bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12885-021-08447-7

Identification of a tumor microenvironment-related seven-gene signature for predicting prognosis in bladder cancer
Cited by: 17
Author(s): Wang Zhi, Lei Tu, Minfeng Chen, Shiyu Tong
Software Mentions: 8
Published: about 5 years ago

10.1186/1471-2105-15-224

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Cited by: 275
Author(s): Krishna R. Kalari, Asha Nair, Jaysheel Bhavsar, Daniel R. O’Brien, Jaime Davila, Matthew A. Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
Software Mentions: 8
Published: about 12 years ago

10.7554/eLife.44036

Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci
Cited by: 38
Author(s): Sonia Sen, Sachin Chanchani, Tony D. Southall, Chris Q. Doe
Software Mentions: 8
Published: over 7 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

10.7554/eLife.52690

Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta
Cited by: 28
Author(s): Eric Engelbrecht, Michel V. Levesque, Liqun He, Michael Vanlandewijck, Anja Nitzsche, Hira Niazi, Andrew Kuo, Sasha A Singh, Masamichi Aikawa, Kristina M. Holton, Richard L. Proia, Mari Kono, William T. Pu, Eric Camerer, Christer Betsholtz, Timothy Hla
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: about 7 years ago

10.3390/cancers13071561

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma
Cited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.58331

An essential role for MEF2C in the cortical response to loss of sleep in mice
Cited by: 19
Author(s): Theresa E. Bjorness, Ashwinikumar Kulkarni, Volodymyr Rybalchenko, Ayako Suzuki, Catherine Bridges, Adam J. Harrington, Christopher W. Cowan, Joseph S. Takahashi, Genevieve Konopka, Robert Greene
Software Mentions: 8
Published: almost 6 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

10.3389/fphar.2021.608778

Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma
Cited by: 0
Author(s): Zhichao Liu, Xi Chen, Ruth Roberts, Ruili Huang, Mike Mikailov, Weida Tong
Software Mentions: 8
Published: over 5 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: over 6 years ago

10.1186/s13058-021-01445-4

Single cell transcriptome atlas of mouse mammary epithelial cells across development
Cited by: 19
Author(s): Bhupinder Pal, Yunshun Chen, Michael J. G. Milevskiy, François Vaillant, Lexie Prokopuk, Caleb A. Dawson, Bianca D. Capaldo, Xiaoyu Song, Felicity C. Jackling, Paul Timpson, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 8
Published: about 5 years ago

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

10.1186/s12906-020-02939-y

A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies
Cited by: 3
Author(s): Mengwei Ni, Xinkui Liu, Ziqi Meng, Shuyu Liu, Shanshan Jia, Yingying Liu, Wei Zhou, Jiarui Wu, Jingyuan Zhang, Siyu Guo, Jialin Li, Haojia Wang, Xiaomeng Zhang
Software Mentions: 8
Published: about 6 years ago

10.1007/s00018-018-2898-5

Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: about 8 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: about 11 years ago

10.1534/g3.119.400185

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: about 7 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 5 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

10.3390/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

10.26508/lsa.201800085

Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 8 years ago

10.1038/s41598-021-87234-7

Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model
Cited by: 9
Author(s): Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-40285-3

Phenotypic and transcriptomic characterization of canine myeloid-derived suppressor cells
Cited by: 22
Author(s): Michelle R. Goulart, Sabina I. Hlavaty, Yu-Mei Chang, Gerry Polton, Anneliese Stell, James A. Perry, Ying Wu, Eshita Sharma, John Broxholme, Avery C. Lee, Balázs Szladovits, Mark Turmaine, John G. Gribben, Dong Xia, Oliver A. Garden
Software Mentions: 7
Published: over 7 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: almost 10 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 6 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: about 5 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: about 8 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

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: over 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

10.18632/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

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 10 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

10.3390/genes11101165

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
Cited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: almost 6 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

10.1186/1471-2105-14-262

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: almost 13 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

10.1016/j.ccell.2020.08.016

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer
Cited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: almost 6 years ago

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: over 6 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

10.1186/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: about 12 years ago

10.1038/s41598-018-37746-6

The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region
Cited by: 22
Author(s): Nora Fernández-Jiménez, Koldo García-Etxebarria, Leticia Plaza-Izurieta, Irati Romero-Garmendia, Amaia Jauregi-Miguel, María Legarda, Szilvia Ecsedi, Ainara Castellanos–Rubio, Vincent Cahais, Cyrille Cuenin, Davide Degli Esposti, Iñaki Irastorza, Héctor Hernández-Vargas, Zdenko Herceg, José Ramón Bilbao
Software Mentions: 7
Published: over 7 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: over 8 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

10.3389/fonc.2021.734873

DNA Methylation Regulator-Meditated Modification Patterns Define the Distinct Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 3
Author(s): Dejian Yuan, Zehong Wei, Yicheng Wang, Cheng Fang, Yujie Zeng, Yang Li, Shangyu Zhang, Jianbo Li, Renkuan Tang
Software Mentions: 7
Published: almost 5 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: over 8 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

10.1371/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

10.1371/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

10.1371/journal.pone.0147249

Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies
Cited by: 43
Author(s): Iddo Z. Ben‐Dov, Veronica M. Whalen, Béatrice Goilav, Klaas E.A. Max, Thomas Tuschl
Software Mentions: 7
Published: over 10 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/s12864-021-07509-1

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

10.3389/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

10.1186/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/fmicb.2020.00995

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography
Cited by: 31
Author(s): Xin Zhou, Jinting Wang, Z.F. Zhang, Wei Li, Wen Chen, Lei Cai
Software Mentions: 7
Published: about 6 years ago

10.1038/s41422-019-0168-1

Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
Cited by: 64
Author(s): Rui Gao, Xingqun Liang, Sirisha Cheedipudi, Julio Cordero, Xiyi Jiang, Qingquan Zhang, Luca Caputo, Stefan Günther, Carsten Kuenne, Yongcheng Ren, Shoumo Bhattacharya, Xuejun Yuan, Guillermo Barreto, Yihan Chen, Thomas Braun, Sylvia M. Evans, Yunfu Sun, Gergana Dobreva
Software Mentions: 7
Published: over 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: over 12 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

10.1186/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

10.3390/ijms21134727

Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies
Cited by: 16
Author(s): Maximilian Fuchs, Fabian Philipp Kreutzer, Lorenz A. Kapsner, Saskia Mitzka, Annette Just, Filippo Perbellini, Cesare M. Terracciano, Xiaoyan Ke, Robert Geffers, Christian Bogdan, Hans‐Ulrich Prokosch, Jan Fiedler, Thomas Thum, Meik Kunz
Software Mentions: 7
Published: about 6 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

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 5 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/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

10.3389/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: almost 6 years ago

10.1371/journal.pone.0219723

Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima
Cited by: 10
Author(s): Gareth A. Pearson, Neusa Martins, Pedro M Madeira, Ester Á. Serrão, Inka Bartsch
Software Mentions: 7
Published: almost 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

10.1186/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

10.1186/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

10.1186/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

10.1186/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

10.1186/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

10.1007/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

10.7554/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: almost 9 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: over 12 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: over 6 years ago

10.1038/s42003-021-01897-6

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Cited by: 9
Author(s): Giorgia Maroni, Mahmoud A. Bassal, Indira Krishnan, Chee Wai Fhu, Virginia Savova, Rapolas Žilionis, Valerie A. Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Barbara Storti, Julio Castaño, Riccardo Panella, Jia Li, Corinne E. Gustafson, Sam Fox, Rachel Levy, Claire Meyerovitz, Peter J. Tramontozzi, Kimberly Vermilya, Assunta De Rienzo, Stefania Crucitta, Daniela S. Bassères, Marla Weetall, Art Branstrom, Alessandra Giorgetti, Raffaele Ciampi, Marzia Del Re, Romano Danesi, Ranieri Bizzarri, Henry Yang, Olivier Kocher, Allon M. Klein, Robert S. Welner, Raphael Bueno, Maria Cristina Magli, John G. Clohessy, Azhar Ali, Daniel G. Tenen, Elena Levantini
Software Mentions: 7
Published: over 5 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

10.1186/1471-2105-14-91

A comparison of methods for differential expression analysis of RNA-seq data
Cited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: over 13 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: over 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

10.7554/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/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: almost 8 years ago

10.1186/s13195-020-00654-x

Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through RNA sequencing analysis
Cited by: 44
Author(s): Daichi Shigemizu, Tomohisa Mori, Shintaro Akiyama, Sayuri Higaki, Hiroshi Watanabe, Takashi Sakurai, Shumpei Niida, Kouichi Ozaki
Software Mentions: 7
Published: about 6 years ago

10.18632/aging.104116

Integrated analysis of a competing endogenous RNA network reveals an 11-lncRNA prognostic signature in ovarian cancer
Cited by: 3
Author(s): Yongjian Zhang, Hu Zhou, Mei‐Yin Zhang, Linan Xing, Chang Yang, Bairong Xia, Ge Lou
Software Mentions: 7
Published: over 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/s13148-019-0651-z

Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
Cited by: 18
Author(s): Shivani Kamdar, Ruth Isserlin, Theodorus van der Kwast, Alexandre R. Zlotta, Gary D. Bader, Neil Fleshner, Bharati Bapat
Software Mentions: 7
Published: over 7 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: over 5 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-018-1438-9

UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Cited by: 80
Author(s): Wenan Chen, Yán Li, John Easton, David Finkelstein, Gang Wu, Xiang Chen
Software Mentions: 7
Published: about 8 years ago

10.1038/sdata.2018.21

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich’s ataxia patients
Cited by: 22
Author(s): Marta Seco-Cervera, Daymé González-Rodríguez, José Santiago Ibáñez-Cabellos, Lorena Peiró-Chova, Federico V. Pallardó, José Luis García-Giménez
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-019-1862-5

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Cited by: 225
Author(s): José Alquicira-Hernández, Anuja Sathe, Hanlee P. Ji, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: over 6 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: over 10 years ago

10.1186/s13059-016-0940-1

A benchmark for RNA-seq quantification pipelines
Cited by: 146
Author(s): Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri D. Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Software Mentions: 7
Published: over 10 years ago

10.1126/sciimmunol.abg0833

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Cited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.678436

Development of an Immune-Related LncRNA Prognostic Signature for Glioma
Cited by: 8
Author(s): Yudong Cao, Hecheng Zhu, Jun Tan, Yin Wu, Quanwei Zhou, Zhaoqi Xin, Zhaoping Wu, Zhipeng Jiang, Youwei Guo, Yirui Kuang, Can Li, Ming Zhao, Xingjun Jiang, Jian Peng, Chao Ren
Software Mentions: 7
Published: about 5 years ago

10.1038/s41597-020-00659-z

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
Cited by: 35
Author(s): Fayaz Seifuddin, Komudi Singh, Abhilash Suresh, Jennifer Judy, Yun Ching Chen, Vijender Chaitankar, Ilker Tunc, Xiangbo Ruan, Ping Li, Yi Chen, Haiming Cao, Richard S. Lee, Fernando S. Goes, Peter P. Zandi, M. Saleet Jafri, Mehdi Pirooznia
Software Mentions: 7
Published: almost 6 years ago

10.3389/fgene.2021.722981

Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Cited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
Software Mentions: 7
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568