bioconductor: limma | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-020-3366-4

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Cited by: 4
Author(s): Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich A. Maus, Thomas Illig, David S. DeLuca
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1716-9

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system
Cited by: 66
Author(s): Rodrigo Pulgar, Christian Hödar, Dante Travisany, Alejandro Zúñiga, Cristina Ruesca Domínguez, Alejandro Maass, Maurício González, Verónica Cambiazo
Software Mentions: 4
Published: about 11 years ago

10.1007/s00592-018-1223-y

Negative pressure wound therapy in the treatment of diabetic foot ulcers may be mediated through differential gene expression
Cited by: 12
Author(s): Sebastian Borys, Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Jerzy Hohendorff, Teresa Koblik, Julita Machlowska, Beata Kieć‐Wilk, Paweł Wołkow, Maciej Małecki
Software Mentions: 4
Published: about 8 years ago

10.1007/s00401-020-02230-x

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
Cited by: 21
Author(s): Sheila Mansouri, Suganth Suppiah, Yasin Mamatjan, Irene Paganini, Jeffrey Liu, Shirin Karimi, Vikas Patil, Farshad Nassiri, Olivia Singh, Yogi Sundaravadanam, Pramod C. Rath, Roberta Sestini, Francesca Gensini, Sameer Agnihotri, Jaishri O. Blakeley, Kimberly Laskie Ostrow, David A. Largaespada, Scott R. Plotkin, Anat Stemmer‐Rachamimov, Marcela Maria Ferrer, Trevor J. Pugh, Kenneth Aldape, Laura Papi, Gelareh Zadeh
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-14-188

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
Cited by: 14
Author(s): George Y. Wu, Hongkai Ji
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-020-70368-5

Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma
Cited by: 16
Author(s): Prithvi Singh, Archana Sharma, Jha R, Shweta Arora, Rafiq Ahmad, Arshad Husain Rahmani, Saleh A. Almatroodi, Ravins Dohare, Mansoor Ali Syed
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-70540-x

Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis
Cited by: 16
Author(s): Shumei Tang, Xiufen Wang, Tianci Deng, Huipeng Ge, Xiangcheng Xiao
Software Mentions: 4
Published: about 6 years ago

10.18632/aging.202170

A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adults
Cited by: 10
Author(s): Chun-Kai Wen, Hongxue Wang, Han Wang, Hao Yuan Mo, Weiying Zhong, Jing Tang, Yuefeng Lu, Wenxian Zhou, Aihua Tan, Yan Liu, Weimin Xie
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-9-164

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Cited by: 32
Author(s): Richard D. Pearson
Software Mentions: 4
Published: over 18 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0031505

Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis
Cited by: 10
Author(s): Zhide Fang, Ruofei Du, Xiangqin Cui
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0052021

Prospective Transcriptomic Pathway Analysis of Human Lymphatic Vascular Insufficiency: Identification and Validation of a Circulating Biomarker Panel
Cited by: 46
Author(s): Shin Lin, Jeanna Kim, Mi-Joung Lee, Leslie Roche, Nancy L. Yang, Philip S. Tsao, Stanley G. Rockson
Software Mentions: 4
Published: almost 14 years ago

10.7554/eLife.18312

PDZD7-MYO7A complex identified in enriched stereocilia membranes
Cited by: 37
Author(s): Clive P. Morgan, Jocelyn F. Krey, M’hamed Grati, Bo Zhao, Shannon Fallen, Abhiraami Kannan-Sundhari, Xue Zhong Liu, Dongseok Choi, Ulrich Müller, Peter G. Barr-Gillespie
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-019-6142-y

DNA methylation profiles capturing breast cancer heterogeneity
Cited by: 19
Author(s): Xiao Chen, Jianying Zhang, Xiaofeng Dai
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.mcpro.2021.100065

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits
Cited by: 5
Author(s): F. Schober, Ilian Atanassov, David Moore, Javier Calvo‐Garrido, Marco F. Moedas, Anna Wedell, Christoph Freyer, Anna Wredenberg
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-020-03935-2

H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection
Cited by: 9
Author(s): Nan Zhou, Ji Bao, Yuping Ning
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-8-449

A comparison of Affymetrix gene expression arrays
Cited by: 59
Author(s): Mark D. Robinson, Terence P. Speed
Software Mentions: 4
Published: almost 19 years ago

10.1038/s41598-020-74798-z

Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients
Cited by: 19
Author(s): Nathalie Acevedo, Rui Benfeitas, Shintaro Katayama, Sören Bruhn, Ann‐Catrin Andersson, Gustav Wikberg, Lena Lundeberg, Jessica M. Lindvall, Dario Greco, Juha Kere, Cilla Söderhäll, Annika Scheynius
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-016-2646-x

A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
Cited by: 25
Author(s): Montserrat Torres-Oliva, Isabel Almudí, Alistair P. McGregor, Nico Posnien
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-75326-9

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress
Cited by: 33
Author(s): Meltem Weger, Daniel Alpern, Antoine Cherix, Sriparna Ghosal, Jocelyn Grosse, Julie Russeil, Rolf Gruetter, E. R. de Kloet, Bart Deplancke, Carmen Sandi
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2018.01715

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period
Cited by: 39
Author(s): Enrique Doster, Pablo Rovira, Noelle Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Steven M. Lakin, Christopher Dean, Lyndsey Linke, Roberta J. Magnuson, Kenneth Jones, Christina Boucher, Jamie Ruiz, K. E. Belk, Paul S. Morley
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-76048-8

Characterization of somatic mutation-associated microenvironment signatures in acute myeloid leukemia patients based on TCGA analysis
Cited by: 4
Author(s): Jun Wang, Feng‐Ting Dao, Lu Yang, Ya‐Zhen Qin
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2017.01808

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Cited by: 36
Author(s): François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-021-07729-5

The holobiont transcriptome of teneral tsetse fly species of varying vector competence
Cited by: 3
Author(s): Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer, Rita V. M. Rio
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.00944

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers
Cited by: 43
Author(s): Tommy Harding, Andrew J. Roger, Alastair G. B. Simpson
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.202558

ENAM gene associated with T classification and inhibits proliferation in renal clear cell carcinoma
Cited by: 8
Author(s): Xiaohan Ren, Shengjie Liang, Yang Li, Yisheng Ji, Lin Li, Chao Qin, Kai Fang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-06789-3

Distinctions between sex and time in patterns of DNA methylation across puberty
Cited by: 11
Author(s): Sarah R. Moore, Kathryn L. Humphreys, Natalie L. Colich, Elena Goetz Davis, David Lin, Julia L. MacIsaac, Michæl S. Kobor, Ian H. Gotlib
Software Mentions: 4
Published: over 6 years ago

10.3389/fmed.2020.615981

DNA Repair-Based Gene Expression Signature and Distinct Molecular Subtypes for Prediction of Clinical Outcomes in Lung Adenocarcinoma
Cited by: 8
Author(s): Bin Hu, Di Liu, Yinqiang Liu, Zhixi Li
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms20204983

Methionine Adenosyltransferase 1a (MAT1A) Enhances Cell Survival During Chemotherapy Treatment and is Associated with Drug Resistance in Bladder Cancer PDX Mice
Cited by: 10
Author(s): Kelly A. Martin, Nicholas R. Hum, Aimy Sebastian, Wei He, Salma Siddiqui, Paramita M. Ghosh, Chong Xian Pan, Ralph de Vere White, Gabriela G. Loots
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-018-0581-1

Methylome profiling of healthy and central precocious puberty girls
Cited by: 28
Author(s): Danielle Bessa, Mariana Maschietto, Carlos F. Aylwin, Ana Pinheiro Machado Canton, Vinícius Nahime Brito, Delanie B Macedo, Marina Cunha-Silva, Heloísa Marcelina Cunha Palhares, Elisabete Aparecida Mantovani Rodrigues de Resende, Maria de Fátima Borges, Berenice B. Mendonca, Irène Netchine, Ana Cristina Victorino Krepischi, Alejandro Lomniczi, Sergio R. Ojeda, Ana Cláudia Latronico
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmed.2021.654635

Multi-Omics Integrative Analysis Uncovers Molecular Subtypes and mRNAs as Therapeutic Targets for Liver Cancer
Cited by: 4
Author(s): Yi Shen, Wei Xiong, Qi Gu, Qin Zhang, Yue Jia, Changsong Liu, Duan Wang
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102824

Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of osteosarcoma
Cited by: 103
Author(s): Chi Zhang, Jinghui Zheng, Zong-Han Lin, Haoyuan Lv, Zhuo-Miao Ye, Yueping Chen, Xiaoyun Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2018.01626

Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Cited by: 23
Author(s): Alejandro M. Labella, Esther García-Rosado, Isabel Bandı́n, Carlos P. Dopazo, Dolores Castro, M. Carmen Alonso, Juan J. Borrego
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers11020263

Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts
Cited by: 2
Author(s): Hanna Najgebauer, Andrew F. Jarnuczak, Andrea Varró, Christopher M. Sanderson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-016-2952-3

Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response
Cited by: 46
Author(s): Marcos Paolinelli, José Manuel Villalobos-Escobedo, Philippe E. Rolshausen, Alfredo Herrera-Estrella, Clara E. Galindo-Sánchez, José Fabricio López-Hernández, Rufina Hernández-Martínez
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-020-76657-3

Distinct regional ontogeny and activation of tumor associated macrophages in human glioblastoma
Cited by: 64
Author(s): Alexander Landry, Michael Balas, Saira Alli, Julian Spears, Zsolt Zádor
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.molcel.2021.06.016

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
Cited by: 31
Author(s): Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlösser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-13-296

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data
Cited by: 167
Author(s): James R. Perkins, J. D. K. Dawes, Stephen B. McMahon, David L.H. Bennett, Christine A. Orengo, Matthias Kohl
Software Mentions: 4
Published: over 14 years ago

10.1186/1471-2105-16-S17-S5

A computational method for drug repositioning using publicly available gene expression data
Cited by: 4
Author(s): K M Shabana, K. A. Abdul Nazeer, Meeta Pradhan, Mathew Palakal
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-017-1915-2

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder
Cited by: 10
Author(s): Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chenglian Feng, Guang Fan
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-9-S2-S12

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Cited by: 30
Author(s): Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì Maria Victoria Grober, Maria Ravo, Angelo Facchiano, Claudia Angelini, Alessandro Weisz
Software Mentions: 4
Published: over 18 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-020-79781-2

Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Cited by: 7
Author(s): Endika Varela-Martínez, Giulia I. Corsi, Christian Anthon, Jan Gorodkin, Begoña M. Jugo
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22052679

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model
Cited by: 15
Author(s): Fábio Pértille, Manuel Álvarez‐Rodríguez, Arthur Nery da Silva, Isabel Barranco, Jordi Roca, Carlos Guerrero-Bosagna, Heriberto Rodríguez-Martinez
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-79704-1

Data-driven detection of subtype-specific differentially expressed genes
Cited by: 9
Author(s): Lulu Chen, Yingzhou Lu, Chiung Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.705511

Screening and Validation of the Hypoxia-Related Signature of Evaluating Tumor Immune Microenvironment and Predicting Prognosis in Gastric Cancer
Cited by: 27
Author(s): Jun‐Peng Pei, Chundong Zhang, Maimaititusun Yusupu, Dong‐Qiu Dai
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-80158-8

Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort
Cited by: 6
Author(s): Nikita Baiju, Torkjel M. Sandanger, Pål Sætrom, Therese Haugdahl Nøst
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.729359

Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy
Cited by: 9
Author(s): Hang Ji, Yixu Ba, Shuai Ma, Kezuo Hou, Shan Mi, Xin Gào, Jiaqi Jin, Qingguo Gong, Ting Liu, Fang Wang, Zhihui Liu, Shupeng Li, Jianyang Du, Shaoshan Hu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12934-016-0434-6

Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain
Cited by: 32
Author(s): Stéphanie Rollero, Jean-Roch Mouret, Isabelle Sanchez, Carole Camarasa, Anne Ortiz‐Julien, Jean‐Marie Sablayrolles, Sylvie Dequin
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0047107

Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos
Cited by: 12
Author(s): Elisa A. Casanova, Michał Okoniewski, Paolo Cinelli
Software Mentions: 4
Published: almost 14 years ago

10.3389/fimmu.2021.676922

DNA Damage Repair Status Predicts Opposite Clinical Prognosis Immunotherapy and Non-Immunotherapy in Hepatocellular Carcinoma
Cited by: 11
Author(s): Yunfei Chen, Wei Xu, Xiaofang Deng, Yu Zhang, Rui Liao, Youzan Li, Hongji Yang, Kai Chen
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-10-373

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers
Cited by: 170
Author(s): Xinxia Peng, Li Yu, Kathie–Anne Walters, Elizabeth Rosenzweig, Sharon Lederer, Lauri Aicher, Sean Proll, Michael G. Katze
Software Mentions: 4
Published: about 17 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: almost 20 years ago

10.1186/s12859-019-2619-6

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics
Cited by: 16
Author(s): Philip Berg, Evan W. McConnell, Leslie M. Hicks, S. Popescu, George V. Popescu
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2017.01351

Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16
Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
Software Mentions: 4
Published: almost 9 years ago

10.3389/fimmu.2019.01063

α7 Nicotinic Acetylcholine Receptor Signaling Modulates Ovine Fetal Brain Astrocytes Transcriptome in Response to Endotoxin
Cited by: 16
Author(s): Mingju Cao, James W. MacDonald, Hai L. Liu, Molly Weaver, Marina Farrel Cortês, Lucien Daniel Durosier, Patrick Burns, Gilles Fecteau, André Desrochers, Jay Schulkin, Marta C. Antonelli, Raphael Bernier, Michael O. Dorschner, Theo K. Bammler, Martin G. Frasch
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.25965

Snail mediates repression of the Dlk1-Dio3 locus in lung tumor-infiltrating immune cells
Cited by: 4
Author(s): Svenja Groeneveld, Julien Faget, Nadine Zangger, Etienne Meylan
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.64680

Urocortin-3 neurons in the mouse perifornical area promote infant-directed neglect and aggression
Cited by: 23
Author(s): Anita E. Autry, Wu Zheng, Vikrant Kapoor, Johannes Kohl, Dhananjay Bambah-Mukku, Nimrod D. Rubinstein, Brenda Marin-Rodriguez, Ilaria Carta, Victoria Sedwick, Ming Tang, Catherine Dulac
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2164-11-50

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data
Cited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: over 16 years ago

10.1186/1471-2164-12-64

Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library
Cited by: 118
Author(s): Pedro López-Romero
Software Mentions: 4
Published: over 15 years ago

10.18632/aging.202365

Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinoma
Cited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cell.2013.03.012

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3
Cited by: 288
Author(s): Joerg Betschinger, Jennifer Nichols, Sabine Dietmann, Philip Corrin, Patrick J. Paddison, Austin Smith
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0035035

MAPK Signaling Determines Anxiety in the Juvenile Mouse Brain but Depression-Like Behavior in Adults
Cited by: 37
Author(s): Benedikt Wefers, Christiane Hitz, Sabine M. Hölter, Dietrich Trümbach, Jens Hansen, Peter Weber, Benno Pütz, Jan M. Deussing, Martin Hrabě de Angelis, Till Roenneberg, Fang Zheng, Christian Alzheimer, Alcino Silva, Wolfgang Wurst, Ralf Kühn
Software Mentions: 4
Published: over 14 years ago

10.3389/fimmu.2021.731751

The CXCL Family Contributes to Immunosuppressive Microenvironment in Gliomas and Assists in Gliomas Chemotherapy
Cited by: 15
Author(s): Zeyu Wang, Yuze Liu, Yuyao Mo, Hao Zhang, Ziyu Dai, Xun Zhang, Weijie Ye, Hui Cao, Zhixiong Liu, Quan Cheng
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2017.01221

PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8+ T Cells
Cited by: 56
Author(s): Jacob S. Bowers, Kinga Majchrzak, Michelle H. Nelson, Bülent Arman Aksoy, Megan Wyatt, Aubrey S. Smith, Stefanie R. Bailey, Lillian R. Neal, Jeff Hammerbacher, Chrystal M. Paulos
Software Mentions: 4
Published: almost 9 years ago

10.3389/fimmu.2021.695806

An Unbiased Machine Learning Exploration Reveals Gene Sets Predictive of Allograft Tolerance After Kidney Transplantation
Cited by: 7
Author(s): Qiang Fu, Divyansh Agarwal, Kevin Deng, Rudy Matheson, Hongji Yang, Wei Liang, Ran Qing, Shaoping Deng, James F. Markmann
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.102820

Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9010149

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species
Cited by: 21
Author(s): Niranjan P. Sahu, Zsolt Merényi, Balázs Bálint, Brigitta Kiss, György Sipos, Rebecca A. Owens, László G. Nagy
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22041632

Construction and Validation of a Prognostic Gene-Based Model for Overall Survival Prediction in Hepatocellular Carcinoma Using an Integrated Statistical and Bioinformatic Approach
Cited by: 8
Author(s): Eskezeia Y. Dessie, Siang-Jyun Tu, Hui-Shan Chiang, Jeffrey J. P. Tsai, Ya‐Sian Chang, Jan-Gowth Chang, Ka-Lok Ng
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-8-146

Analysis of probe level patterns in Affymetrix microarray data
Cited by: 15
Author(s): A. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson
Software Mentions: 4
Published: over 19 years ago

10.3389/fimmu.2021.667875

TNF-Alpha Pathway Alternation Predicts Survival of Immune Checkpoint Inhibitors in Non-Small Cell Lung Cancer
Cited by: 9
Author(s): Anqi Lin, Hongman Zhang, Hua Meng, Ze Deng, Tianqi Gu, Peng Luo, Jian Zhang
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-82853-6

Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia
Cited by: 19
Author(s): Kornphimol Kulthong, Guido Hooiveld, Loes P. M. Duivenvoorde, Ignacio Miro Estruch, Victor Augustus Marin, Meike van der Zande, Hans Bouwmeester
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-82976-w

Integrated analysis identifies oxidative stress genes associated with progression and prognosis in gastric cancer
Cited by: 29
Author(s): Zhengyuan Wu, Lin Wang, Zhenpei Wen, Jun Yao
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9020459

A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions
Cited by: 6
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Carlos Lax, Marta Silva, Javier Capilla, Eusebio Navarro, Victoriano Garre
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-84647-2

Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)
Cited by: 8
Author(s): Timothy I. Shaw, Li Dong, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony A. High, Kanisha Kavdia, Vishwajeeth Pagala, Bridget Shaner, Deqing Pei, John Easton, Laura J. Janke, Shaina N. Porter, Xiaotu Ma, Cheng Cheng, Shondra M. Pruett-Miller, John K. Choi, Jiyang Yu, Junmin Peng, Wei Gu, A. Thomas Look, James R. Downing, Jinghui Zhang
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cell.2016.09.037

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Cited by: 818
Author(s): Biola M. Javierre, Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns, Steven W. Wingett, Csilla Várnai, Michiel J. Thiecke, Frances Burden, Samantha Farrow, Antony J. Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G. Stunnenberg, John A. Todd, Daniel R. Zerbino, Oliver Stegle, Willem H. Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms22031332

The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling
Cited by: 4
Author(s): Daniel Pensold, Julia Gehrmann, Georg Pitschelatow, Asa Walberg, Kai Braunsteffer, Julia Reichard, Amin Ravaei, Jenice Linde, Angelika Lampert, Ivan G. Costa, Geraldine Zimmer-Bensch
Software Mentions: 4
Published: over 5 years ago

10.1186/s13075-020-02195-y

Increased serum calpain activity is associated with HMGB1 levels in systemic sclerosis
Cited by: 9
Author(s): Ji-Na Zheng, Yang Li, Yue-Mei Yan, Yong Yu, Wenqi Shao, Qiang Wang
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2018.00183

Network-Based Predictors of Progression in Head and Neck Squamous Cell Carcinoma
Cited by: 20
Author(s): Nasim Sanati, Ovidiu D. Iancu, Guanming Wu, Jan Jacobs, Shannon K. McWeeney
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2021.591623

Identification of Prognostic Biomarkers and Correlation With Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network
Cited by: 3
Author(s): Zhaoxia Pu, Yuanyuan Zhu, Xiaofang Wang, Yun Zhong, Fang Peng, Yiya Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.628136

Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-86536-0

Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study
Cited by: 6
Author(s): Binisha H. Mishra, Pashupati P. Mishra, Emma Raitoharju, Saara Marttila, Nina Mononen, Harri Sievänen, Jorma Viikari, Markus Juonala, Marika Laaksonen, Nina Hutri‐Kähönen, Mika Kähönen, Olli T. Raitakari, Terho Lehtimäki
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-87540-0

Identification of novel autophagy-related lncRNAs associated with a poor prognosis of colon adenocarcinoma through bioinformatics analysis
Cited by: 43
Author(s): Danni Wu, Zhenhua Yin, Yisheng Ji, Lin Li, Yunxin Li, F. Meng, Xiaohan Ren, Ming Xu
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2021.680369

Identification of MX2 as a Novel Prognostic Biomarker for Sunitinib Resistance in Clear Cell Renal Cell Carcinoma
Cited by: 27
Author(s): Yuang Wei, Xinglin Chen, Xiaohan Ren, Bao Wang, Qian Zhang, Hengtao Bu, Ji Qian, Pengfei Shao
Software Mentions: 4
Published: about 5 years ago

10.1186/s12868-021-00622-7

Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm
Cited by: 7
Author(s): Yutong Pan, Jianing Lu, Biao Yang, Cameron Lenahan, Jianmin Zhang, Anwen Shao
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203184

The circadian clock is associated with prognosis and immune infiltration in stomach adenocarcinoma
Cited by: 13
Author(s): Zhihao Huang, Aoxiao He, Jiakun Wang, Hongmei Lü, Rongguiyi Zhang, Linquan Wu, Qian Feng
Software Mentions: 4
Published: about 5 years ago

10.1186/s12935-021-02069-6

Integrative analysis of ceRNA network reveals functional lncRNAs associated with independent recurrent prognosis in colon adenocarcinoma
Cited by: 11
Author(s): Yinling Mao, Jiachen Lv, Li Jiang, Yihui Wang
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2019.00159

A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures
Cited by: 22
Author(s): Adib Shafi, Tin Nguyen, Azam Peyvandipour, Hung Son Nguyen, Sorin Drăghici
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.648329

Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis
Cited by: 10
Author(s): Wanchen Ning, Aneesha Acharya, Zhenjie Sun, Anthony Chukwunonso Ogbuehi, Cong Liu, Shiting Hua, Qiyun Ou, Muhui Zeng, Xiangqiong Liu, Yupei Deng, Rainer Haak, Dirk Ziebolz, Gerhard Schmalz, George Pelekos, Yan Wang, Xianda Hu
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.599261

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Cited by: 53
Author(s): Komudi Singh, Yunching Chen, Shakiba Hassanzadeh, Han Kim, Jennifer Judy, Fayaz Seifuddin, Ilker Tunc, Michael N. Sack, Mehdi Pirooznia
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-87759-x

SIRT1 promotes lipid metabolism and mitochondrial biogenesis in adipocytes and coordinates adipogenesis by targeting key enzymatic pathways
Cited by: 58
Author(s): Yasser Majeed, Najeeb Halabi, Aisha Madani, Rudolf Engelke, Aditya Bhagwat, Houari Abdesselem, Maha Victor Agha, Muneera Vakayil, Raphael Jean Courjaret, Neha Goswami, Hisham Ben Hamidane, Mohamed A. Elrayess, Arash Rafii, Johannes Graumann, Frank Schmidt, Nayef Mazloum
Software Mentions: 4
Published: over 5 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776