bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1016/j.celrep.2015.12.012

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR
Cited by: 27
Author(s): Kobe Yuen, Baoshan Xu, Ian D. Krantz, Jennifer L. Gerton
Software Mentions: 3
Published: over 10 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20202921

Immune-associated biomarkers for early diagnosis of Parkinson’s disease based on hematological lncRNA–mRNA co-expression
Cited by: 8
Author(s): Kecheng Lei, Liwen Zhang, Yijing He, Hui Sun, Weifang Tong, Yawei Xu, Lingjing Jin
Software Mentions: 3
Published: over 5 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

10.1016/j.celrep.2019.04.113

Molecular Logic of Spinocerebellar Tract Neuron Diversity and Connectivity
Cited by: 33
Author(s): Min Won Baek, Vilas Menon, Thomas M. Jessell, Adam W. Hantman, Jeremy S. Dasen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41438-018-0020-7

Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)
Cited by: 49
Author(s): Jason P. Londo, Alisson P. Kovaleski, Jacquelyn Lillis
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2016.00682

Transcriptomic Analysis Identifies Differentially Expressed Genes (DEGs) Associated with Bolting and Flowering in Radish (Raphanus sativus L.)
Cited by: 17
Author(s): Shaoping Nie, Chao Li, Yan Wang, Liang Xu, Everlyne M. Muleke, Mingjia Tang, Xiaochuan Sun, Liwang Liu
Software Mentions: 3
Published: over 10 years ago

10.1093/gigascience/giaa009

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas
Cited by: 15
Author(s): Maosheng Chen, Longjian Niu, Miaomiao Zhao, Chuan-Jia Xu, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Hua He, Chaoqi Hou, Zeng-Fu Xu
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2020.108453

The Microfluidic Environment Reveals a Hidden Role of Self-Organizing Extracellular Matrix in Hepatic Commitment and Organoid Formation of hiPSCs
Cited by: 23
Author(s): Federica Michielin, Giovanni Giuseppe Giobbe, Camilla Luni, Qianjiang Hu, Ida Maroni, Michael Orford, Anna Manfredi, Lucio Di Filippo, Anna L. David, Davide Cacchiarelli, Paolo De Coppi, Simon Eaton, Nicola Elvassore
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00813-16

Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
Cited by: 24
Author(s): Jozef Dingemans, Pieter Monsieurs, Sung-Huan Yu, Aurélie Crabbé, Konrad U. Förstner, Anne Malfroot, Pierre Cornélis, Rob Van Houdt
Software Mentions: 3
Published: almost 10 years ago

10.3389/fonc.2020.00979

High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes
Cited by: 42
Author(s): Mairene Coto‐Llerena, Caner Ercan, Venkatesh Kancherla, Stephanie Taha‐Mehlitz, Serenella Eppenberger‐Castori, Savas D. Soysal, Charlotte K.Y. Ng, Martin Bolli, Markus von Flüe, Guillaume Nicolas, Luigi Terracciano, Melpomeni Fani, Salvatore Piscuoglio
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.540094

Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis
Cited by: 16
Author(s): Qiwei Yang, Weiwei Chu, Wei Yang, Yan-Qiong Cheng, Chuanmin Chu, Xiuwu Pan, Jianqing Ye, Jun Cao, Sishun Gan, Xingang Cui
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0204426

Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses
Cited by: 7
Author(s): Chunman Zuo, Yuhong Tang, Fang Hao, Yiming Liu, Xunzhong Zhang, Bingyu Zhao, Ying Xu
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13071-018-2817-5

Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii
Cited by: 21
Author(s): Bradley J. Main, Amanda Everitt, Anthony J. Cornel, Fereydoun Hormozdiari, Gregory C. Lanzaro
Software Mentions: 3
Published: over 8 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: about 5 years ago

10.1016/j.celrep.2015.11.040

Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome
Cited by: 37
Author(s): Ana Tufegdžić Vidaković, Oscar M. Rueda, Stephin J. Vervoort, Ankita Batra, Mae A. Goldgraben, Santiago Uribe-Lewis, Wendy Greenwood, Paul J. Coffer, Alejandra Bruna, Carlos Caldas
Software Mentions: 3
Published: over 10 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 years ago

10.3389/fonc.2019.00613

Identification of Biomarkers for Controlling Cancer Stem Cell Characteristics in Bladder Cancer by Network Analysis of Transcriptome Data Stemness Indices
Cited by: 92
Author(s): Shen Pan, Yunhong Zhan, Xiaonan Chen, Bin Wu, Bitian Liu
Software Mentions: 3
Published: about 7 years ago

10.1128/mBio.01950-18

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
Cited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: about 7 years ago

10.1155/2021/3212878

Peripheral Blood Cells from Patients with Hodgkin’s and Diffuse Large B Cell Lymphomas May Be a Better Source of Candidate Diagnostic miRNAs Than Circulating miRNAs
Cited by: 0
Author(s): Ewa Paszkiewicz‐Kozik, Agnieszka Paziewska, Maria Kulecka, Michalina Dąbrowska, Anna Kluska, Aneta Bałabas, Magdalena Piątkowska, Filip Ambrożkiewicz, J. Tajer, W. Osiadacz, Joanna Romejko‐Jarosińska, Martyna Kotarska, Natalia Żeber‐Lubecka, Jakub Karczmarski, Lidia Popławska, Michał Mikula, Piotr Rutkowski, Jan Walewski, Jerzy Ostrowski
Software Mentions: 3
Published: over 5 years ago

10.1089/cell.2018.0008

Porcine Fetal-Derived Fibroblasts Alter Gene Expression and Mitochondria to Compensate for Hypoxic Stress During Culture
Cited by: 4
Author(s): Bethany R. Mordhorst, Shaun Murphy, Martin Schauflinger, Shirley Rojas-Salazar, Tieming Ji, Susanta K. Behura, Kevin D. Wells, Jonathan A. Green, Randall S. Prather
Software Mentions: 3
Published: about 8 years ago

10.1038/s41422-018-0103-x

Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens
Cited by: 105
Author(s): Gongbo Fu, Weijian Huang, Min Zeng, Zhou Xu, Hongping Wu, Changcheng Liu, Han Wu, Jun Weng, Hong‐Dan Zhang, Yongchao Cai, Charles Ashton, Min Ding, Dan Tang, Baohua Zhang, Yi Gao, Weifeng Yu, Bo Zhai, Zhiying He, Hongyang Wang, He‐Xin Yan
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.8260

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Cited by: 4
Author(s): Necla Koçhan, G. Yazgı Tütüncü, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner
Software Mentions: 3
Published: over 6 years ago

10.1038/cr.2017.124

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
Cited by: 152
Author(s): Changsong Zou, A Chen, Li Xiao, H.-A. Müller, Peter Ache, Georg Haberer, M Zhang, Jia Wei, Ping Deng, Ru Huang, Daniel Lang, Li Feng, Dong Zhan, Xiaoyong Wu, H Zhang, Jennifer Böhm, Ruirui Liu, Lana Shabala, Rainer Hedrich, J-K Zhu
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-01526-5

Gene co-expression network analysis identifies porcine genes associated with variation in metabolizing fenbendazole and flunixin meglumine in the liver
Cited by: 8
Author(s): Jeremy Howard, M.S. Ashwell, Ronald E. Baynes, James D. Brooks, James L. Yeatts, Christian Maltecca
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2021.574196

Identification of the Functions and Prognostic Values of RNA Binding Proteins in Bladder Cancer
Cited by: 18
Author(s): Yue Wu, Zheng Liu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 3
Published: about 5 years ago

10.1042/BSR20200295

Identification of hub driving genes and regulators of lung adenocarcinoma based on the gene Co-expression network
Cited by: 5
Author(s): Zihao Xu, Zilong Wu, Jiatang Xu, Jingtao Zhang, Bentong Yu
Software Mentions: 3
Published: over 6 years ago

10.1016/j.stem.2020.05.004

Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease
Cited by: 302
Author(s): Elisa Giacomelli, Viviana Meraviglia, Giulia Campostrini, Amy Cochrane, Xu Cao, Ruben W.J. van Helden, Ana Krotenberg Garcia, Maria Mircea, Sarantos Kostidis, Richard P. Davis, Berend J. van Meer, Carolina R. Jost, Abraham J. Koster, Hailiang Mei, David G. Míguez, Aat A. Mulder, Mario Ledesma-Terrón, Giulio Pompilio, Luca Sala, Daniela Salvatori, Roderick C. Slieker, Elena Sommariva, Antoine A.F. de Vries, Martin Giera, Stefan Semrau, Leon G.J. Tertoolen, Valeria V. Orlova, Milena Bellin, Christine L. Mummery
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms19092657

Comparative Transcriptomics Identifies Novel Genes and Pathways Involved in Post-Traumatic Osteoarthritis Development and Progression
Cited by: 26
Author(s): Aimy Sebastian, Jiun Chiun Chang, Melanie E. Mendez, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms20236090

Disclosure of the Molecular Mechanism of Wheat Leaf Spot Disease Caused by Bipolaris sorokiniana through Comparative Transcriptome and Metabolomics Analysis
Cited by: 21
Author(s): Wei Ye, Taomei Liu, Weiyang Zhang, Saini Li, Muzi Zhu, Haohua Li, Yali Kong, Luoshan Xu
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-020-00796-5

Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma
Cited by: 73
Author(s): Hechen Huang, Zhigang Ren, Xingxing Gao, Xiaoyi Hu, Yuan Zhou, Jianwen Jiang, Haifeng Lü, Shengyong Yin, Junfang Ji, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-020-02110-3

Cis and trans effects differentially contribute to the evolution of promoters and enhancers
Cited by: 26
Author(s): Kaia Mattioli, Winona Oliveros, Chiara Gerhardinger, Daniel Andergassen, Philipp G. Maass, John L. Rinn, Marta Melé
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.00215-20

Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Cited by: 56
Author(s): Myra Hosmillo, Yasmin Chaudhry, Komal Nayak, Frédéric Sorgeloos, Bon‐Kyoung Koo, Alessandra Merenda, Reidun Lillestøl, Lydia N Drumright, Matthias Zilbauer, Ian Goodfellow
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: almost 9 years ago

10.3390/cells9122700

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion
Cited by: 6
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Claudia Krüger, Miloslav Juříček, Helena Štorchová
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.10576

A novel similarity score based on gene ranks to reveal genetic relationships among diseases
Cited by: 3
Author(s): Dongmei Luo, Chengdong Zhang, Liwan Fu, Yuening Zhang, Yue‐Qing Hu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-14083-8

Profiling of miRNAs and target genes related to cystogenesis in ADPKD mouse models
Cited by: 32
Author(s): Yu Mi Woo, Do Yeon Kim, Nam Jin Koo, Yong Min Kim, Sun Young Lee, Je Yeong Ko, Yubin Shin, Bo Hye Kim, Hyowon Mun, Seonju Choi, Eun Ji Lee, Jeong Oh Shin, Eun Young Park, Jinwoong Bok, Jong Hoon Park
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-13176-8

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans
Cited by: 11
Author(s): Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, Heike Hadrys, George Amato, Rob DeSalle
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13068-019-1630-5

Responses of Methanosarcina barkeri to acetate stress
Cited by: 21
Author(s): Pinjing He, Haowen Duan, Wenfeng Han, Yang Liu, Liming Shao
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms19082300

Transcriptomic Analyses of Root Restriction Effects on Phytohormone Content and Signal Transduction during Grape Berry Development and Ripening
Cited by: 12
Author(s): Lu Feng, Ji Cao, Shiping Wang, Ling Jiang, Xian Li, Chongde Sun
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.00265

Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer
Cited by: 12
Author(s): Yan Wang, Steven Chen, Xi Rao, Yunlong Liu
Software Mentions: 3
Published: over 6 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

10.1128/mBio.01628-20

Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway
Cited by: 11
Author(s): Siqi Hong, Yan Li, Paul J. Kaminski, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2019.00009

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data
Cited by: 60
Author(s): Aanchal Mongia, Debarka Sengupta, Angshul Majumdar
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-020-01758-0

Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Cited by: 14
Author(s): Xiao Han, Yi An, Yangyan Zhou, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 3
Published: about 6 years ago

10.1186/s13068-019-1612-7

Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement
Cited by: 7
Author(s): Yin Li, Min Tu, Yaping Feng, Wenqing Wang, Joachim Messing
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.3631

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
Cited by: 34
Author(s): Van L.T. Hoang, Lisa Tom, Xiu-Cheng Quek, Jean-Marie Tan, Elizabeth Payne, Lynlee L. Lin, Sudipta Sinnya, Anthony P. Raphael, Duncan Lambie, Ian H. Frazer, Marcel E. Dinger, H. Peter Soyer, Tarl W. Prow
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-020-02150-9

A novel antiviral lncRNA, EDAL, shields a T309 O-GlcNAcylation site to promote EZH2 lysosomal degradation
Cited by: 34
Author(s): Baokun Sui, Dong Chen, Wei Liu, Qiong Wu, Bin Tian, Yingying Li, Jing Hou, Shiyong Liu, Juan Xie, Hao Jiang, Zhidan Luo, Lei Lv, Fei Huang, Ruiming Li, Chengguang Zhang, Yuling Tian, Min Cui, Ming Zhou, Huanchun Chen, Zhen F. Fu, Yi Zhang, Ling Zhao
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells8090986

RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications
Cited by: 19
Author(s): Kai Sen Tan, Anand Kumar Andiappan, Bernett Lee, Yan Yan, Jing Liu, See Aik Tang, Josephine Lum, Ting He, Yew Kwang Ong, Mark Thong, Hui Fang Lim, Hyung-Jin Choi, Olaf Rötzschke, Vincent Chow, De Yun Wang
Software Mentions: 3
Published: about 7 years ago

10.1038/s41408-021-00440-4

Relapsed multiple myeloma demonstrates distinct patterns of immune microenvironment and malignant cell-mediated immunosuppression
Cited by: 22
Author(s): Alissa Visram, Surendra Dasari, Emilie Anderson, Shaji Kumar, Taxiarchis Kourelis
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2019.00101

Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels
Cited by: 19
Author(s): Loes A. Oosterhoff, Hedwig S. Kruitwagen, Monique E. van Wolferen, Bas W. M. van Balkom, Michal Mokrý, Nico Lansu, Noortje A.M. van den Dungen, Louis C. Penning, Talitha C.F. Spanjersberg, Johannes W. de Graaf, Tomas Veenendaal, Flin Zomerdijk, Joost O. Fledderus, Bart Spee, Frank G. van Steenbeek
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2018.00291

Transcriptome Analyses Reveal Adult Metabolic Syndrome With Intrauterine Growth Restriction in Pig Models
Cited by: 21
Author(s): Linyuan Shen, Mailin Gan, Shunhua Zhang, Jideng Ma, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Jinyong Wang, Xuewei Li, Lianqiang Che, Li Zhu
Software Mentions: 3
Published: about 8 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

10.3390/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: about 8 years ago

10.3390/cells10092376

Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli
Cited by: 4
Author(s): Kimberly Wellman, Rui Fu, Amber Baldwin, Juilee Rege, Elisabeth Murphy, William E. Rainey, Neelanjan Mukherjee
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-13012-z

Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome
Cited by: 30
Author(s): Zhiyuan Chen, Darren E. Hagen, Tieming Ji, Christine G. Elsik
Software Mentions: 3
Published: almost 9 years ago

10.3390/cells10092289

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Cited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: almost 5 years ago

10.1128/mBio.03533-20

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 5 years ago

10.1186/s12979-015-0038-8

Hormetic effect of rotenone in primary human fibroblasts
Cited by: 13
Author(s): Shiva Marthandan, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Stephan Diekmann
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-017-11379-7

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium
Cited by: 12
Author(s): Woncheoul Park, Deivendran Rengaraj, Dong Yong Kil, Heebal Kim, Hak-Kyo Lee, Ki Duk Song
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-11237-6

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer
Cited by: 162
Author(s): Rachel Purcell, Tina Visnovska, Patrick J. Biggs, Sebastian Schmeier, Frank Frizelle
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13020-020-00339-5

Identification of drug targets and potential molecular mechanisms for Wantong Jingu Tablet extract in treatment of rheumatoid arthritis: bioinformatics analysis of fibroblast-like synoviocytes
Cited by: 6
Author(s): Zhaodong Li, Fanghua Qi, Fan Li
Software Mentions: 3
Published: about 6 years ago

10.1186/s13742-015-0091-4

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
Cited by: 52
Author(s): Liang Wu, Xiaolong Zhang, Zhikun Zhao, Ling Wang, Bo Li, Guibo Li, Michael Dean, Qichao Yu, Yanhui Wang, Xinxin Lin, Weijian Rao, Zhanlong Mei, Yang Li, Runze Jiang, Huan Yang, Fuqiang Li, Guoyun Xie, Liqin Xu, Kui Wu, Jie Zhang, Jianghao Chen, Ting Wang, Karsten Kristiansen, Xiuqing Zhang, Yingrui Li, Huanming Yang, Jian Wang, Yong Hou, Xun Xu
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms21207603

Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development
Cited by: 8
Author(s): Shuo Sun, Changyu Yi, Jing Ma, Shoudong Wang, Marta Peirats‐Llobet, Mathew G. Lewsey, James Whelan, Huixia Shou
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13148-020-00980-9

Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction
Cited by: 8
Author(s): Fieke Terstappen, Jorg J.A. Calis, Nina D. Paauw, Jaap A. Joles, Bas B. van Rijn, Michal Mokrý, Torsten Plösch, A. Titia Lely
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-018-0451-x

Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma
Cited by: 20
Author(s): Thomas Sanford, Maxwell V. Meng, Reema Railkar, Piyush K. Agarwal, Sima P. Porten
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.32920

Association mapping from sequencing reads using k-mers
Cited by: 82
Author(s): Atif Rahman, Ingileif B. Hallgrímsdóttir, Michael B. Eisen, Lior Pachter
Software Mentions: 3
Published: about 8 years ago

10.1186/s13148-020-00916-3

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease
Cited by: 11
Author(s): Dingailu Ma, Irfete S. Fetahu, Mei Wang, Rui Fang, Jia-hui Li, Huan Liu, Tobin Gramyk, Isabella Iwanicki, Sophie Zhaotao Gu, Winnie Xu, Li Tan, Feizhen Wu, Yujiang Geno Shi
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.00321

Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach
Cited by: 4
Author(s): Yangyang Pang, Long He, Yameng Song, Xiaozhe Song, Jiahuan Lv, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2015.00174

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations
Cited by: 44
Author(s): Ovidiu D. Iancu, Alexandre M. Colville, Denesa Oberbeck, Priscila Darakjian, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 3
Published: over 11 years ago

10.1093/gbe/evv117

Variation in the X:Autosome Distribution of Male-Biased Genes amongDrosophila melanogasterTissues and Its Relationship with Dosage Compensation
Cited by: 28
Author(s): Ann Kathrin Huylmans, John Parsch
Software Mentions: 3
Published: about 11 years ago

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-020-00955-w

Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs
Cited by: 4
Author(s): Iraia Muñoa-Hoyos, John Halsall, Manu Araolaza, Carl Ward, Idoia García, Itziar Urizar-Arenaza, Marta Gianzo Citores, Paloma García, Bryan M. Turner, Nerea Subirán
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13073-019-0697-8

Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4
Cited by: 37
Author(s): Jitske van den Bulk, Els M.E. Verdegaal, Dina Ruano, Marieke E. Ijsselsteijn, Marten Visser, Ruud van der Breggen, Thomas Duhen, Manon van der Ploeg, Natasja L. de Vries, Jan Oosting, Koen Peeters, Andrew D. Weinberg, Arantza Farina Sarasqueta, Sjoerd H. van der Burg, Noel F.C.C. de Miranda
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.5443

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus albaL.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2019.01215

Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome
Cited by: 8
Author(s): Gabriella Farries, Kenneth Bryan, C. L. McGivney, Paul A. McGettigan, K. F. Gough, John A. Browne, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21113870

Time-course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air
Cited by: 5
Author(s): Habibu Aliyu, Teresa Mohr, Don A. Cowan, Pieter De Maayer, Anke Neumann
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-020-0715-x

A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons
Cited by: 29
Author(s): Sergio Espeso-Gil, Tobias B. Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan K. Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J. Bannon, Panagiotis Roussos, John F. Crary, Zhiping Weng, Stefano Marenco, Barbara K. Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang, Schahram Akbarian
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-021-01043-3

Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations
Cited by: 14
Author(s): Jiayi Pei, Maike Schuldt, Emília Nagyová, Zhujie Gu, Said el Bouhaddani, Loukia Yiangou, Manon A. A. Jansen, Jorg J.A. Calis, Larissa M. Dorsch, Christian Snijders Blok, Noortje A.M. van den Dungen, Nico Lansu, Bastiaan J. Boukens, Igor R. Efimov, Michelle Michels, Marianne C. Verhaar, Roel de Weger, Aryan Vink, Frank G. van Steenbeek, Annette F. Baas, Richard P. Davis, Hae‐Won Uh, Diederik W.D. Kuster, Caroline Cheng, Michal Mokrý, Jolanda van der Velden, Folkert W. Asselbergs, Magdaléna Harakaľová
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.01109

Identification of Immune-Related Prognostic Genes and LncRNAs Biomarkers Associated With Osteosarcoma Microenvironment
Cited by: 12
Author(s): Tao Zhang, Yingli Nie, Haifa Xia, Yanbin Zhang, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 3
Published: about 6 years ago

10.1007/s12551-018-0494-4

The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond
Cited by: 37
Author(s): Jessica C. Mar
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-10648-9

Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C
Cited by: 31
Author(s): Haifei Wang, Jiying Wang, Chao Ning, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jianfeng Liu
Software Mentions: 3
Published: about 9 years ago

10.3389/fphar.2021.596535

The Widely Used Antihelmintic Drug Albendazole is a Potent Inducer of Loss of Heterozygosity
Cited by: 3
Author(s): Luiza Sheyla Evenni Porfírio Will Castro, Wietske Pieters, Mir Farshid Alemdehy, Muhammad Aslam, Olimpia Alessandra Buoninfante, Jonne A. Raaijmakers, Bas Pilzecker, Paul C.M. van den Berk, Hein te Riele, René H. Medema, Rozangela Curi Pedrosa, Heinz Jacobs
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-018-0508-x

H3K27 acetylation and gene expression analysis reveals differences in placental chromatin activity in fetal growth restriction
Cited by: 39
Author(s): Nina D. Paauw, A. Titia Lely, Jaap A. Joles, Arie Franx, Floris Groenendaal, Michal Mokrý, Bas B. van Rijn
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-09963-y

Infection with the Makona variant results in a delayed and distinct host immune response compared to previous Ebola virus variants
Cited by: 30
Author(s): Krista Versteeg, Andrea Menicucci, Courtney Woolsey, Chad E. Mire, Joan B. Geisbert, Robert W. Cross, Krystle N. Agans, Daniel R. Jeske, Ilhem Messaoudi, Thomas W. Geisbert
Software Mentions: 3
Published: about 9 years ago

10.1186/s13071-017-2326-y

Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii
Cited by: 4
Author(s): Jingru Zhang, Jiacheng Huang, Feng Zhu, Jian Zhang
Software Mentions: 3
Published: about 9 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

10.3390/ijms19051399

High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients
Cited by: 14
Author(s): Sara De Iudicibus, Marianna Lucafò, Nicola Vitulo, Stefano Martelossi, Rosanna Zimbello, Fabio De Pascale, Claudio Forcato, Samuele Naviglio, Alessia Di Silvestre, Marco Gerdol, Gabriele Stocco, Giorgio Valle, Alessandro Ventura, Matteo Bramuzzo, Giuliana Decorti
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-020-02046-8

MAUDE: inferring expression changes in sorting-based CRISPR screens
Cited by: 14
Author(s): Carl G. de Boer, John J. Ray, Nir Hacohen, Aviv Regev
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.43877

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential mediator of epithelial fusion
Cited by: 27
Author(s): Holly Hardy, James Prendergast, Aara Patel, Sunit Dutta, Violeta Trejo-Reveles, Hannah Kröger, Andrea R. Yung, Lisa V. Goodrich, Brian P. Brooks, Jane C. Sowden, Joe Rainger
Software Mentions: 3
Published: about 7 years ago

10.3389/fphys.2019.00214

Understanding Molecular Mechanisms of the Brain Through Transcriptomics
Cited by: 14
Author(s): Wei Wang, Guang-Zhong Wang
Software Mentions: 3
Published: over 7 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

10.1128/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

10.3390/biomedicines9060629

Activin-A Induces Early Differential Gene Expression Exclusively in Periodontal Ligament Fibroblasts from Fibrodysplasia Ossificans Progressiva Patients
Cited by: 8
Author(s): Ton Schoenmaker, Michal Mokrý, Dimitra Micha, Coen Netelenbos, Nathalie Bravenboer, Marjolijn Gilijamse, Elisabeth M. W. Eekhoff, Teun J. de Vries
Software Mentions: 3
Published: about 5 years ago

10.1002/hed.25537

Association between loss of Y chromosome and poor prognosis in male head and neck squamous cell carcinoma
Cited by: 21
Author(s): Robert Hollows, Wenbin Wei, Jean‐Baptiste Cazier, Hisham Mehanna, Gabriella Parry, Graham Halford, Paul G. Murray
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-08239-9

The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals
Cited by: 17
Author(s): Sabrina Jenull, Michael Tscherner, Megha Gulati, Clarissa J. Nobile, Neeraj Chauhan, Karl Kuchler
Software Mentions: 3
Published: about 9 years ago

10.1155/2020/1971284

Immune-Related lncRNA Risk Signatures Predict Survival of IDH Wild-Type and MGMT Promoter Unmethylated Glioblastoma
Cited by: 3
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 3
Published: about 6 years ago

10.3390/v13061140

Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp
Cited by: 8
Author(s): Rebecca S. Millard, Lisa K. Bickley, Kelly S. Bateman, Audrey Farbos, Diana Minardi, Karen Moore, Stuart Ross, Grant D. Stentiford, Charles R. Tyler, Ronny van Aerle, Eduarda M. Santos
Software Mentions: 3
Published: about 5 years ago

10.1016/j.gpb.2020.12.001

Tissue-specific Gene Expression Changes Are Associated with Aging in Mice
Cited by: 19
Author(s): Akash Srivastava, Emanuel Barth, Maria A. Ermolaeva, Madlen Guenther, Christiane Frahm, Manja Marz, Otto W. Witte
Software Mentions: 3
Published: about 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568