robert Manak
Software Mentions: 2
Published: over 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

10.1038/cr.2017.25

De novo DNA methylation during monkey pre-implantation embryogenesis
Cited by: 42
Author(s): Fei Gao, Yuyu Niu, Yi Sun, Hanlin Lu, Yongchang Chen, Siguang Li, Yu Kang, Yuan Luo, Chenyang Si, Juehua Yu, Li Chang, Nianqin Sun, Wei Si, Hong Wang, Weizhi Ji, Tao Tan
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.115.021386

Identification of Genes Uniquely Expressed in the Germ-Line Tissues of the Jewel WaspNasonia vitripennis
Cited by: 15
Author(s): Patrick M. Ferree, Christopher Fang, Mariah Mastrodimos, Bruce A. Hay, Henry Amrhein, Omar S. Akbari
Software Mentions: 2
Published: almost 10 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

10.1038/s41422-021-00477-x

Formative pluripotent stem cells show features of epiblast cells poised for gastrulation
Cited by: 42
Author(s): Xiaoxiao Wang, Yunlong Xiang, Yang Yu, Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh‐Chang, Hongmei Wang, Naihe Jing, Wei Xie, Lei Li
Software Mentions: 2
Published: over 4 years ago

10.1016/j.cellsig.2007.01.010

Genomic tagging of endogenous Type IIβ Phosphatidylinositol 5-phosphate 4-kinase in DT40 cells reveals a nuclear localisation
Cited by: 31
Author(s): Jonathan P. Richardson, Minchuan Wang, Jonathan H. Clarke, Ketan Patel, Robin F. Irvine
Software Mentions: 2
Published: over 18 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

10.3390/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

10.1534/g3.118.200901

Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14
Cited by: 14
Author(s): Daniel Miller, Carmy Forney, Mark Rochman, Stacey A Cranert, Jeffery Habel, Jeffrey K. Rymer, Arthur Lynch, Connor Schroeder, Josh Lee, Amber Sauder, Quinton Smith, Mehak Chawla, Michael Trimarchi, Xiaoming Lu, Ellen Fjellman, Michael Brusilovsky, Artem Barski, Stephen N. Waggoner, Matthew T. Weirauch, Marc E. Rothenberg, Leah C. Kottyan
Software Mentions: 2
Published: over 6 years ago

10.1093/database/bav103

WaspAtlas: aNasonia vitripennisgene database and analysis platform
Cited by: 17
Author(s): Nathaniel J. Davies, Eran Tauber
Software Mentions: 2
Published: almost 11 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

10.1093/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

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