Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: limma

https://packages.ecosyste.ms/registries/bioconductor.org/packages/limma

Linear Models for Microarray Data
3 versions
Latest release: about 1 year ago
314 dependent packages
4,663,292 downloads total

Papers Mentioning limma 7,776

10.1186/s13045-021-01131-0
High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis
Cited by: 16
Author(s): Bo Ren, Jinshou Yang, Yuming Wang, Gang Ye, Huanyu Wang, Chen Yuan, Ruiyuan Xu, Xu-Ning Fan, Lei You, Taiping Zhang, Yupei Zhao
Software Mentions: 6
Published: over 3 years ago
10.7150/ijms.51918
Exploration of the relationship between tumor mutation burden and immune infiltrates in colon adenocarcinoma
Cited by: 3
Author(s): Rong Ouyang, Zhongzhuan Li, Peng Peng, Jinxiu Zhang, Jun Li, Mengbin Qin, Jiean Huang
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pgen.1008531
ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: almost 5 years ago
10.7150/ijms.46456
Lipid Metabolism is the common pathologic mechanism between Type 2 Diabetes Mellitus and Parkinson's disease
Cited by: 6
Author(s): Xi Zhang, Yu Fan, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13045-018-0679-0
Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
Cited by: 31
Author(s): Benoît Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez‐Bougie, Sophie Maïga, Alban Gaignard, David Chiron, Emmanuelle Ménoret, Steven Le Gouill, Philippe Moreau, Martine Amiot, Catherine Pellat‐Deceunynck
Software Mentions: 6
Published: about 6 years ago
10.1186/s12864-016-2849-1
Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs
Cited by: 26
Author(s): M. S. Islam, Christine Große‐Brinkhaus, Maren Pröll, Muhammad Jasim Uddin, Sharmin Aqter Rony, Dawit Tesfaye, Ernst Tholen, Michael Hölker, K. Schellander, Christiane Neuhoff
Software Mentions: 6
Published: over 8 years ago
10.1186/s12859-018-2096-3
A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip
Cited by: 32
Author(s): Zhenxing Wang, Xiaoliang Wu, Yadong Wang
Software Mentions: 6
Published: over 6 years ago
10.1186/1471-2105-10-201
A-MADMAN: Annotation-based microarray data meta-analysis tool
Cited by: 35
Author(s): Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
Software Mentions: 6
Published: over 15 years ago
10.1186/1471-2105-12-92
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Cited by: 5
Author(s): Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
Software Mentions: 6
Published: over 13 years ago
10.1007/s00018-020-03485-z
Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
Cited by: 17
Author(s): Tiziana Caputo, Van Du T. Tran, Nasim Bararpour, Carine Winkler, Gabriela Aguileta, Bao Khanh Trang, Greta Maria Paola Giordano Attianese, Anne Wilson, Aurélien Thomas, Marco Pagni, Nicolas Guex, Béatrice Desvergne, Federica Gilardi
Software Mentions: 6
Published: over 4 years ago
10.3389/fgene.2019.00025
LncRNAs GIHCG and SPINT1-AS1 Are Crucial Factors for Pan-Cancer Cells Sensitivity to Lapatinib
Cited by: 20
Author(s): Zhen Xiang, Shuzheng Song, Zhenggang Zhu, Wenhong Sun, Jaron E. Gifts, Sam Q. Sun, Qiushi Shauna Li, Yingyan Yu, Keqin Kathy Li
Software Mentions: 6
Published: almost 6 years ago
10.1111/acel.13381
Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
Cited by: 7
Author(s): Rebecca L. McIntyre, Simone Denis, Rashmi Kamble, Marte Molenaars, Michael Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli, Aldo Jongejan, Morten Scheibye‐Knudsen, Riekelt H. Houtkooper, Georges E. Janssens
Software Mentions: 6
Published: over 3 years ago
10.7150/ijms.61309
Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Ke Zhu, Aiqun Xu, Wanli Xia, Pulin Li, Rui Han, Enze Wang, Sijing Zhou, Ran Wang
Software Mentions: 6
Published: almost 4 years ago
10.1155/2021/5583400
Identification and Validation of Autophagy-Related Gene Nomograms to Predict the Prognostic Value of Patients with Cervical Cancer
Cited by: 3
Author(s): Jinqun Jiang, Hongxing Xu, Yihao Wang, Hai Lü
Software Mentions: 6
Published: over 3 years ago
10.1186/s13029-017-0063-4
DEApp: an interactive web interface for differential expression analysis of next generation sequence data
Cited by: 63
Author(s): Yan Li, Jorge Andrade
Software Mentions: 5
Published: almost 8 years ago
10.1186/s13029-019-0071-7
eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
Cited by: 34
Author(s): Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
Software Mentions: 5
Published: almost 6 years ago
10.18632/aging.102278
Association between promoter DNA methylation and gene expression in the pathogenesis of ischemic stroke
Cited by: 20
Author(s): Guo-Xiong Deng, Ning Xu, Qi Huang, Jin-Yue Tan, Zhao Zhang, Xianfeng Li, Jinru Wei
Software Mentions: 5
Published: about 5 years ago
10.1186/s12859-021-04095-7
Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression
Cited by: 5
Author(s): Qinghong Dai, Tao Liu, Yongchao Gao, Honghao Zhou, Xiong Li, Wei Zhang
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-93863-9
MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Cited by: 6
Author(s): Sofia Zanotti, Suzanne Vanhauwaert, Christophe Van Neste, Volodimir Olexiouk, Jolien Van Laere, Marlies Verschuuren, Joni Van der Meulen, Liselot Mus, Kaat Durinck, Laurentijn Tilleman, Dieter Deforce, Filip Van Nieuwerburgh, Michael D. Hogarty, Bieke Decaesteker, Winnok H. De Vos, Frank Speleman
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-016-0951-7
Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer
Cited by: 18
Author(s): Mengyun Wu, Xiaofei Zhang, Dao‐Qing Dai, Le Ou-Yang, Yuan Zhu, Hong Yan
Software Mentions: 5
Published: almost 9 years ago
10.1007/s00122-020-03712-y
The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding
Cited by: 38
Author(s): Liangliang Gao, Dal Hoe Koo, Philomin Juliana, Trevor W. Rife, Daljit Singh, Cristiano Lemes da Silva, Thomas Lux, Kevin M. Dorn, Marshall Clinesmith, Paula Silva, Xu Wang, Manuel Spannagl, Cécile Monat, Bernd Friebe, Burkhard Steuernagel, Gary J. Muehlbauer, Sean Walkowiak, Curtis Pozniak, Ravi P. Singh, Nils Stein, Martin Mascher, Allan K. Fritz, Jesse Poland
Software Mentions: 5
Published: about 4 years ago
10.1186/s12864-020-6739-1
The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster
Cited by: 17
Author(s): Ben Harrison, Lu Wang, Erika Gajda, Elise V. Hoffman, Brian Y. Chung, Scott D. Pletcher, Daniel Raftery, Daniel Promislow
Software Mentions: 5
Published: over 4 years ago
10.1186/s12859-016-1154-y
Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffery Rubnitz, Jatinder K. Lamba, Bernie J. Daigle, Deborah C. Hay Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun T. Ajayi, Fatih Şen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas Jackson, John Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane E. Grill, Jie Na, Jeanette E. Eckel‐Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison A Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M Scotty DePriest, James N. MacLeod, H. Marblestone Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Smalter Hall, Philip Kreisle, Jessica Lasher, B.K. Oakes, Allison Speer, Maximilian Valentine, Naga Satya V Rao Nagisetty, Rony Jose, Robert J. Rooney, David S. Hains
Software Mentions: 5
Published: over 8 years ago
10.1111/acel.13230
COVID‐19 is an emergent disease of aging
Cited by: 91
Author(s): Didac Santesmasses, José Pedro Castro, Aleksandr Zenin, Anastasia V. Shindyapina, Maxim V. Gerashchenko, Bohan Zhang, Csaba Kerepesi, Sun Hee Yim, П. О. Федичев, Vadim N. Gladyshev
Software Mentions: 5
Published: about 4 years ago
10.3389/fcell.2020.588041
Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: about 4 years ago
10.1186/1471-2105-6-306
WebArray: an online platform for microarray data analysis
Cited by: 72
Author(s): Xiaoqin Xia, Michael McClelland, Yipeng Wang
Software Mentions: 5
Published: about 19 years ago
10.1038/s41598-020-67690-3
Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: over 4 years ago
10.3389/fcell.2020.00552
Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1
Cited by: 15
Author(s): Wee Siang Teo, Holly Holliday, N. Karthikeyan, Aurélie Cazet, Daniel Roden, Kate Harvey, Christina Valbirk Konrad, Reshma Murali, Binitha Anu Varghese, Archana P. Thankamony, Chia-Ling Chan, Andrea McFarland, Simon Junankar, Sunny Ye, Jessica Yang, Iva Nikolić, Jaynish S. Shah, Laura A. Baker, Ewan K.A. Millar, Matthew J. Naylor, Christopher J. Ormandy, Sunil R. Lakhani, Warren Kaplan, Albert S. Mellick, Sandra A. O’Toole, Alexander Swarbrick, Radhika Nair
Software Mentions: 5
Published: over 4 years ago
10.1186/1471-2164-9-124
Can subtle changes in gene expression be consistently detected with different microarray platforms?
Cited by: 48
Author(s): Paola Pedotti, Peter A C ‘t Hoen, Erno Vreugdenhil, Geert J. Schenk, Rolf H. A. M. Vossen, Yavuz Ariyürek, Mattias de Hollander, Rowan Kuiper, G.J.B. van Ommen, Johan T. den Dunnen, Judith M. Boer, Renée X. de Menezes
Software Mentions: 5
Published: over 16 years ago
10.1038/s41598-020-61649-0
Epigenome-wide association study for perceived discrimination among sub-Saharan African migrants in Europe - the RODAM study
Cited by: 6
Author(s): Loes C. van der Laan, Karlijn Meeks, Felix P Chilunga, Charles Agyemang, Andrea Venema, Marcel M.A.M. Mannens, Mohammad Hadi Zafarmand, Kerstin Klipstein‐Grobusch, Liam Smeeth, Adebowale Adeyemo, Peter Henneman
Software Mentions: 5
Published: over 4 years ago
10.3389/fcell.2021.723103
A Calcium-Related Immune Signature in Prognosis Prediction of Patients With Glioma
Cited by: 1
Author(s): Cha Lin, Jian Chen, Zhaoying Su, Pei Liu, Zheyu Liu, Chenchen Zhu, Dakang Xu, Lin Zhang, Xu Pei, Ganqiang Liu, Xinjian Liu
Software Mentions: 5
Published: about 3 years ago
10.3389/fcell.2021.690542
Predicting Panel of Metabolism and Immune-Related Genes for the Prognosis of Human Ovarian Cancer
Cited by: 7
Author(s): Lingyun Zhang, Wenwen Sun, Weimin Ren, Jinguo Zhang, Guoxiong Xu
Software Mentions: 5
Published: over 3 years ago
10.18632/aging.202559
Infertility network and hub genes for nonobstructive azoospermia utilizing integrative analysis
Cited by: 6
Author(s): Baoquan Han, Zihui Yan, Shuai Yu, Wei Ge, Yaqi Li, Yan Wang, Bo Yang, Wei Shen, Hui Jiang, Zhongyi Sun
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.570336
A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 10
Author(s): Yi Zhang, Ping Chen, Qiang Zhou, Hongyan Wang, Qingquan Hua, Jie Wang, Hongliang Zhong
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1008783
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics
Cited by: 23
Author(s): Georgia Doing, Katja Koeppen, Patricia Occipinti, Colleen E. Harty, Deborah A. Hogan
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pgen.1005819
Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: almost 9 years ago
10.1186/1741-7007-7-70
Genetical genomic determinants of alcohol consumption in rats and humans
Cited by: 136
Author(s): Boris Tabakoff, Laura Saba, Morton P. Printz, Pam Flodman, Colin A. Hodgkinson, David Goldman, George F. Koob, H. G. Richardson, Katerina Kechris, Richard L. Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, M Dongier, Katherine M. Conigrave, John B. Whitfield, John B. Saunders, Bridget F. Grant, Paula L. Hoffman
Software Mentions: 5
Published: about 15 years ago
10.1186/s12864-017-4007-9
Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: over 7 years ago
10.1186/s12864-015-1546-9
Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)
Cited by: 31
Author(s): Andriy Kovalchuk, Tommaso Raffaello, Emad Jaber, Susanna Keriö, Rajendra P. Ghimire, W. Walter Lorenz, Jeffrey F. D. Dean, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 5
Published: over 9 years ago
10.1186/1471-2105-14-263
Ontology based molecular signatures for immune cell types via gene expression analysis
Cited by: 12
Author(s): Terrence F. Meehan, Nicole Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl
Software Mentions: 5
Published: over 11 years ago
10.3389/fcvm.2021.631650
Integrated DNA Methylation and Gene Expression Analysis Identified S100A8 and S100A9 in the Pathogenesis of Obesity
Cited by: 7
Author(s): Ningyuan Chen, Miao Liu, Wei Lin, Donghua Zou, Ling Huang, Jian Huang, Wei Shi, Li-Lin Li, Yu-Xing Luo, Hao Liang, Shang‐Ling Pan, Junhua Peng
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-021-04046-2
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Cited by: 0
Author(s): Heeju Noh, Hua Ziyi, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Software Mentions: 5
Published: almost 4 years ago
10.1186/1471-2164-12-326
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Cited by: 19
Author(s): Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, A.M. Mosquera, E. A. Gonzalez, Juan José Lozano, Matthew Ingham, Juliane C. Dohm, María Noguera, Robert Kofler, José Antonio del Rı́o, Mònica Bayés, Heinz Himmelbauer, Lauro Sumoy
Software Mentions: 5
Published: over 13 years ago
10.1038/s41598-019-57108-0
Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pntd.0007361
Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya
Cited by: 3
Author(s): David P. Tchouassi, Ephantus J. Muturi, Samwel O. Arum, Chang‐Hyun Kim, Christopher J. Fields, Baldwyn Torto
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pcbi.0040006
Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
Cited by: 45
Author(s): Michał Okoniewski, Crispin Miller
Software Mentions: 5
Published: almost 17 years ago
10.1186/s12864-020-07225-2
Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice
Cited by: 25
Author(s): Pabodha Hettige, Uzma Tahir, Kiisa C. Nishikawa, Matthew J. Gage
Software Mentions: 5
Published: about 4 years ago
10.18632/aging.101341
Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: almost 7 years ago
10.1186/s12859-019-2697-5
GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
Cited by: 5
Author(s): Karl Stamm, Aoy Tomita‐Mitchell, Serdar Bozdag
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pcbi.1002963
Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
Cited by: 39
Author(s): Gabriela V. Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, J. Wilson-McManus, Robert Balshaw, Paul Keown, Christoph H. Borchers, Bruce M. McManus, Raymond T. Ng, W. Robert McMaster
Software Mentions: 5
Published: over 11 years ago
10.1186/s40478-019-0805-4
Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pcbi.1002887
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: almost 12 years ago
10.1186/1471-2105-13-326
A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
Cited by: 29
Author(s): Oliver P. Günther, Virginia Chen, Gabriela Cohen Freue, Robert Balshaw, Scott J. Tebbutt, Zsuzsanna Hollander, Mandeep Takhar, W. Robert McMaster, Bruce M. McManus, Paul Keown, Raymond T. Ng
Software Mentions: 5
Published: about 12 years ago
10.1093/femsyr/foab011
Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production
Cited by: 2
Author(s): Leonie Baumann, Tyler W. Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Software Mentions: 5
Published: almost 4 years ago
10.1186/1471-2164-11-32
Integrative analysis of the heat shock response in Aspergillus fumigatus
Cited by: 76
Author(s): Daniela Albrecht, Reinhard Guthke, Axel A. Brakhage, Olaf Kniemeyer
Software Mentions: 5
Published: almost 15 years ago
10.1186/1471-2105-14-174
PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: over 11 years ago
10.1038/s41598-019-48589-0
Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells
Cited by: 7
Author(s): Juan Bautista Menendez-Gonzalez, Samantha Sinnadurai, Alex Gibbs, Leigh-anne Thomas, Maria Konstantinou, Alfonso Garcia-Valverde, Magali Boyer, Zhengke Wang, Ashleigh S. Boyd, Allison Blair, Rhys G. Morgan, Neil P. Rodrigues
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-019-48435-3
Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
Cited by: 22
Author(s): Junbo Zou, Herzl Chai, Xiaofei Zhang, Deliang Guo, Jia Tai, Yu Wang, Yulin Liang, Fang Wang, Jiangxue Cheng, Jing Wang, Yajun Shi
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pcbi.1004847
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Cited by: 40
Author(s): Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James Stevens
Software Mentions: 5
Published: over 8 years ago
10.18632/aging.102841
Identification of biomarkers related to CD8+ T cell infiltration with gene co-expression network in clear cell renal cell carcinoma
Cited by: 47
Author(s): Jiaxing Lin, Meng Yu, Xiao Xu, Yutao Wang, Haotian Xing, Jing An, Jieping Yang, Chaozhi Tang, Dan Sun, Yuyan Zhu
Software Mentions: 5
Published: almost 5 years ago
10.3389/fnagi.2021.686066
Significant Difference of Immune Cell Fractions and Their Correlations With Differential Expression Genes in Parkinson’s Disease
Cited by: 13
Author(s): Yilin Huang, Huisheng Liu, Jiaqi Hu, Chongyin Han, Zhenggang Zhong, Wei Luo, Yuhu Zhang, Fei Ling
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-017-06355-0
Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Cited by: 5
Author(s): Prashanna Balaji Venkatasubramanian, Gamze Toydemir, Nicole de Wit, Edoardo Saccenti, Vítor A. P. Martins dos Santos, Peter van Baarlen, Jerry M. Wells, María Suárez-Diez, Jurriaan J. Mes
Software Mentions: 5
Published: over 7 years ago
10.3389/fgene.2021.672674
Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer
Cited by: 10
Author(s): Jianfeng Zheng, Jialu Guo, Huizhi Zhang, Benben Cao, XU Guomin, Zhifen Zhang, Jinyi Tong
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-017-01767-4
Systems Immunology of Diabetes-Tuberculosis Comorbidity Reveals Signatures of Disease Complications
Cited by: 78
Author(s): César Augusto Prada-Medina, Kiyoshi F. Fukutani, Nathella Pavan Kumar, Leonardo Gil-Santana, Subash Babu, Flávio Lichtenstein, Kim West, Sivakumar Shanmugam, Pradeep A. Menon, Vijay Viswanathan, Bruno B. Andrade, Hidehiko Nakaya, Hardy Kornfeld
Software Mentions: 5
Published: over 7 years ago
10.1038/s41598-017-07238-0
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders
Cited by: 32
Author(s): Jyoti Rani, Inna Mittal, Atreyi Pramanik, Namita Singh, Namita Dube, Smriti Sharma, Bhanwar Lal Puniya, Muthukurussi Varieth Raghunandanan, Ahmed Mobeen, Srinivasan Ramachandran
Software Mentions: 5
Published: over 7 years ago
10.3389/fcvm.2021.663509
Development and Validation of a Random Forest Diagnostic Model of Acute Myocardial Infarction Based on Ferroptosis-Related Genes in Circulating Endothelial Cells
Cited by: 14
Author(s): Yifan Chen, Jianfeng Shi, Jun Pu
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2020.579709
Potential of Immune-Related Genes as Biomarkers for Diagnosis and Subtype Classification of Preeclampsia
Cited by: 8
Author(s): Ying Wang, Zhen Li, Guanhua Song, Jun Wang
Software Mentions: 5
Published: about 4 years ago
10.1186/s12920-021-00928-9
Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of esophageal squamous cell carcinoma
Cited by: 8
Author(s): Mingdi Liu, Faping Li, Bin Liu, Yong‐Ping Jian, Dan Zhang, Honglan Zhou, Yishu Wang, Zhixiang Xu
Software Mentions: 5
Published: over 3 years ago
10.1038/srep31479
Pancreas-enriched miRNAs are altered in the circulation of subjects with diabetes: a pilot cross-sectional study
Cited by: 131
Author(s): Attila A. Seyhan, Yury O. Nunez Lopez, Hui Xie, Fanchao Yi, Clayton E. Mathews, Magdalena Pasarica, Richard E. Pratley
Software Mentions: 5
Published: over 8 years ago
10.1038/srep36055
Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions
Cited by: 28
Author(s): Betty Hebecker, Sebastian Vlaic, Theresia Conrad, Michael Bauer, Sascha Brunke, Mario Kapitan, Jörg Linde, Bernhard Hube, Ilse D. Jacobsen
Software Mentions: 5
Published: about 8 years ago
10.1186/1471-2164-13-351
The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon
Cited by: 38
Author(s): Kusum Sharma, Nicholas Gillum, J Lomax Boyd, Amy K. Schmid
Software Mentions: 5
Published: over 12 years ago
10.1038/srep31669
Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells
Cited by: 3
Author(s): Mariam El-Ashmawy, Melissa Coquelin, Krishna Luitel, Kimberly Batten, Jerry W. Shay
Software Mentions: 5
Published: over 8 years ago
10.1186/s12864-015-2040-0
Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study
Cited by: 27
Author(s): Philip Shaw, Sastra Chaotheing, Pavita Kaewprommal, Jittima Piriyapongsa, Chayaphat Wongsombat, Nattida Suwannakitti, Pongpisid Koonyosying, Chairat Uthaipibull, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan
Software Mentions: 5
Published: about 9 years ago
10.1038/srep29251
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data
Cited by: 21
Author(s): Tin Nguyen, Diana Diaz, Rebecca Tagett, Sorin Drăghici
Software Mentions: 5
Published: over 8 years ago
10.1186/1471-2105-6-98
ProGenExpress: Visualization of quantitative data on prokaryotic genomes
Cited by: 6
Author(s): Michael Watson
Software Mentions: 5
Published: over 19 years ago
10.1186/s12864-017-4100-0
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates
Cited by: 61
Author(s): Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 5
Published: about 7 years ago
10.1186/s12859-020-03633-z
PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients
Cited by: 10
Author(s): Young‐Chul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal, Minjung Kim
Software Mentions: 5
Published: over 4 years ago
10.1038/srep20533
Gene regulatory network inference using fused LASSO on multiple data sets
Cited by: 114
Author(s): Nooshin Omranian, Jeanne M. O. Eloundou-Mbebi, Bernd Mueller‐Roeber, Zoran Nikoloski
Software Mentions: 5
Published: almost 9 years ago
10.1038/s41597-020-0527-2
Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain
Cited by: 6
Author(s): Kimberly A. Aldinger, Andrew E. Timms, James W. MacDonald, Hanna K. McNamara, Jennifer Herstein, Theo K. Bammler, Oleg V. Evgrafov, James A. Knowles, Pat Levitt
Software Mentions: 5
Published: over 4 years ago
10.18632/aging.103809
Landscape of transcription and expression regulated by DNA methylation related to age of donor and cell passage in adipose-derived mesenchymal stem cells
Cited by: 3
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Yuju Ma, Zhizhai Luo, Fengyao Wu, Xinheng Liu, Yu Liu, Steven Mo, Zhongquan Qi, Hong-Mian Li
Software Mentions: 5
Published: about 4 years ago
10.1038/srep21911
Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: almost 9 years ago
10.1038/sdata.2018.136
A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: over 6 years ago
10.1186/1471-2105-14-47
A survey of protein interaction data and multigenic inherited disorders
Cited by: 6
Author(s): Antonio M. Mora, Katerina Michalickova, Ian Donaldson
Software Mentions: 5
Published: almost 12 years ago
10.1155/2021/8895723
Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients
Cited by: 14
Author(s): Zhiqiang Zha, Peiling Zhang, Dailing Li, Guolong Liu, Lin Lü
Software Mentions: 5
Published: almost 4 years ago
10.15252/msb.20209888
Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: about 4 years ago
10.3390/diagnostics10040188
Profiling of Circulating microRNAs in Prostate Cancer Reveals Diagnostic Biomarker Potential
Cited by: 21
Author(s): Jacob Fredsøe, Anne Rasmussen, Peter Mouritzen, Marianne Bjerre, Peter Busch Østergren, Mikkel Fode, Michael Borre, Karina D. Sørensen
Software Mentions: 5
Published: over 4 years ago
10.18632/aging.102983
Survival-associated alternative splicing signatures in non-small cell lung cancer
Cited by: 21
Author(s): Delong Zhao, Chuantao Zhang, Man Jiang, Yongjie Wang, Liang Yu, Li Wang, Kang Qin, Faisal Rehman
Software Mentions: 5
Published: over 4 years ago
10.1186/s12931-019-1085-z
Airway host-microbiome interactions in chronic obstructive pulmonary disease
Cited by: 82
Author(s): Zhang Wang, Barbara Maschera, Simon Lea, Umme Kolsum, David Michalovich, Stephanie Van Horn, Christopher Traini, James R. Brown, Edith M. Hessel, Dave Singh
Software Mentions: 5
Published: over 5 years ago
10.1242/dev.160614
Distinct prophase arrest mechanisms in human male meiosis
Cited by: 24
Author(s): Sabrina Z. Jan, Aldo Jongejan, Cindy M. Korver, Saskia K.M. van Daalen, Ans M.M. van Pelt, Sjoerd Repping, Geert Hamer
Software Mentions: 5
Published: almost 7 years ago
10.1016/j.molp.2020.07.010
The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense
Cited by: 25
Author(s): Roland E. Schwarzenbacher, Grace Wardell, Joost H. M. Stassen, Emily Guest, Peijun Zhang, Estrella Luna, Jurriaan Ton
Software Mentions: 5
Published: about 4 years ago
10.1186/s12859-020-03691-3
Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Cited by: 31
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 5
Published: over 4 years ago
10.1186/1471-2164-15-132
Major aging-associated RNA expressions change at two distinct age-positions
Cited by: 17
Author(s): Marius Gheorghe, M.M.J. Snoeck, Michael Emmerich, Thomas Bäck, Jelle J. Goeman, Vered Raz
Software Mentions: 5
Published: almost 11 years ago
10.18632/aging.102819
Expression and prognostic value of long non-coding RNA H19 in glioma via integrated bioinformatics analyses
Cited by: 33
Author(s): Yi Xiao, Zi-peng Zhu, LI Jian-xiong, Jie Yao, Haitao Jiang, Ran Ran, Xueyuan Li, Zhiqiang Li
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12864-020-06811-8
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development
Cited by: 3
Author(s): Haley S. Toups, Noé Cochetel, D. J. Gray, Grant R. Cramer
Software Mentions: 5
Published: over 4 years ago
10.1186/s12864-018-4652-7
Impact on birth weight of maternal smoking throughout pregnancy mediated by DNA methylation
Cited by: 41
Author(s): Stephanie H. Witt, Josef Frank, Maria Gilles, Maren Lang, Jens Treutlein, Fabian Streit, Isabella Wolf, Verena Peus, Barbara Scharnholz, Tabea Send, Stefanie Heilmann‐Heimbach, Sugirthan Sivalingam, Helene Dukal, Jana Strohmaier, Marc Sütterlin, Janine Arloth, Manfred Laucht, Markus M. Nöthen, Michael Deuschle, Marcella Rietschel
Software Mentions: 5
Published: over 6 years ago
10.1186/1744-8069-10-7
A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat
Cited by: 72
Author(s): James R. Perkins, Ana Antunes-Martins, Margarita Calvo, John Grist, Werner Rust, RM Schmid, Tobias Hildebrandt, Matthias Kohl, Christine A. Orengo, Stephen B. McMahon, David L.H. Bennett
Software Mentions: 5
Published: almost 11 years ago
10.1155/2020/6937475
A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma
Cited by: 18
Author(s): Yingkun Xu, Xiunan Li, Yaling Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu
Software Mentions: 5
Published: about 4 years ago
10.1093/database/bau068
yStreX: yeast stress expression database
Cited by: 11
Author(s): Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranović
Software Mentions: 5
Published: almost 11 years ago
10.1073/pnas.1822046116
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: over 5 years ago
10.1186/s12864-019-6127-x
Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake
Cited by: 9
Author(s): Haibo Li, Kristina M. Feye, Yet Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Dekkers, Nicholas K. Gabler, Christopher K. Tuggle
Software Mentions: 5
Published: about 5 years ago