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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: almost 6 years ago

10.1186/s12915-019-0674-0

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
Cited by: 24
Author(s): Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel J. Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce B. J. van Meurs, Rick Jansen, Peter A.C. ’t Hoen, Andrew J. Sharp, Szymon M. Kiełbasa
Software Mentions: 3
Published: over 7 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 14 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 12 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 12 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
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 7 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: about 9 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 13 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 18 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 20 years ago

10.1186/1471-2164-15-86

Finding the missing honey bee genes: lessons learned from a genome upgrade
Cited by: 349
Author(s): Christine G. Elsik, Kim C. Worley, Anna Bennett, Martin Beye, Francisco Câmara, Christopher P. Childers, Dirk C. de Graaf, Griet Debyser, Jixin Deng, Bart Devreese, Eran Elhaik, Jay D. Evans, Leonard J. Foster, Dan Graur, Roderic Guigó, Katharina J. Hoff, Michael Holder, Matthew E. Hudson, Greg J. Hunt, Huaiyang Jiang, Vandita Joshi, Radhika S. Khetani, Peter Kosarev, Christie Kovar, Jian Ma, Ryszard Maleszka, Robin F. A. Moritz, Monica Muñoz-Torres, Terence Murphy, Donna M. Muzny, Irene Newsham, Justin Reese, Hugh M. Robertson, Gene E. Robinson, Olav Rueppell, Victor Solovyev, Mario Stanke, Eckart Stolle, Jennifer M. Tsuruda, Matthias Van Vaerenbergh, Robert M. Waterhouse, Daniel Weaver, Charles W. Whitfield, Yuanqing Wu, Evgeny M. Zdobnov, Lan Zhang, Dianhui Zhu, Richard A. Gibbs
Software Mentions: 3
Published: almost 13 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 15 years ago

10.1186/s12864-018-4556-6

The deregulated microRNAome contributes to the cellular response to aneuploidy
Cited by: 12
Author(s): Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann, Zuzana Storchová
Software Mentions: 3
Published: over 8 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 7 years ago

10.1186/1471-2148-10-90

Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes
Cited by: 56
Author(s): Chenhong Li, Jean-Jack M. Riethoven, Lan Ma
Software Mentions: 3
Published: almost 17 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: almost 17 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 7 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 15 years ago

10.1186/s12864-016-2539-z

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Cited by: 117
Author(s): Laurence Ettwiller, John A. Buswell, Erbay Yigit, Ira Schildkraut
Software Mentions: 3
Published: over 10 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 7 years ago

10.1186/s12864-015-2285-7

cChIP-seq: a robust small-scale method for investigation of histone modifications
Cited by: 13
Author(s): Cristina Valensisi, Jo Ling Liao, Colin Andrus, Stephanie L. Battle, R. David Hawkins
Software Mentions: 3
Published: almost 11 years ago

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 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: over 6 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: about 11 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 6 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 6 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 9 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 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 9 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 8 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: almost 6 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: about 5 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 17 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 14 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 6 years ago

10.7717/peerj.5067

Horizontally transferred genes in the ctenophoreMnemiopsis leidyi
Cited by: 7
Author(s): Alexandra M. Hernandez, Joseph F. Ryan
Software Mentions: 3
Published: over 8 years ago

10.3389/fbioe.2014.00088

Discovery of Proteinâ€“lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
Cited by: 55
Author(s): Junhao Li, Shun Liu, Ling‐Ling Zheng, Jie Wu, Wenju Sun, Zelin Wang, Hui Zhou, Liang‐Hu Qu, Jianhua Yang
Software Mentions: 3
Published: almost 12 years ago

10.3389/fcvm.2018.00159

Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells
Cited by: 22
Author(s): Pierre R. Moreau, Tiit Örd, Nicholas Downes, Henri Niskanen, Maria Bouvy-Liivrand, Einari Aavik, Seppo Ylä‐Herttuala, Minna U. Kaikkonen
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13567-020-00850-5

Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection
Cited by: 18
Author(s): Bee-Oh Lim, Sang–Wook Kim, kyu sang lim, Chang Gi Jeong, Seung Chai Kim, Sang Myeong Lee, Choi Kyu Park, M.F.W. te Pas, Haesu Gho, Tae Hun Kim, Kyung Tai Lee, Won Il Kim, Jun Mo Kim
Software Mentions: 3
Published: about 6 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 8 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 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 14 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 5 years ago

10.3389/fcell.2021.666303

Lgr4 Regulates Oviductal Epithelial Secretion Through the WNT Signaling Pathway
Cited by: 3
Author(s): Xue Tan, Lingling Zhang, Tianqi Li, Jia Zhan, Kun Qiao, Haili Wu, Shenfei Sun, Meina Huang, Fangxi Zhang, Meixing Zhang, Changwei Li, Li R, Hongjie Pan
Software Mentions: 3
Published: about 5 years ago

10.3389/fnagi.2017.00249

DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment
Cited by: 48
Author(s): Lara Ianov, Alberto Riva, Ashok Kumar, Thomas C. Foster
Software Mentions: 3
Published: over 9 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 20 years ago

10.3389/fbioe.2014.00064

Uncovering RNA Editing Sites in Long Non-Coding RNAs
Cited by: 41
Author(s): Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Antonio Montalvo, Graziano Pesole
Software Mentions: 3
Published: almost 12 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: over 11 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 8 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 6 years ago

10.1186/s13072-018-0216-y

The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm
Cited by: 11
Author(s): Dong Cheng, Tingcai Cheng, Xi Yang, Quan Zhang, Jianfeng Fu, Tieshan Feng, Jiao Gong, Qingyou Xia
Software Mentions: 3
Published: about 8 years ago

10.1186/1756-8935-7-35

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes
Cited by: 12
Author(s): Raghunath Chatterjee, Ximiao He, Di Huang, Peter Fitzgerald, Andrew D. Smith, Charles Vinson
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13072-019-0325-2

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans
Cited by: 10
Author(s): Alexis V. Stutzman, April S. Liang, Vera Beilinson, Kohta Ikegami
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13072-020-00350-y

Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver
Cited by: 15
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-017-0123-7

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
Cited by: 64
Author(s): Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark, Clare Stirzaker
Software Mentions: 3
Published: over 9 years ago

10.1186/s13072-020-00338-8

The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure
Cited by: 6
Author(s): Dana M. Freeman, Dan Lou, Yanqiang Li, Suzanne N. Martos, Zhibin Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-021-00386-8

Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
Cited by: 20
Author(s): Bradley P. Balaton, Oriol Fornés, Wyeth W. Wasserman, Carolyn J. Brown
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-016-1227-y

PGen: large-scale genomic variations analysis workflow and browser in SoyKB
Cited by: 25
Author(s): Yang Liu, Saad Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, João Vitor Maldonado dos Santos, Babu Valliyodan, Prasad Calyam, Nirav Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi
Software Mentions: 3
Published: about 10 years ago

10.15252/embr.201745000

<scp>KAP</scp> 1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control
Cited by: 83
Author(s): Christopher H.C. Tie, Liane Fernandes, Lucía Conde, Luisa Robbez‐Masson, Rebecca P. Sumner, Thomas P. Peacock, Maria T. Rodriguez-Plata, Greta Mickute, Robert J. Gifford, Greg J. Towers, Javier Herrero, Helen M. Rowe
Software Mentions: 3
Published: over 8 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 9 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 8 years ago

10.15252/emmm.201606711

Gene signature driving invasive mucinous adenocarcinoma of the lung
Cited by: 72
Author(s): Minzhe Guo, Koichi Tomoshige, Michael Meister, Thomas Muley, Takuya Fukazawa, Tomoshi Tsuchiya, Rebekah Karns, Arne Warth, Iris M. Fink-Baldauf, Takeshi Nagayasu, Yoshio Naomoto, Yan Xu, Marcus Mall, Yutaka Maeda
Software Mentions: 3
Published: over 9 years ago

10.1002/ece3.484

Cis‐regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch ( Carpodacus mexicanus )
Cited by: 11
Author(s): Niclas Backström, Daria Shipilina, Mozes P. K. Blom, Scott V. Edwards
Software Mentions: 3
Published: over 13 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: over 5 years ago

10.1186/s12864-016-2542-4

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA
Cited by: 6
Author(s): Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert Wilson, Chadrick E. Denlinger, Dennis K. Watson, Paul E. Anderson
Software Mentions: 3
Published: over 10 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 18 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 7 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 9 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: over 5 years ago

10.1080/15592294.2018.1429857

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta
Cited by: 34
Author(s): Sungsam Gong, Michelle D. Johnson, Justyna Dopierała, Francesca Gaccioli, Ulla Sovio, Miguel Constância, Gordon C. S. Smith, D. Stephen Charnock-Jones
Software Mentions: 3
Published: over 8 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 5 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 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 9 years ago

10.1371/journal.pone.0254444

Using Assessment Design Decision Framework in understanding the impact of rapid transition to remote education on student assessment in health-related colleges: A qualitative study
Cited by: 8
Author(s): Myriam Jaam, Zachariah Nazar, Daniel Rainkie, Diana Alsayed Hassan, Farhat Hussain, Salah Kassab, Abdelali Agouni
Software Mentions: 3
Published: over 5 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 11 years ago

10.1371/journal.pone.0165395

TCGA Expedition: A Data Acquisition and Management System for TCGA Data
Cited by: 56
Author(s): Uma Chandran, Olga Medvedeva, M. Michael Barmada, Philip D. Blood, Anish Chakka, Soumya Luthra, Antonio M. Ferreira, Kim F. Wong, Adrian V. Lee, Zhihui Zhang, Robert Budden, James R. Scott, Annerose Berndt, Jeremy M. Berg, Rebecca S. Jacobson
Software Mentions: 3
Published: about 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 11 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: over 12 years ago

10.1371/journal.pone.0233191

Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene
Cited by: 3
Author(s): Jaafar Alomairi, Anne Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan T M Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean-Christophe Andrau, Denis Puthier, Tom Sexton, Salvatore Spicuglia
Software Mentions: 3
Published: over 6 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 6 years ago

10.1186/1471-2164-15-S9-S2

TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancer
Cited by: 60
Author(s): Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi
Software Mentions: 3
Published: almost 12 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 11 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 11 years ago

10.1371/journal.pone.0073953

Human Melanoma Cells Over-Express Extracellular Matrix 1 (ECM1) Which Is Regulated by TFAP2C
Cited by: 18
Author(s): Geeta Lal, Piedad Gómez Contreras, Mikhail V. Kulak, George W. Woodfield, Thomas B. Bair, Frederick E. Domann, Ronald J. Weigel
Software Mentions: 3
Published: about 13 years ago

10.12688/f1000research.11352.2

New chimeric RNAs in acute myeloid leukemia
Cited by: 8
Author(s): Florence Rufflé, Jérôme Audoux, Anthony Boureux, Sacha Beaumeunier, Jean‐Baptiste Gaillard, Elias Bou Samra, André Mégarbané, Bruno Cassinat, Christine Chomienne, Ronnie Alves, Sébastien Riquier, Nicolas Gilbert, Jean-Marc Lemaı̂tre, Delphine Bacq‐Daian, Anne Laure Bougé, Philippe Naveilhan, Thérèse Commes
Software Mentions: 3
Published: almost 9 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 6 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: over 7 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 10 years ago

10.1038/srep37622

HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Cited by: 33
Author(s): Marco De Martino, Floriana Forzati, Marianna Marfella, Simona Pellecchia, Claudio Arra, Luigi Terracciano, Alfredo Fusco, Francesco Esposito
Software Mentions: 3
Published: almost 10 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 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 7 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 8 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 9 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 7 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 8 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 11 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 6 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 8 years ago

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