bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41597-020-0352-7

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
Cited by: 69
Author(s): Won-Hee Kang, Young Mi Sim, Namjin Koo, Jae Do Nam, Junesung Lee, Nayoung Kim, Hakgi Jang, Yongmin Kim, Seon-In Yeom
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.664178

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: over 3 years ago

10.1042/BSR20211451

Identification of a glycolysis-related lncRNA prognostic signature for clear cell renal cell carcinoma
Cited by: 7
Author(s): Wei Ma, Manli Zhong, Xiaowu Liu
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: over 4 years ago

10.3389/fcell.2021.684643

Development of an Individualized Ubiquitin Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yue Wu, Xi Zhang, Wa Xian, Huan Feng, Bintao Hu, Zhiyao Deng, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.33480

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
Cited by: 86
Author(s): David A. Knowles, Courtney K Burrows, John Blischak, Kristen Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 5
Published: over 6 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
Software Mentions: 5
Published: about 6 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: over 6 years ago

10.1042/BSR20203231

Identification of an autophagy-related gene signature predicting overall survival for hepatocellular carcinoma
Cited by: 5
Author(s): Wenfang Xu, Wenxiu Guo, Ping Lü, Ding Ma, Lei Liu, Fudong Yu
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12860-020-00295-w

Molecular docking and machine learning analysis of Abemaciclib in colon cancer
Cited by: 14
Author(s): José Liñares-Blanco, Cristian R. Munteanu, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: about 8 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0186794

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health
Cited by: 16
Author(s): Vittoria Roncalli, Andrew E. Christie, Stephanie A. Sommer, Matthew Cieslak, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0101467

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation
Cited by: 22
Author(s): Panu Somervuo, Jouni Kvist, Suvi Ikonen, Petri Auvinen, Lars Paulín, Patrik Koskinen, Liisa Holm, Minna Taipale, Anne Duplouy, Annukka Ruokolainen, Suvi Saarnio, Jukka Sirén, Jukka Kohonen, Jukka Corander, Mikko J. Frilander, Virpi Ahola, Ilkka Hanski
Software Mentions: 4
Published: over 10 years ago

10.1016/j.celrep.2021.108860

COX2 regulates senescence secretome composition and senescence surveillance through PGE2
Cited by: 30
Author(s): S. Goncalves, Kai Yin, Yoko Itō, Adelyne Chan, Ioana Olan, Sarah Gough, Liam Cassidy, Eva M. Serrao, Stephen Smith, Andrew Young, Masashi Narita, Matthew Hoare
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-47363-6

Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma
Cited by: 20
Author(s): Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Luíza Ferreira de Araújo, Isabela Ichihara de Barros, Kamila Chagas Peronni, Greice Andreotti de Molfetta, Carlos Alberto Oliveira de Biagi, Enilza Maria Espreáfico, Josane F. Sousa, Wilson A. Silva
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: almost 7 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: almost 9 years ago

10.1111/jcmm.14779

Four transcription profile–based models identify novel prognostic signatures in oesophageal cancer
Cited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0214559

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus cattle rumen tissue
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Zan Liu, Jiuzhou Song
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: over 6 years ago

10.1155/2015/862130

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library
Cited by: 29
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian D. Lehmann, Jennifer A. Pietenpol, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 6 years ago

10.3389/fcimb.2021.723481

Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence
Cited by: 6
Author(s): Jodie Ackland, Ashley Heinson, David W. Cleary, Myron Christodoulides, Tom Wilkinson, Karl J. Staples
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-52841-y

Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma
Cited by: 3
Author(s): Petros Tsantoulis, Mauro Delorenzi, Ivan Bièche, Sophie Vacher, Pascale Mariani, Nathalie Cassoux, Alexandre Houy, Marc‐Henri Stern, Sergio Román-Román, Pierre‐Yves Dietrich, Arnaud Roth, Wulfran Cacheux
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/6784138

Identification of FOS as a Candidate Risk Gene for Liver Cancer by Integrated Bioinformatic Analysis
Cited by: 10
Author(s): Jinwu Hu, Guangyu Ding, Pei-Yao Fu, Wei‐Guo Tang, Qiqing Sun, Xiao‐Dong Zhu, Ying‐Hao Shen, Ji Zhou, Jia Fan, Hui–Chuan Sun, Cheng Huang
Software Mentions: 4
Published: over 4 years ago

10.3390/v13040593

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes
Cited by: 23
Author(s): Yashu Song, Robert Hanner, Bin Meng
Software Mentions: 4
Published: over 3 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: about 7 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 11 years ago

10.3389/fimmu.2020.580219

Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants’ Mimics Wild Type Infection
Cited by: 4
Author(s): Alberto Gómez‐Carballa, Ruth Barral-Arca, Miriam Cebey-López, María José Currás-Tuala, Sara Pischedda, José Gómez-Rial, Dominic Habgood-Coote, Jethro Herberg, Myrsini Kaforou, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0252452

Comprehensive analysis of lncRNA biomarkers in kidney renal clear cell carcinoma by lncRNA-mediated ceRNA network
Cited by: 4
Author(s): Ke Gong, Ting Xie, Yiliao Luo, Hui Guo, Jinlan Chen, Zhiping Tan, Yifeng Yang, Li Xie
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: about 6 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2021.607121

Loss of Ciliary Gene Bbs8 Results in Physiological Defects in the Retinal Pigment Epithelium
Cited by: 7
Author(s): Sandra Schneider, Rossella De Cegli, Jayapriya Nagarajan, Viola Kretschmer, Peter Andreas Matthiessen, Daniela Intartaglia, Nathan Hotaling, Marius Ueffing, Karsten Boldt, Iván Conte, Helen May-Simera
Software Mentions: 4
Published: almost 4 years ago

10.3390/nu12123858

Effects of Daily Raspberry Consumption on Immune-Metabolic Health in Subjects at Risk of Metabolic Syndrome: A Randomized Controlled Trial
Cited by: 18
Author(s): Maximilien Franck, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette, Marie‐Claude Vohl
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 7 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-52903-1

Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness
Cited by: 46
Author(s): S. Luján Marco, Ettore Caroppo, Craig S. Niederberger, Joan‐Carles Arce, Ingrid Sadler‐Riggleman, Daniel Beck, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: about 4 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: almost 4 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: over 3 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 9 years ago

10.3390/biomedicines9060646

Identification of MicroRNAs as Viable Aggressiveness Biomarkers for Prostate Cancer
Cited by: 11
Author(s): Luis Javier Martínez-González, Victor Sánchez-Conde, Jose María González-Cabezuelo, Alba Antúnez-Rodríguez, Eduardo Andrés-León, Inmaculada Robles-Fernández, José A. Lorente, Fernando Vázquez-Alonso, María Jesús Álvarez-Cubero
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: over 4 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2019.00603

Genome-Wide Identification of Circular RNAs Revealed the Dominant Intergenic Region Circularization Model in Apostichopus japonicus
Cited by: 15
Author(s): Xuelin Zhao, Xuemei Duan, Jianping Fu, Yina Shao, Weiwei Zhang, Ming Guo, Chenghua Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: almost 5 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 10 years ago

10.3389/fcell.2021.670854

Integrative Analysis of DNA Methylation and Transcriptome Identifies a Predictive Epigenetic Signature Associated With Immune Infiltration in Gliomas
Cited by: 7
Author(s): Jianlei Zhang, Yin Jiang, Li Luo, Dongzhou Huang, Dongfeng Zhai, Ge Wang, Ning Xu, Minqiang Yang, Ying Song, Guopei Zheng, Qiong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12870-020-02757-x

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains
Cited by: 5
Author(s): Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma‐Silva, Fábio Pinheiro
Software Mentions: 4
Published: about 4 years ago

10.1038/s41396-019-0508-7

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
Cited by: 53
Author(s): Adrien Assié, Nikolaus Leisch, Dimitri V. Meier, Harald R. Gruber‐Vodicka, Halina E. Tegetmeyer, Anke Meyerdierks, Manuel Kleiner, Tjorven Hinzke, Samantha B. Joye, Matthew Saxton, Nicole Dubilier, Jillian M. Petersen
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 4 years ago

10.3389/fcimb.2021.652837

Potential Roles of Oral Microbiota in the Pathogenesis of Immunoglobin A Nephropathy
Cited by: 6
Author(s): Jiawei He, Xu‐Jie Zhou, Ping Hou, Yan-Na Wang, Tao Gan, Yang Li, Yang Liu, Lijun Liu, Sufang Shi, Li Zhu, Jicheng Lv, Hong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1038/srep24375

RNA-seq analysis for detecting quantitative trait-associated genes
Cited by: 33
Author(s): Minseok Seo, Kwondo Kim, Joon Yoon, Jin Young Jeong, Hyun-Jeong Lee, Seoae Cho, Heebal Kim
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0251121

Melanocytes determine angiogenesis gene expression across human tissues
Cited by: 3
Author(s): Shirly Freilikhman, Marianna Halasi, Alal Eran, Irit Adini
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0235763

Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Cited by: 17
Author(s): Juan Jin, Lei Yang, Dingyu Fan, Xuxin Liu, Qing Hao
Software Mentions: 4
Published: about 4 years ago

10.1111/jcmm.15271

Systematic prediction of key genes for ovarian cancer by co‐expression network analysis
Cited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 4 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2021.657917

PSMC5 Promotes Proliferation and Metastasis of Colorectal Cancer by Activating Epithelial–Mesenchymal Transition Signaling and Modulating Immune Infiltrating Cells
Cited by: 8
Author(s): Zengyou He, Xiao Yang, Ling Huang, Leqi Zhou, Sen Zhang, Jing Ping Sun, Min Zheng, Junjun Ma, Bo Feng, Lu Zang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2021.667177

CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer
Cited by: 20
Author(s): Enhao Li, Xiaobao Yang, Yuzhang Du, Guanzheng Wang, David Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.628136

Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.658736

A Prognostic Model Based on the Immune-Related lncRNAs in Colorectal Cancer
Cited by: 16
Author(s): Fen Qin, Houxi Xu, Guoli Wei, Ji Yi, Jialin Yu, Canhong Hu, Chunyi Yuan, Yuzhu Ma, Jun Qian, Lingchang Li, Jiege Huo
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2019.01269

An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients
Cited by: 27
Author(s): Yuhang Liu, Bingxin Liu, Guoying Jin, Jia Zhang, Xue Wang, Yuyang Feng, Zehua Bian, Bojian Fei, Yuan Yin, Zhaohui Huang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0109262

De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Cited by: 48
Author(s): Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: about 13 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: about 4 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: about 3 years ago

Projects: bioconductor: edgeR

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