bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fpls.2018.01632

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus
Cited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: almost 8 years ago

10.3390/biom11050695

Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis
Cited by: 10
Author(s): Xiaomin Hu, Liang Gong, Ronggang Zhou, Ziying Han, Ji Li, Yan Zhang, Shuyang Zhang, Dong Wu
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2018.01625

Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
Cited by: 9
Author(s): Shirin Akhter, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, Jens F. Sundström
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12859-019-2974-3

miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer
Cited by: 11
Author(s): Emmy Borgmästars, Hendrik A de Weerd, Zelmina Lubovac-Pilav, Malin Sund
Software Mentions: 8
Published: about 7 years ago

10.1042/BSR20203676

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis
Cited by: 7
Author(s): Zhenchao Ma, Jingyu Xu, Lixin Ru, Weihua Zhu
Software Mentions: 8
Published: over 5 years ago

10.18632/aging.203266

Clinical significance and prognostic role of an immune-related gene signature in gastric adenocarcinoma
Cited by: 4
Author(s): Rui Mao, Kehao Liu, Nana Zhao, Pengsen Guo, Yingxin Wu, Zheng Wang, Yanjun Liu, Tongtong Zhang
Software Mentions: 8
Published: about 5 years ago

10.1186/1471-2105-14-219

TCC: an R package for comparing tag count data with robust normalization strategies
Cited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: about 13 years ago

10.1186/s12859-021-04125-4

Censcyt: censored covariates in differential abundance analysis in cytometry
Cited by: 0
Author(s): Reto Gerber, Mark D. Robinson
Software Mentions: 8
Published: over 5 years ago

10.1155/2020/5843874

Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney
Cited by: 1
Author(s): Xiaoqing Wang, Xiangyu Wu, Tianyou Li, Meng Cui, Lichao Zhu, Gang Wang, Feng Guo
Software Mentions: 8
Published: about 6 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: over 11 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 5 years ago

10.1038/s41419-021-03552-8

Transcriptional profiling reveals the transcription factor networks regulating the survival of striatal neurons
Cited by: 12
Author(s): Lin Yang, 智慧蘇, Zi-Wu Wang, Zhenmeiyu Li, Zicong Shang, Heng Du, Shuai Liu, Dashi Qi, Zhengang Yang, Zhejun Xu, Zhuangzhi Zhang
Software Mentions: 8
Published: over 5 years ago

10.1038/s41419-021-03525-x

Loss of retinoic acid receptor-related receptor alpha (Rorα) promotes the progression of UV-induced cSCC
Cited by: 6
Author(s): Guolong Zhang, Guorong Yan, Fu Zhuo, Yuhao Wu, Fei Wu, Zhe Zheng, Shiji Fang, Ying Gao, Xiao Bao, Yeqiang Liu, Xiuli Wang, Sibo Zhu
Software Mentions: 8
Published: over 5 years ago

10.1186/s12859-017-1803-9

XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation
Cited by: 11
Author(s): Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson‐Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodríguez, Yidong Chen
Software Mentions: 8
Published: almost 9 years ago

10.1186/s12964-021-00728-9

Multi-omics analysis of tumor angiogenesis characteristics and potential epigenetic regulation mechanisms in renal clear cell carcinoma
Cited by: 28
Author(s): Wenzhong Zheng, Shiqiang Zhang, Huan Guo, Xiaobao Chen, Zhangcheng Huang, Shaoqin Jiang, Mengqiang Li
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: over 14 years ago

10.18632/oncotarget.13467

Effects of <i>Abies sibirica</i> terpenes on cancer- and aging-associated pathways in human cells
Cited by: 9
Author(s): Anna V. Kudryavtseva, George S. Krasnov, Anastasiya V. Lipatova, B. Ya. Alekseev, Faniya Maganova, Mikhail Shaposhnikov, Maria S. Fedorova, Anastasiya V. Snezhkina, Alexey Moskalev
Software Mentions: 8
Published: almost 10 years ago

10.1186/1471-2105-16-S11-S4

Epiviz: a view inside the design of an integrated visual analysis software for genomics
Cited by: 3
Author(s): Florin Chelaru, Héctor Corrada Bravo
Software Mentions: 7
Published: about 11 years ago

10.1093/gbe/evab144

CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation
Cited by: 17
Author(s): Galen Martin, Danelle Seymour, Brandon S. Gaut
Software Mentions: 7
Published: about 5 years ago

10.3390/cancers13092126

Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
Cited by: 7
Author(s): Syuzo Kaneko, Toutai Mitsuyama, Kouya Shiraishi, Noriko Ikawa, Kanto Shozu, Ai Dozen, Hidenori Machino, Ken Asada, Masaaki Komatsu, Asako Kukita, Kenbun Sone, Hiroshi Yoshida, Noriko Motoi, Shinya Hayami, Yutaka Yoneoka, Tomoyasu Kato, Takashi Kohno, Toru Natsume, Gottfried von Keudell, Vassiliki Saloura, Hiroki Yamaue, Ryuji Hamamoto
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers12082310

Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma
Cited by: 15
Author(s): Haitang Yang, Duo Xu, Yang Zhang, Feng Yao, Heng Zhao, Ralph A. Schmid, Ren‐Wang Peng
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-021-02372-5

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers12071788

Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data
Cited by: 44
Author(s): Jinjia Wei, Kaitang Huang, Zixi Chen, Meiling Hu, Yunmeng Bai, Shudai Lin, Hongli Du
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: almost 9 years ago

10.3390/cancers12030690

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo
Cited by: 17
Author(s): Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-02082-4

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells
Cited by: 22
Author(s): Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xun Chu, Sheng Yi, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan, Lei Yang
Software Mentions: 7
Published: about 6 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: about 12 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: over 7 years ago

10.3389/fpls.2020.619404

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I
Cited by: 18
Author(s): Abdellah Barakate, Jamie Orr, Miriam Schreiber, Isabelle Colas, Dominika Lewandowska, Nicola McCallum, Malcolm Macaulay, Jenny Morris, Mikel Arrieta, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-021-07593-3

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0230945

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River
Cited by: 3
Author(s): Jason T. Payne, Colin R. Jackson, Justin Millar, Clifford A. Ochs
Software Mentions: 7
Published: over 6 years ago

10.3389/fpls.2019.01581

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
Cited by: 24
Author(s): Tomás Carrasco-Valenzuela, Claudia Muñoz-Espinoza, Aníbal Riveros, Romina Pedreschi, Pere Arús, Reinaldo Campos-Vargas, Claudio Meneses
Software Mentions: 7
Published: almost 7 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: almost 13 years ago

10.1186/s12967-021-02936-w

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: about 5 years ago

10.3389/fonc.2021.674394

Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 5 years ago

10.18632/aging.103999

CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients
Cited by: 12
Author(s): Tianjie Liu, Qing Xia, Haibao Zhang, Zixi Wang, Wenjie Yang, Xiao Gu, Tao Hou, Yule Chen, Xinqi Pei, Guodong Zhu, Dalin He, Lei Li, Shan Xu
Software Mentions: 7
Published: almost 6 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 9 years ago

10.3389/fonc.2020.00061

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: over 6 years ago

10.18632/aging.203208

miRNAs generated from Meg3-Mirg locus are downregulated during aging
Cited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2021.639631

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca
Cited by: 11
Author(s): Piotr M. Kopec, Katarzyna Mikołajczyk, E. Jajor, A. Perek, Joanna Nowakowska, Christian Obermeier, Harmeet Singh Chawla, M. Korbas, I. Bartkowiak-Broda, Wojciech M. Karłowski
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-021-02466-0

Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.28275

Concentration dependent chromatin states induced by the bicoid morphogen gradient
Cited by: 76
Author(s): Colleen E Hannon, Shelby A. Blythe, Eric Wieschaus
Software Mentions: 7
Published: about 9 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-14-262

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Cited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: about 13 years ago

10.1186/s12920-021-01081-z

Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
Cited by: 2
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 7
Published: almost 5 years ago

10.7554/eLife.66788

An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma
Cited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-017-3938-5

A permutation-based non-parametric analysis of CRISPR screen data
Cited by: 26
Author(s): Gaoxiang Jia, Xinlei Wang, Guanghua Xiao
Software Mentions: 7
Published: about 9 years ago

10.3389/fimmu.2020.585168

Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.13503

A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types
Cited by: 50
Author(s): Yasuyuki Shima, Ken Sugino, Chris M. Hempel, Masami Shima, Praveen Taneja, James B. Bullis, Sonam Mehta, Carlos Lois, Sacha B. Nelson
Software Mentions: 7
Published: over 10 years ago

10.1186/s12864-018-5390-6

Stability of methods for differential expression analysis of RNA-seq data
Cited by: 14
Author(s): Bingqing Lin, Zhen Pang
Software Mentions: 7
Published: over 7 years ago

10.1186/1471-2164-15-452

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Cited by: 52
Author(s): Arun Kommadath, Hua Bao, Adriano S. Arantes, Graham Plastow, Christopher K. Tuggle, Shawn M. D. Bearson, Le Luo Guan, Paul Stothard
Software Mentions: 7
Published: over 12 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: over 5 years ago

10.1128/mSystems.00086-17

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota
Cited by: 8
Author(s): Eric J. de Muinck, Knut E.A. Lundin, Pål Trosvik
Software Mentions: 7
Published: almost 9 years ago

10.1186/s12864-017-4304-3

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence
Cited by: 71
Author(s): Hana Hall, Patrick S Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, R. W. Doerge, Vikki M. Weake
Software Mentions: 7
Published: almost 9 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 7 years ago

10.3389/fgene.2020.566579

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma
Cited by: 12
Author(s): Lan Jiang, Xiaolong Zhu, Hui Yang, Tianbing Chen, Kun Lv
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12885-020-06777-6

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Cited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-018-4934-0

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola
Cited by: 30
Author(s): Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason, Guangyu Sun
Software Mentions: 7
Published: about 8 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-018-4896-2

Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands
Cited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: about 8 years ago

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 5 years ago

10.1128/mBio.02880-19

Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection
Cited by: 33
Author(s): Changjiang Wang, Christian V. Forst, Tsui-Wen Chou, Adam Geber, Minghui Wang, Wissam Hamou, Melissa Smith, Robert Sebra, Bin Zhang, Bin Zhou, Elodie Ghedin
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 10 years ago

10.3389/fimmu.2019.00488

The Association Between Vitamin D and Multiple Sclerosis Risk: 1,25(OH)2D3 Induces Super-Enhancers Bound by VDR
Cited by: 24
Author(s): Ming Lu, Bennet J McComish, Kathryn P. Burdon, Bruce Taylor, Heinrich Körner
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pgen.1009294

Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-017-3580-2

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data
Cited by: 37
Author(s): Yevhen Vainshtein, Karsten Rippe, Vladimir B. Teif
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: almost 6 years ago

10.18632/aging.103949

Analysis of DNA methylation-driven genes for predicting the prognosis of patients with colorectal cancer
Cited by: 3
Author(s): Boshi Fu, Du Cheng, Zhuona Wu, Mingwei Li, Yi Zhao, Xinli Liu, Huizhe Wu, Minjie Wei
Software Mentions: 7
Published: almost 6 years ago

10.3389/fcell.2020.576996

Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients With Glioblastoma: A Multiomic Analysis
Cited by: 9
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-016-1180-9

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Cited by: 21
Author(s): Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma
Software Mentions: 7
Published: about 10 years ago

10.1002/1878-0261.12911

LncRNA NKX2‐1‐AS1 promotes tumor progression and angiogenesis via upregulation of SERPINE1 expression and activation of the VEGFR‐2 signaling pathway in gastric cancer
Cited by: 39
Author(s): Fei Teng, Ju‐Xiang Zhang, Yi Chen, Xiaodong Shen, Chang Su, Yanjiao Guo, Pu‐Hua Wang, Chencheng Shi, Ming Lei, Yiou Cao, Shao‐Qun Liu
Software Mentions: 7
Published: over 5 years ago

10.15252/emmm.201809910

Overcoming resistance to anabolic SARM therapy in experimental cancer cachexia with an HDAC inhibitor
Cited by: 16
Author(s): Sophia G. Liva, Yu Chou Tseng, Anees M. Dauki, Michael G. Sovic, Trang Vu, Sally E. Henderson, Yi Chiu Kuo, Jason Benedict, Xiaoli Zhang, Bryan Remaily, Samuel K. Kulp, Moray J. Campbell, Tanios Bekaii‐Saab, Mitch A. Phelps, Ching Shih Chen, Christopher C. Coss
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: almost 6 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-017-02932-5

Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus
Cited by: 25
Author(s): Lina Wang, Chuanai Cao, Shuangshuang Zheng, Haiyang Zhang, Panjing Liu, Qian Ge, Jingrui Li, Zhonghai Ren
Software Mentions: 7
Published: over 9 years ago

10.1186/s12859-018-2370-4

GPrank: an R package for detecting dynamic elements from genome-wide time series
Cited by: 7
Author(s): Hande Topa, Antti Honkela
Software Mentions: 7
Published: almost 8 years ago

10.1242/dmm.039297

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Cited by: 10
Author(s): Christopher Nash, Nadia Boufaied, Dunarel Badescu, Yu Chang Wang, Miltiadis Paliouras, Mark Trifiro, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-020-3433-x

RASflow: an RNA-Seq analysis workflow with Snakemake
Cited by: 30
Author(s): Xiaokang Zhang, Inge Jonassen
Software Mentions: 7
Published: over 6 years ago

10.3389/fonc.2021.657094

LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-016-2816-x

EventPointer: an effective identification of alternative splicing events using junction arrays
Cited by: 28
Author(s): Juan Pablo Romero, Ander Muniategui, Fernando J. de Miguel, Ander Aramburu, Luis M. Montuenga, Rubén Pı́o, Ángel Rubio
Software Mentions: 7
Published: about 10 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: about 9 years ago

10.1186/s12859-018-2435-4

Single sample scoring of molecular phenotypes
Cited by: 230
Author(s): Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons, Melissa J. Davis
Software Mentions: 7
Published: almost 8 years ago

10.1038/s41416-019-0571-x

Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: almost 7 years ago

10.1074/mcp.RA120.002105

MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures
Cited by: 70
Author(s): Ting Huang, Meena Choi, Manuel Tzouros, Sabrina Golling, Nikhil J. Pandya, Balázs Bánfai, Tom Dunkley, Olga Vitek
Software Mentions: 7
Published: almost 6 years ago

10.3389/fonc.2020.01409

Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Cited by: 43
Author(s): Yin Wu, Xingjun Jiang, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Xianyong Fu, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Chao Ren, Guihua Tang
Software Mentions: 7
Published: about 6 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: about 13 years ago

10.1038/s41437-019-0251-x

Genetic and genomic analysis of the seed-filling process in maize based on a logistic model
Cited by: 14
Author(s): Yin Su, Pengcheng Li, Yongsheng Xu, Jun Li, Tiantian Yang, Jie Wei, Shaohang Xu, Junjie Yu, Huiying Fang, Li Xue, Dejun Hao, Zefeng Yang, Chenwu Xu
Software Mentions: 7
Published: about 7 years ago

10.1042/BSR20204340

TIGIT-related transcriptome profile and its association with tumor immune microenvironment in breast cancer
Cited by: 8
Author(s): Qin Zhang, Chaowei Gao, Jianqiang Shao, Zunyi Wang
Software Mentions: 7
Published: over 5 years ago

10.1007/s00401-021-02263-w

Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease
Cited by: 143
Author(s): Emma Gerrits, Nieske Brouwer, Susanne M. Kooistra, Maya E. Woodbury, Yannick Vermeiren, Mirjam Lambourne, Jan Mulder, Markus P. Kummer, Thomas Möller, Knut Biber, Wilfred F. A. den Dunnen, Peter Paul De Deyn, Bart J. L. Eggen, Erik Boddeke
Software Mentions: 7
Published: over 5 years ago

10.1111/jcmm.15252

CA9 transcriptional expression determines prognosis and tumour grade in tongue squamous cell carcinoma patients
Cited by: 9
Author(s): Chenyu Guan, Dai-qiao Ouyang, Yongjie Qiao, Kan Li, Guanghui Zheng, Xiaomei Lao, Sien Zhang, Guiqing Liao, Yujie Liang
Software Mentions: 7
Published: over 6 years ago

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
Cited by: 7
Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-020-06888-1

A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples
Cited by: 6
Author(s): Huamei Li, Ingo G. H. Schmidt‐Wolf, Wenglong Ming, Xiao Sun, Hongde Liu
Software Mentions: 7
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568