10.1186/1471-2164-15-570

Comparing reference-based RNA-Seq mapping methods for non-human primate data
Cited by: 33
Author(s): Ashlee M. Benjamin, Marshall Nichols, Thomas W. Burke, Geoffrey S. Ginsburg, Joseph E. Lucas
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pcbi.1003501

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Cited by: 75
Author(s): Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
Software Mentions: 3
Published: over 12 years ago

10.1242/dev.199628

LncRNA <i>HBL1</i> is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: over 5 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.1242/bio.031245

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation
Cited by: 18
Author(s): Jian Xu, Benjamin L. Kidder
Software Mentions: 3
Published: over 8 years ago

10.1007/s00125-017-4500-3

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes
Cited by: 121
Author(s): Michele Solimena, Anke M. Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno‐Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B. Wollheim, Gustavo Baretton, Raphaël Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer‐Puttlitz, Ugo Boggi, Hans‐Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xénarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A. Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-020-6482-7

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression
Cited by: 15
Author(s): Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou, Shuisheng Hou
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 10 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: over 11 years ago

10.1038/srep24964

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Cited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 10 years ago

10.3390/biology10090885

Metabolic Regulation of Sugar Assimilation for Lipid Production in Aspergillus oryzae BCC7051 through Comparative Transcriptome Perspective
Cited by: 5
Author(s): Tayvich Vorapreeda, Bhimabol Khongto, Chinae Thammarongtham, Tanawut Srisuk, Kobkul Laoteng
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1002968

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Cited by: 199
Author(s): Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, J Stamatoyannopoulos, Jason Ernst, M Kellis, Bing Ren
Software Mentions: 3
Published: over 13 years ago

10.3390/ijms22189693

Fetal Brain Elicits Sexually Conflicting Transcriptional Response to the Ablation of Uterine Forkhead Box A2 (Foxa2) in Mice
Cited by: 5
Author(s): Pramod Dhakal, Monica Strawn, Ananya Samal, Susanta K. Behura
Software Mentions: 3
Published: about 5 years ago

10.3390/ph14010041

Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients
Cited by: 4
Author(s): Hana Votavová, Zuzana Urbanová, David Kundrát, Michaela Dostálová Merkerová, Martin Vostrý, Monika Hruba, Jaroslav Čermák, Monika Beličková
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: about 10 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 10 years ago

10.1155/2020/9369341

Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients
Cited by: 6
Author(s): Shuwen Han, Yang Xi, Miao Da, Jingying Xu, Zhuang Jing, Gao Wei-li
Software Mentions: 3
Published: over 6 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-018-4627-8

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse
Cited by: 44
Author(s): Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luís Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño‐Pachón, Sérgio Akira Uyemura, Taísa Magnani Dinamarco
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/6827057

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database
Cited by: 11
Author(s): Wenqing Zhou, Yongkui Pang, Yunmin Yao, Huiying Qiao
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms22189799

Identification of miR-199a-5p, miR-214-3p and miR-99b-5p as Fibrosis-Specific Extracellular Biomarkers and Promoters of HSC Activation
Cited by: 7
Author(s): Catherine Jane Messner, Saskia Schmidt, Dilek Özkul, Carine Gaiser, Luigi Terracciano, Stephan Krähenbühl, Laura Suter‐Dick
Software Mentions: 3
Published: about 5 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 8 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: over 12 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: almost 11 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: about 11 years ago

10.1186/s40478-018-0569-2

ABCA1 haplodeficiency affects the brain transcriptome following traumatic brain injury in mice expressing human APOE isoforms
Cited by: 16
Author(s): Emilie L. Castranio, Cody M. Wolfe, Kyong Nyon Nam, Florent Letronne, Nicholas F. Fitz, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 3
Published: over 8 years ago

10.1038/srep02898

Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study
Cited by: 15
Author(s): Brooke L. Fridley, Gregory D. Jenkins, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland, Ann L. Oberg
Software Mentions: 3
Published: about 13 years ago

10.1186/s12864-017-4170-z

Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda
Cited by: 35
Author(s): Karina Lucas Silva‐Brandão, Renato J. Horikoshi, Daniel Bernardi, Celso Omoto, Antônio Figueira, Marcelo Mendes Brandão
Software Mentions: 3
Published: about 9 years ago

10.1186/s40246-019-0199-1

Transcriptome-wide analysis of differentially expressed chemokine receptors, SNPs, and SSRs in the age-related macular degeneration
Cited by: 22
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Lijuan Fan, Zhengmao Hu, Huang Hu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-2376-0

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum
Cited by: 19
Author(s): Stanford Kwenda, Vladimir Gorshkov, Aiyagari Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: about 6 years ago

10.1016/j.ebiom.2018.02.017

Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis
Cited by: 45
Author(s): Giulia Fregni, Mathieu Quinodoz, Emely Möller, Joanna A. Vuille, Sabine Galland, Carlo Fusco, Patricia Martin, Igor Letovanec, Paolo Provero, Carlo Rivolta, Nicolò Riggi, Ivan Stamenkovic
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms21010364

Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mice
Cited by: 25
Author(s): Aimy Sebastian, Deepa K. Murugesh, Melanie E. Mendez, Nicholas R. Hum, Naiomy Deliz Rios‐Arce, Jillian L. McCool, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5745-7

Cold acclimation triggers major transcriptional changes in Drosophila suzukii
Cited by: 29
Author(s): Thomas Enriquez, Hervé Colinet
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07099-4

Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed
Cited by: 3
Author(s): Xi Liu, Frédéric Herault, Christian Diot, Erwan Corre
Software Mentions: 3
Published: about 6 years ago

10.3390/ani9060313

Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
Cited by: 11
Author(s): Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Yan Hua, Fuping Zhao, Longchao Zhang, Lixian Wang
Software Mentions: 3
Published: over 7 years ago

10.1152/physiolgenomics.00123.2014

Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout
Cited by: 14
Author(s): Tamsyn M. Uren Webster, Janice A. Shears, Karen Moore, Eduarda M. Santos
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-15-954

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Cited by: 33
Author(s): Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xinwei Sun, Yan Meng, Paul Stothard, Graham Plastow, Christopher K. Tuggle, James M. Reecy, Eric R. Fritz-Waters, Samuel M. Abrams, Joan K. Lunney, Leluo Guan
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-017-4285-2

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis
Cited by: 15
Author(s): Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst, Joel Schick
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-017-3973-2

Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars
Cited by: 37
Author(s): Rugang Yu, Dan Li, Xiaodong Du, Shenglan Xia, Caifeng Liu, Gangrong Shi
Software Mentions: 3
Published: about 9 years ago

10.1038/s41597-019-0117-3

Metagenomics and transcriptomics data from human colorectal cancer
Cited by: 5
Author(s): Tina Visnovska, Patrick J. Biggs, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: over 7 years ago

10.1128/mSystems.00358-21

Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments
Cited by: 16
Author(s): Sean Ting-Shyang Wei, Yi Lung Chen, Yu Wei Wu, Tien Yu Wu, Yi Li Lai, Po Hsiang Wang, Wael Ismail, Tzong‐Huei Lee, Yin-Ru Chiang
Software Mentions: 3
Published: over 5 years ago

10.3390/ani10111944

Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Cited by: 12
Author(s): Shijun Li, Sayed Haidar Abbas Raza, Chunping Zhao, Gong Chen, Zan Liu
Software Mentions: 3
Published: about 6 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 9 years ago

10.18632/aging.202714

High expression of CD52 in adipocytes: a potential therapeutic target for obesity with type 2 diabetes
Cited by: 3
Author(s): Rui Mao, Fan Yang, Yu Zhang, Hongtao Liu, Pengsen Guo, Yanjun Liu, Tongtong Zhang
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: over 9 years ago

10.1155/2020/3980742

The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity
Cited by: 21
Author(s): Wei Hu, Yuanlin Ding, Shu Wang, Lin Xu, Haibing Yu
Software Mentions: 3
Published: over 6 years ago

10.1093/ecco-jcc/jjaa021

A Pilot Integrative Analysis of Colonic Gene Expression, Gut Microbiota, and Immune Infiltration in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Association of Disease With Bile Acid Pathways
Cited by: 75
Author(s): Mohammed Nabil Quraishi, Animesh Acharjee, Andrew D Beggs, Richard D. Horniblow, Chris Tselepis, Georgios V. Gkoutos, Subrata Ghosh, Amanda E. Rossiter, Nicholas J. Loman, Willem van Schaik, David R. Withers, Julian R.F. Walters, Gideon Hirschfield, Tariq Iqbal
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07560-y

Factors affecting the rapid changes of protein under short-term heat stress
Cited by: 4
Author(s): Bingjin Wu, Jian-Wen Qiao, Xiaoming Wang, Manshuang Liu, Shengbao Xu, Dianjun Sun
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00451-19

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer
Cited by: 24
Author(s): Sarah Tomkovich, Raad Z. Gharaibeh, Christine M. Dejea, Jillian L. Pope, Jinmai Jiang, Kathryn Winglee, Josée Gauthier, Rachel C. Newsome, Ye Yang, Anthony A. Fodor, Thomas D. Schmittgen, Cynthia L. Sears, Christian Jobin
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00416-19

Genomewide Analysis of Mode of Action of the <i>S</i> -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Cited by: 13
Author(s): Arijit Bhattacharya, Meenakshi Sharma, Charles Packianathan, Barry P. Rosen, Philippe Leprohon, Marc Ouellette
Software Mentions: 3
Published: about 7 years ago

10.3390/ijms22179120

Identifying the Main Functional Pathways Associated with Cognitive Resilience to Alzheimer’s Disease
Cited by: 11
Author(s): Marta Pérez-González, Sara Badesso, Elena Lorenzo, Elizabeth Guruceaga, Alberto Pérez-Mediavilla, Ana Garcı́a-Osta, Mar Cuadrado‐Tejedor
Software Mentions: 3
Published: about 5 years ago

10.3390/jcm8111928

B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells
Cited by: 12
Author(s): Claudia De Vitis, Giacomo Corleone, Valentina Salvati, Francesca Ascenzi, Matteo Pallocca, Francesca De Nicola, Maurizio Fanciulli, Simona Di Martino, Sara Bruschini, Christian Napoli, Alberto Rícci, Massimiliano Bassi, Federico Venuta, Erino Angelo Rendina, Gennaro Ciliberto, Rita Mancini
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-3433-4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.1172/JCI97007

Hypothalamic loss of Snord116 recapitulates the hyperphagia of Prader-Willi syndrome
Cited by: 73
Author(s): Joseph Polex-Wolf, Brian Lam, Rachel Larder, John Tadross, Debra Rimmington, Fàtima Bosch, Verónica Jiménez Cenzano, Eduard Ayuso, Marcella Kl, Kara Rainbow, Anthony P. Coll, Stephen O’Rahilly, Giles S.H. Yeo
Software Mentions: 3
Published: almost 9 years ago

10.1002/jcp.29046

Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma
Cited by: 11
Author(s): Jia Wang, Qiujing Zhang, Qingqing Zhu, Chengxiang Li, Xueli Nan, Fuxia Wang, Lihua Fang, Jie Liu, Chao Xie, Shuai Fu, Bao-Liang Song
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4675-0

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Cited by: 31
Author(s): Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Sharon Benjamini, Shoval Miyara, M. Ruzal, Manfred Grabherr, Nima Rafati, Anna Maja Molin, Ken Pendavis, Shane C. Burgess, Leif Andersson, Miriam Friedman‐Einat
Software Mentions: 3
Published: over 8 years ago

10.14814/phy2.13019

Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
Cited by: 19
Author(s): Sindre Lee, Frode Norheim, Torgrim M. Langleite, Hans Jørgen Noreng, Trygve H. Storås, Lydia A. Afman, Gary Frost, Jimmy D. Bell, E. Louise Thomas, Kristoffer Jensen Kolnes, Daniel S. Tangen, Hans Kristian Stadheim, Gregor D. Gilfillan, Hanne Løvdal Gulseth, Kåre I. Birkeland, Jørgen Jensen, Christian A. Drevon, Torgeir Holen
Software Mentions: 3
Published: about 10 years ago

10.18632/aging.101541

Comprehensive analysis of circRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of atherosclerosis in rabbits
Cited by: 129
Author(s): Feng Zhang, Ruyou Zhang, Xiaoyu Zhang, Yingnan Wu, Xiaoying Li, Shuang Zhang, Wen-ying Hou, Yu Ding, Jiawei Tian, Lei Sun, Xiangdong Kong
Software Mentions: 3
Published: about 8 years ago

10.1242/bio.039917

Characterization and comparative analyses of transcriptomes of cloned and <i>in vivo</i> fertilized porcine pre-implantation embryos
Cited by: 7
Author(s): Xiaoyan He, Cheng Tan, Zicong Li, Chengfa Zhao, Junsong Shi, Rong Zhou, Xingwang Wang, Gelong Jiang, Guangyan Cai, Dewu Liu, Zhenfang Wu
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2018.00294

Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline
Cited by: 23
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Lei Yu, Yanling Wang, Philip L. De Jager, David A. Bennett
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-018-5017-y

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: about 8 years ago

10.3390/antibiotics9100715

Aureolic Acid Group of Agents as Potential Antituberculosis Drugs
Cited by: 2
Author(s): Julia Bespyatykh, Dmitry Bespiatykh, Maja V. Malakhova, Ksenia M. Klimina, Andrey Bespyatykh, Anna M. Varizhuk, Anna N. Tevyashova, Tatiana A Nikolenko, Galina E. Pozmogova, Elena N. Ilina, Egor Shitikov
Software Mentions: 3
Published: about 6 years ago

10.1111/jcmm.16596

Interplay between SARS‐CoV‐2 and human long non‐coding RNAs
Cited by: 32
Author(s): Maryam Moazzam-Jazi, Hossein Lanjanian, Samaneh Maleknia, Mehdi Hedayati, Maryam S. Daneshpour
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00216-19

Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space
Cited by: 19
Author(s): Neil D. Ritchie, Tom Evans
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: about 10 years ago

10.1111/jcmm.15980

A novel autophagy‐related lncRNA prognostic risk model for breast cancer
Cited by: 74
Author(s): Xiaoying Li, Feng Jin, Yang Li
Software Mentions: 3
Published: almost 6 years ago

10.1111/jcmm.15687

Development of a prognostic gene signature based on an immunogenomic infiltration analysis of osteosarcoma
Cited by: 14
Author(s): Yan Yu, Hongliang Zhang, Tingting Ren, Yi Huang, Xin Liang, Wei Wang, Jianfang Niu, Yu Han, Wei Guo
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.102393

Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma
Cited by: 12
Author(s): Mingdong Li, Shengrong Long, Jinqu Hu, Zan Wang, Chao Geng, Shaowu Ou
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-4900-x

Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)
Cited by: 24
Author(s): Zhiqiang Tian, Lina Sun, Yanyan Li, Linfa Quan, Huaijiang Zhang, Wentao Yan, Qiang Yue, Qiu GuiSheng
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1111/jcmm.15193

To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancer
Cited by: 45
Author(s): Jiazhi Jiang, Yaqiong Bi, Xiaoping Li, Donghu Yu, Xin Yan, Jie Yao, Tongzu Liu, Li Sheng
Software Mentions: 3
Published: over 6 years ago

10.3390/antiox9121190

Differential Sex-Dependent Regulation of the Alveolar Macrophage miRNome of SP-A2 and co-ex (SP-A1/SP-A2) and Sex Differences Attenuation after 18 h of Ozone Exposure
Cited by: 7
Author(s): Nithyananda Thorenoor, David S. Phelps, Joanna Floros
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21030861

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways
Cited by: 21
Author(s): Yingdan Yuan, Bo Zhang, Xinggang Tang, Jinchi Zhang, Jie Lin
Software Mentions: 3
Published: almost 7 years ago

10.1111/jcmm.15183

PTBP1 modulates osteosarcoma chemoresistance to cisplatin by regulating the expression of the copper transporter SLC31A1
Cited by: 33
Author(s): Cheng Cheng, Qiuyue Ding, Zhicai Zhang, Shangyu Wang, Botao Zhong, Xin Huang
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/btw585

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Cited by: 124
Author(s): Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2018.00610

Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues
Cited by: 26
Author(s): Alexandre A. Lussier, Tamara S. Bodnar, Matthew Mingay, Alexandre Morin, Martin Hirst, Michæl S. Kobor, Joanne Weinberg
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2021.583568

Aberrantly DNA Methylated-Differentially Expressed Genes in Pancreatic Cancer Through an Integrated Bioinformatics Approach
Cited by: 4
Author(s): Haifeng Sun, Rui Xin, Changjun Zheng, Ge Huang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1006088

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Cited by: 21
Author(s): Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 3
Published: over 8 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12918-018-0637-z

Systems biology analysis reveals new insights into invasive lung cancer
Cited by: 2
Author(s): Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang
Software Mentions: 3
Published: almost 8 years ago

10.3390/antiox9090884

The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System
Cited by: 7
Author(s): Dionysios V. Chartoumpekis, Panos G. Ziros, Ilias Georgakopoulos-Soares, Alexander Smith, Ana C. Marques, Mark Ibberson, Peter Kopp, Ioannis Habeos, Ioannis P. Trougakos, Nicholas K.H. Khoo, Gerasimos P. Sykiotis
Software Mentions: 3
Published: about 6 years ago

10.7150/jca.59348

Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1
Cited by: 5
Author(s): Yaoxin Fan, Lin Wang, Yang Ding, Qiuju Sheng, Chong Zhang, Yanwei Li, Chao Han, Bao-Liang Lu, Xiao-guang Dou
Software Mentions: 3
Published: almost 6 years ago

10.1128/mSphere.00659-20

MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus
Cited by: 8
Author(s): Byoung Sik Kim, Jong-Hwan Kim, Sunghee Choi, Shinhye Park, Eun-Young Lee, Sung-Cheol Koh, Choong‐Min Ryu, Seon‐Young Kim, Myung Hee Kim
Software Mentions: 3
Published: about 6 years ago

10.1128/mSphere.00065-20

Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous
Cited by: 3
Author(s): Pilar Martínez-Moya, Sebastián Campusano, Pamela Córdova, Alberto Paradela, Dionisia Sepúlveda, Jennifer Alcaı́no, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.50472

High Expression of RhoBTB3 Predicts Favorable Chemothrapy Outcomes in non-M3 Acute Myeloid Leukemia
Cited by: 3
Author(s): Shuanghui Yang, Wei Liu, Jie Peng, Yajing Xu, Yanfeng Liu, Yan Li, Minyuan Peng, Zhao Ouyang, Cong Chen, Enyi Liu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00342

P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes
Cited by: 9
Author(s): Heeyoun Bunch, Hyeseung Choe, Jong Bum Kim, Doo Sin Jo, Soyeon Jeon, Sang-Hwa Lee, Dong‐Hyung Cho, Keunsoo Kang
Software Mentions: 3
Published: over 7 years ago

10.1128/mSphere.00378-19

Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats
Cited by: 15
Author(s): Julia M. McGonigle, Jeremiah A. Bernau, Brenda B. Bowen, William J. Brazelton
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2021.620241

Integrated Transcriptomic and Epigenetic Study of PCOS: Impact of Map3k1 and Map1lc3a Promoter Methylation on Autophagy
Cited by: 11
Author(s): Yanmin Qin, Ting Li, Hui Zhao, Zhanrui Mao, Chunmei Ding, Yani Kang
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.49138

LINC00184 involved in the regulatory network of ANGPT2 via ceRNA mediated miR-145 inhibition in gastric cancer
Cited by: 13
Author(s): Haiyan Piao, Shuai Guo, Haoyi Jin, Yue Wang, Jun Zhang
Software Mentions: 3
Published: almost 6 years ago

10.7150/jca.38796

A Combined four-mRNA Signature Associated with Lymphatic Metastasis for Prognosis of Colorectal Cancer
Cited by: 7
Author(s): Xueping Li, Zhang Qiang, Liang Zhao, Longyang Jiang, Aoshuang Qi, Wei Qian, Xinyue Song, Wei Lin, Liwen Zhang, Yimeng Zhao, Xuemei Lv, Lin Zhao
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2020.00486

Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn’s Disease and Identification of Potential Causal Genes Through Integration With Disease Associations
Cited by: 14
Author(s): Seulgi Jung, Wenting Liu, Jiwon Baek, Jung Won Moon, Byong Duk Ye, Ho‐Su Lee, Sang Hyoung Park, Suk Kyun Yang, Buhm Han, Jing Liu, Kyuyoung Song
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms19061697

Comparative Analyses of Anatomical Structure, Phytohormone Levels, and Gene Expression Profiles Reveal Potential Dwarfing Mechanisms in Shengyin Bamboo (Phyllostachys edulis f. tubaeformis)
Cited by: 19
Author(s): Tao Wang, Lei Liu, Xiaojing Wang, Lisong Liang, Jin-Jun Yue, Lubin Li
Software Mentions: 3
Published: over 8 years ago

10.7150/jca.34723

Signatures of circulating microRNA in four sarcoma subtypes
Cited by: 11
Author(s): Hanna Koseła-Paterczyk, Agnieszka Paziewska, Maria Kulecka, Aneta Bałabas, Anna Kluska, Michalina Dąbrowska, Magdalena Piątkowska, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Jakub Karczmarski, Michał Mikula, Piotr Rutkowski, Jerzy Ostrowski
Software Mentions: 3
Published: almost 7 years ago

10.7150/jca.35801

Identification of a six-lncRNA signature based on a competing endogenous RNA network for predicting the risk of tumour recurrence in bladder cancer patients
Cited by: 8
Author(s): Danfeng Zhao, Qiang Peng, Lu Wang, Cong Li, Yulin Lv, Yong Liu, Zhichao Wang, Ruizhe Fang, Jiaqi Wang, Zhongqing Liu, Wanhai Xu
Software Mentions: 3
Published: almost 7 years ago

10.3390/cancers13081903

Circular RNA in Chemonaive Lymph Node Negative Colon Cancer Patients
Cited by: 0
Author(s): I. van den Berg, Marcel Smid, Robert R.J. Coebergh van den Braak, Carolien H.M. van Deurzen, Vanja de Weerd, John A. Foekens, Jan N.M. IJzermans, John W.M. Martens, Saskia M. Wilting
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.31675

Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data
Cited by: 9
Author(s): Jianwei Liu, Rong Li, Xiwen Liao, Bang-li Hu, Jia Yu
Software Mentions: 3
Published: almost 8 years ago