bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/s12935-021-02008-5

Prognostic signature composed of transcription factors accurately predicts the prognosis of gastric cancer patients
Cited by: 4
Author(s): Liqun Zhou, Zhiqing Chen, You Wu, Hao Lü, Lin Xin
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-016-1143-5

Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
Cited by: 98
Author(s): Xiaoqi Zheng, Zhang Nai-qian, Hua‐Jun Wu, Hao Wu
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-017-1156-8

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types
Cited by: 88
Author(s): Simone Ecker, Lu Chen, Véra Pancaldi, Frederik Otzen Bagger, José Marı́a Fernández, Enrique Carrillo de Santa Pau, David Juan, Alice Mann, Stephen Watt, Francesco Paolo Casale, Nikolaos Sidiropoulos, Nicolas Rapin, Angelika Merkel, Hendrik G. Stunnenberg, Oliver Stegle, Mattia Frontini, Kate Downes, Tomi Pastinen, Taco W. Kuijpers, Daniel Rico, Alfonso Valencia, Stephan Beck, Nicole Soranzo, Dirk S. Paul
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-016-1131-9

Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
Cited by: 237
Author(s): Maarten van Iterson, Erik W. van Zwet, Bastiaan T. Heijmans, Peter A.C. ’t Hoen, Joyce B. J. van Meurs, Ritsert C. Jansen, Lude Franke, Dorret I. Boomsma, René Pool, Jenny van Dongen, Jouke Jan Hottenga, Marleen J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen, Casper G. Schalkwijk, Cisca Wijmenga, Sasha Zhernakova, Ettje F. Tigchelaar, P. Eline Slagboom, Marian Beekman, Joris Deelen, Diana van Heemst, Jan H. Veldink, Leonard H van den Berg, Cornelia M. van Duijn, Bert A. Hofman, Aaron Isaacs, André G. Uitterlinden, P. Mila Jhamai, Michaël Verbiest, H. Eka D. Suchiman, Marijn Verkerk, Ruud van der Breggen, Jeroen van Rooij, Nico Lakenberg, Hailiang Mei, M.A. van Galen, Jan Bot, Dasha V. Zhernakova, Peter van ’t Hof, Patrick Deelen, Irene Nooren, Matthijs Moed, Martijn Vermaat, René Luijk, Marc Jan Bonder, Freerk van Dijk, Wibowo Arindrarto, Szymon M. Kiełbasa, Morris A. Swertz
Software Mentions: 3
Published: over 9 years ago

10.1002/stem.2095

Molecular Mechanisms Mediating Retinal Reactive Gliosis Following Bone Marrow Mesenchymal Stem Cell Transplantation
Cited by: 62
Author(s): Alessia Tassoni, Alex Gutteridge, Amanda C. Barber, Andrew Osborne, Keith R Martin
Software Mentions: 3
Published: about 11 years ago

10.3389/fneur.2021.612817

An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition
Cited by: 5
Author(s): Maryam Jangjoo, Sarah J. Goodman, Sanaa Choufani, Brett Trost, Stephen W. Scherer, Elizabeth Kelley, Muhammad Ayub, Rob Nicolson, Stelios Georgiades, Jennifer Crosbie, Russell Schachar, Evdokia Anagnostou, Eyal Grunebaum, Rosanna Weksberg
Software Mentions: 3
Published: over 5 years ago

10.1002/stem.2558

New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells
Cited by: 17
Author(s): Carmel O'Brien, Hun S. Chy, Qi Zhou, Shiri Blumenfeld, Jack Lambshead, Xiaodong Liu, Joshua Kie, Bianca D. Capaldo, Tung Liang Chung, Timothy E. Adams, Tram Phan, John D. Bentley, William J. McKinstry, Karen Oliva, Paul McMurrick, Yu-Chieh Wang, Fernando Rossello, Geoffrey J. Lindeman, Di Chen, Thierry Jardé, Amander T. Clark, Helen E. Abud, Jane E. Visvader, Christian M. Nefzger, José M. Polo, Jeanne F. Loring, Andrew L. Laslett
Software Mentions: 3
Published: over 9 years ago

10.1186/s12935-021-02000-z

An immune-related model based on INHBA, JAG2 and CCL19 to predict the prognoses of colon cancer patients
Cited by: 3
Author(s): Xuankun Yang, Yan Jia, Yahui Jiang, Yaxu Wang
Software Mentions: 3
Published: over 5 years ago

10.1016/j.exphem.2020.10.002

HOXA9/IRX1 expression pattern defines two subgroups of infant MLL-AF4-driven acute lymphoblastic leukemia
Cited by: 8
Author(s): Vasiliki Symeonidou, Katrin Ottersbach
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22052442

Immunogenomic Identification for Predicting the Prognosis of Cervical Cancer Patients
Cited by: 10
Author(s): Qun Wang, Aurelia Vattai, Theresa� Vilsmaier, Till Kaltofen, Alexander Steger, Doris Mayr, Sven Mahner, Udo Jeschke, H Heidegger
Software Mentions: 3
Published: over 5 years ago

10.1002/2211-5463.12759

Delivery of platelet <i>TPM3</i> mRNA into breast cancer cells via microvesicles enhances metastasis
Cited by: 29
Author(s): Bing Yao, Shuang Qu, Ruifeng Hu, Wen Gao, Shidai Jin, Junyi Ju, Quan Zhao
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.jcmgh.2021.05.020

Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation
Cited by: 11
Author(s): Gaurav V. Sarode, Kari Neier, Noreene M. Shibata, Yuanjun Shen, Dmitry A. Goncharov, Elena A. Goncharova, Tagreed A. Mazi, Nikhil Joshi, Matthew L. Settles, Janine M. LaSalle, Valentina Medici
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.650213

Predicting the Key Genes Involved in Aortic Valve Calcification Through Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Dinghui Wang, Tianhua Xiong, Wenlong Yu, Bin Liu, Jing Wang, Kaihu Xiao, Sheng Qiang
Software Mentions: 3
Published: over 5 years ago

10.1186/1752-0509-8-12

Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
Cited by: 10
Author(s): Nadia M. Penrod, Jason H. Moore
Software Mentions: 3
Published: over 12 years ago

10.3390/nu13051413

Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study
Cited by: 4
Author(s): Mariana Lizbeth Rodríguez-López, José Jaime Martínez‐Magaña, David Ruiz‐Ramos, Ana Rosa Sepúlveda García, Laura González, Carlos Alfonso Tóvilla-Zárate, Emmanuel Sarmiento, Isela Esther Juárez‐Rojop, Humberto Nicolini, Thelma Beatriz González‐Castro, Alma Delia Genis‐Mendoza
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0063419

HMGA1: A Master Regulator of Tumor Progression in Triple-Negative Breast Cancer Cells
Cited by: 102
Author(s): Sandeep N. Shah, Leslie Cope, Weijie Poh, Amy Belton, Suheeta Roy, C. Conover Talbot, Saraswati Sukumar, David L. Huso, Linda M.S. Resar
Software Mentions: 3
Published: over 13 years ago

10.3389/fcell.2021.694769

Comparison of Genome-Wide DNA Methylation Profiles of Human Fetal Tissues Conceived by in vitro Fertilization and Natural Conception
Cited by: 4
Author(s): Ye Liu, Xinzhu Li, Songchang Chen, Li Wang, Ya‐Jing Tan, Xiaocui Li, Lin Tang, Junyu Zhang, Dandan Wu, Yanting Wu, Xinmei Liu, Yimin Zhu, Jian‐Zhong Sheng, Jiexue Pan, Li Jin, He‐Feng Huang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41419-021-03955-7

LncRNA RCAT1 promotes tumor progression and metastasis via miR-214-5p/E2F2 axis in renal cell carcinoma
Cited by: 22
Author(s): Renbo Guo, Benkui Zou, Yiran Liang, Jiasheng Bian, Jian Xu, Qian Zhou, Chao Zhang, Tao Chen, Mei Yang, Huansheng Wang, Fajun Pei, Zhonghua Xu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0159197

Comparative Transcriptome Profiling of Human Foreskin Fibroblasts Infected with the Sylvio and Y Strains of Trypanosoma cruzi
Cited by: 22
Author(s): Genevieve A. Houston-Ludlam, Ashton T. Belew, Najib M. El-Sayed
Software Mentions: 3
Published: about 10 years ago

10.1038/celldisc.2015.35

Discovery of a highly potent glucocorticoid for asthma treatment
Cited by: 8
Author(s): Yuanzheng He, Jingjing Shi, Wei Yi, Xin Ren, Xiang Gao, Jianshuang Li, Nanyan Wu, Kevin Weaver, Qian Xie, Sok Kean Khoo, Tao Yang, Xiaozhu Huang, Karsten Melcher, H. Eric Xu
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-40963-2

DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood
Cited by: 27
Author(s): Kelly M. Bakulski, John Dou, Nan Lin, Stephanie J. London, Justin A. Colacino
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2020.561907

DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
Cited by: 19
Author(s): Laura Smyth, Christopher Patterson, Elizabeth Swan, Alexander P. Maxwell, Amy Jayne McKnight
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.ccell.2018.06.007

PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells
Cited by: 133
Author(s): Athena Georgilis, Sabrina Klotz, Christopher J. Hanley, Nicolás Herranz, Benedikt Weirich, Beatriz Morancho, Ana Carolina Leote, Luana D’Artista, Suchira Gallage, Marco Seehawer, Thomas Carroll, Gopuraja Dharmalingam, Keng Boon Wee, Massimiliano Mellone, Joaquim Pombo, Danijela Heide, Ernesto Guccione, Joaquı́n Arribas, Nuno L. Barbosa‐Morais, Mathias Heikenwälder, Gareth J. Thomas, Lars Zender, Jesús Gil
Software Mentions: 3
Published: about 8 years ago

10.1111/jcmm.16502

Novel COL4A1‐VEGFD gene fusion in myofibroma
Cited by: 5
Author(s): Guillaume Dachy, Sylvie Fraïtag, Boutaina Boulouadnine, Sabine Cordi, Jean‐Baptiste Demoulin
Software Mentions: 3
Published: over 5 years ago

10.1177/1533033819853237

Comprehensive Analysis of lncRNA–miRNA– mRNA Network Ascertains Prognostic Factors in Patients with Colon Cancer
Cited by: 20
Author(s): Zhenzhen Gao, Peng Fu, Zuwei Yu, Fuxi Zhen, Weimin Fan
Software Mentions: 3
Published: over 7 years ago

10.1111/jcmm.16536

FABP5 enhances malignancies of lower‐grade gliomas via canonical activation of NF‐κB signaling
Cited by: 19
Author(s): Yichang Wang, Alafate Wahafu, Wei Wu, Jianyang Xiang, Longwei Huo, Xudong Ma, Ning Wang, Hao Líu, Xia Bai, Dongze Xu, Wei Xie, Maode Wang, Jia Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12989-016-0115-y

An acetyl-L-carnitine switch on mitochondrial dysfunction and rescue in the metabolomics study on aluminum oxide nanoparticles
Cited by: 39
Author(s): Xiaobo Li, Chengcheng Zhang, Xin Zhang, Shizhi Wang, Qingtao Meng, Shenshen Wu, Hongbao Yang, Yankai Xia, Rui Chen
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0056274

Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness
Cited by: 7
Author(s): Annalisa Buniello, Rachel E. Hardisty-Hughes, Johanna Pass, Eva Bober, Richard J.H. Smith, Karen P. Steel
Software Mentions: 3
Published: over 13 years ago

10.1186/s12969-019-0313-x

10th Congress of International Society of Systemic Auto-Inflammatory Diseases (ISSAID)
Cited by: 21
Author(s):
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0113496

Synergy: A Web Resource for Exploring Gene Regulation in Synechocystis sp. PCC6803
Cited by: 4
Author(s): Niklas Mähler, Otilia Cheregi, Christiane Funk, Sergiu Netotea, Torgeir R. Hvidsten
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0131627

Ensemble Methods for MiRNA Target Prediction from Expression Data
Cited by: 29
Author(s): Thuc Duy Le, Junpeng Zhang, Lin Liu, Jiuyong Li
Software Mentions: 3
Published: about 11 years ago

10.1186/s12957-021-02333-z

Identification of uterine leiomyosarcoma-associated hub genes and immune cell infiltration pattern using weighted co-expression network analysis and CIBERSORT algorithm
Cited by: 12
Author(s): Xiaoyun Shen, Zhujuan Yang, Sheng Feng, Yi Li
Software Mentions: 3
Published: about 5 years ago

10.7150/thno.42986

The molecular landscape and microenvironment of salivary duct carcinoma reveal new therapeutic opportunities
Cited by: 25
Author(s): Mélissa Alame, Emmanuel Cornillot, Valère Cacheux, Guillaume Tosato, Marion Four, Laura de Oliveira, Stéphanie Gofflot, Philippe Delvenne, Evgenia Turtoi, Simon Cabello-Aguilar, Masahiko Nishiyama, Andrei Turtoï, Valérie Costes‐Martineau, Jacques Colinge
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0007397

Interplay between proinflammatory cytokines, miRNA, and tissue lesions in Anisakis-infected Sprague-Dawley rats
Cited by: 21
Author(s): Jerko Hrabar, Željka Trumbić, Ivana Bočina, Ivana Bušelić, Anamarija Vrbatović, Ivona Mladineo
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0007152

Host and parasite responses in human diffuse cutaneous leishmaniasis caused by L. amazonensis
Cited by: 52
Author(s): Stephen M Christensen, Ashton T. Belew, Najib M. El-Sayed, Wagner Luiz Tafuri, Fernando Tobias Sílveira, David M. Mosser
Software Mentions: 3
Published: over 7 years ago

10.1186/s12886-020-01365-5

Identification of lncRNA–miRNA–mRNA regulatory network associated with primary open angle glaucoma
Cited by: 24
Author(s): Minwen Zhou, Bing Lu, Wei Tan, Mingshui Fu
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: over 12 years ago

10.1186/s12957-021-02196-4

Comprehensive analyses of correlation and survival reveal informative lncRNA prognostic signatures in colon cancer
Cited by: 13
Author(s): Meng Gao, Yang Guo, Yifu Xiao, Xuequn Shang
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2018.00742

Transcriptomic Characterization of the Human Habenula Highlights Drug Metabolism and the Neuroimmune System
Cited by: 22
Author(s): Bernard Le Foll, Leon French
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0035322

Nuclear Reprogramming: Kinetics of Cell Cycle and Metabolic Progression as Determinants of Success
Cited by: 23
Author(s): Sebastian T. Balbach, Telma C. Esteves, Franchesca D. Houghton, Marcin Siatkowski, Martin J. Pfeiffer, Chizuko Tsurumi, Benoı̂t Kanzler, Georg Fuellen, Michele Boiani
Software Mentions: 3
Published: over 14 years ago

10.7150/thno.47938

Identification of a Tumor Microenvironment-relevant Gene set-based Prognostic Signature and Related Therapy Targets in Gastric Cancer
Cited by: 49
Author(s): Wangyu Cai, Zi-Nan Dong, Xiao-Teng Fu, Lingyun Lin, Lin Wang, Guodong Ye, Qin Luo, Yuchao Chen
Software Mentions: 3
Published: over 6 years ago

10.7150/thno.44456

Cartilage Oligomeric Matrix Protein promotes epithelial-mesenchymal transition by interacting with Transgelin in Colorectal Cancer
Cited by: 57
Author(s): Weilong Zhong, Huiqin Hou, Tianyu Li, Shuai Su, Xiaonan Xi, Yusheng Liao, Runxiang Xie, Ge Jin, Xiang Liu, Lanping Zhu, Hongxia Zhang, Xueli Song, Cheng Yang, Tao Sun, Hailong Cao, Bangmao Wang
Software Mentions: 3
Published: over 6 years ago

10.3389/fnins.2012.00156

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs
Cited by: 13
Author(s): Sergei A. Manakov, Andrew Morton, Anton J. Enright, Seth G. N. Grant
Software Mentions: 3
Published: over 14 years ago

10.1210/jc.2017-00881

Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors
Cited by: 42
Author(s): Mariana Bisarro dos Reis, Mateus Camargo Barros-Filho, Fábio Albuquerque Marchi, Caroline Moraes Beltrami, Hellen Kuasne, Clóvis Antônio Lopes Pinto, Srikant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Sílvia Regina Rogatto
Software Mentions: 3
Published: about 9 years ago

10.1016/j.celrep.2020.108533

USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells
Cited by: 10
Author(s): Paul van den Berk, Cesare Lancini, Michela Serresi, María Pilar Sánchez-Bailón, Danielle Hulsman, Colin C. Pritchard, Ji‐Ying Song, Matthias Jürgen Schmitt, Ellen Tanger, Oliver Popp, Philipp Mertins, Ivo J. Huijbers, Heinz Jacobs, Maarten van Lohuizen, Gaetano Gargiulo, Elisabetta Citterio
Software Mentions: 3
Published: almost 6 years ago

10.3389/pore.2021.580801

A Five-Genes Based Diagnostic Signature for Sepsis-Induced ARDS
Cited by: 9
Author(s): Ning Xu, Hui Guo, Xurui Li, Qian Zhao, Jianguo Li
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-40857-3

Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p
Cited by: 23
Author(s): Benjamin Goeppert, Felicia Truckenmueller, Alessandro Ori, Valerie Fritz, Thomas Albrecht, Angelika Fraas, Dominique Scherer, Rosa González Silos, Carsten Sticht, Norbert Gretz, Arianeb Mehrabi, Melanie Bewerunge-Hudler, Stefan Pusch, Justo Lorenzo Bermejo, Péter Dietrich, Peter Schirmacher, Marcus Renner, Stephanie Roessler
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.501376

Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans
Cited by: 10
Author(s): M.G. Sterken, R. Bevers, Rita J. M. Volkers, J.A.G. Riksen, J.E. Kammenga, L. Basten Snoek
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00727

Integrative Bioinformatics Approaches to Screen Potential Prognostic Immune-Related Genes and Drugs in the Cervical Cancer Microenvironment
Cited by: 14
Author(s): Zitong Zhao, Jigang Li, He Li, Na-Yi Yuan Wu, Peilin Ouyang, Shan Liu, Jifeng Cai, Jing Wang
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.1172/JCI97007

Hypothalamic loss of Snord116 recapitulates the hyperphagia of Prader-Willi syndrome
Cited by: 73
Author(s): Joseph Polex-Wolf, Brian Lam, Rachel Larder, John Tadross, Debra Rimmington, Fàtima Bosch, Verónica Jiménez Cenzano, Eduard Ayuso, Marcella Kl, Kara Rainbow, Anthony P. Coll, Stephen O’Rahilly, Giles S.H. Yeo
Software Mentions: 3
Published: over 8 years ago

10.1111/cns.13688

TROAP regulates cell cycle and promotes tumor progression through Wnt/β‐Catenin signaling pathway in glioma cells
Cited by: 17
Author(s): Zongqing Zhao, Xiujie Wu, Yalin Cheng, Yunfei Zhou, Xi-Meng Ma, Jian Zhang, Xueyuan Heng, Fang Fěng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12891-021-04662-2

Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method
Cited by: 3
Author(s): Arezou Lari, Hamid Gholami Pourbadie, Ali Sharifi‐Zarchi, Maryam Akhtari, Leila Nejatbakhsh Samimi, Ahmadreza Jamshidi, Mahdi Mahmoudi
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.00647

Identification of a Hypoxia-Associated Signature for Lung Adenocarcinoma
Cited by: 49
Author(s): Zhuomao Mo, Ling Yu, Zhirui Cao, Hao Hu, Shaoju Luo, Shijun Zhang
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0112102

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling
Cited by: 84
Author(s): W. Clay Spencer, Rebecca McWhirter, Tyne Miller, Pnina Strasbourger, Owen Thompson, LaDeana W. Hillier, Robert H. Waterston, David M. Miller
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0217273

The prediction of early preeclampsia: Results from a longitudinal proteomics study
Cited by: 73
Author(s): Adi L. Tarca, Roberto Romero, Neta Benshalom-Tirosh, Nándor Gábor Than, Dereje W. Gudicha, Bogdan Done, Percy Pacora, Tinnakorn Chaiworapongsa, Bogdan Panaitescu, Dan Tirosh, Nardhy Gómez-López, Sorin Drăghici, Sonia S. Hassan, Offer Erez
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.683173

Expression of AOX1 Predicts Prognosis of Clear Cell Renal Cell Carcinoma
Cited by: 3
Author(s): Luyang Xiong, Yuchen Feng, Wei Hu, Jiahong Tan, Shusheng Li, Hongjie Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2021.687979

Identification of Potential Prognostic Biomarkers Associated With Cancerometastasis in Skin Cutaneous Melanoma
Cited by: 3
Author(s): Yang Li, Shanshan Lyu, Zhe Gao, Weifeng Zha, Ping Wang, Yuxi Shan, Jianzhong He, Suyang Huang
Software Mentions: 3
Published: about 5 years ago

10.7150/thno.46460

Cisplatin prevents breast cancer metastasis through blocking early EMT and retards cancer growth together with paclitaxel
Cited by: 44
Author(s): Haitao Wang, Sen Guo, Seung Jin Kim, Fangyuan Shao, Joshua W. K. Ho, Kuan Un Wong, Zhengqiang Miao, Dapeng Hao, Ming Zhao, Jun Xu, Jianming Zeng, Koon Ho Wong, Lijun Di, Ada Hang Heng Wong, Xiaoling Xu, Chu Xia Deng
Software Mentions: 3
Published: over 5 years ago

10.1186/1475-2867-9-12

Gene expression profiling predicts a three-gene expression signature of endometrial adenocarcinoma in a rat model
Cited by: 9
Author(s): Sandra Karlsson, Björn Olsson, Karin Klinga‐Levan
Software Mentions: 3
Published: over 17 years ago

10.1038/s41419-021-03932-0

An integrative transcriptome study reveals Ddit4/Redd1 as a key regulator of cancer cachexia in rodent models
Cited by: 14
Author(s): Mengyuan Niu, Li Li, Zhonglan Su, Lulu Wei, Wenyuan Pu, Chen Zhao, Yibing Ding, Junaid Wazir, Wangsen Cao, Shiyu Song, Qian Gao, Hongwei Wang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0145316

High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers
Cited by: 27
Author(s): Catherine Mooney, Rana Raoof, Hany El‐Naggar, Amaya Sanz‐Rodriguez, Eva M. Jiménez-Mateos, David C. Henshall
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: over 7 years ago

10.1186/s12935-019-0859-1

Eleven genes associated with progression and prognosis of endometrial cancer (EC) identified by comprehensive bioinformatics analysis
Cited by: 54
Author(s): Jinhui Liu, Shulin Zhou, Siyue Li, Yi Jiang, Yicong Wan, Xiaoling Ma, Wenjun Cheng
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.7515

Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy
Cited by: 7
Author(s): Jiang Cui, Shaofei Wu, Lei Jiang, Zhichao Gao, Xiaorui Li, Yangyang Duan, Na Li, Tao Sun
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0203824

Dissecting cancer heterogeneity based on dimension reduction of transcriptomic profiles using extreme learning machines
Cited by: 11
Author(s): Kejun Wang, Xin Duan, Feng Gao, Wei Wang, Liangliang Liu, Xin Wang
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms22179595

Regulation of the Golgi Apparatus by p38 and JNK Kinases during Cellular Stress Responses
Cited by: 6
Author(s): Cathrine Nordgaard, Maxim A. X. Tollenaere, Ana Martinez Del Val, Dorte B. Bekker-Jensen, Melanie Blasius, Jesper V. Olsen, Simon Bekker‐Jensen
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1008155

The alternative cap-binding complex is required for antiviral defense in vivo
Cited by: 18
Author(s): Anna Gebhardt, Valter Bergant, Daniel Schnepf, Markus Moser, Arno Meiler, Dieudonnée Togbe, Claire Mackowiak, Line S. Reinert, Søren R. Paludan, Bernhard Ryffel, Alexey Stukalov, Peter Staeheli, Andreas Pichlmair
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0201553

Striatal transcriptome of a mouse model of ADHD reveals a pattern of synaptic remodeling
Cited by: 11
Author(s): Anastasia Sorokina, Michael C. Saul, Tassia M. Goncalves, Joseph V. Gogola, Petra Majdak, Sandra L. Rodriguez-Zas, Justin S. Rhodes
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms22115902

NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells
Cited by: 6
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Hans Drexler
Software Mentions: 3
Published: over 5 years ago

10.3390/jcm10051057

Gene Expression Landscape of SDH-Deficient Gastrointestinal Stromal Tumors
Cited by: 9
Author(s): Valentina Indio, Angela Schipani, Margherita Nannini, Milena Urbini, Alessandro Rizzo, Antonio De Leo, Annalisa Altimari, Valerio Di Scioscio, Daria Messelodi, Giuseppe Tarantino, Annalisa Astolfi, Maria Abbondanza Pantaleo
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.54999

Progressive stretch enhances growth and maturation of 3D stem-cell-derived myocardium
Cited by: 28
Author(s): Kun Lü, Thomas Seidel, Xiaochun Cao-Ehlker, Tatjana Dorn, Aarif M.N. Batcha, Christine Schneider, María Eugenia Aubet Semmler, Tilmann Volk, Alessandra Moretti, Andreas Dendorfer, Roland Tomasi
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01867-2

Identification of a tumor microenvironment-related gene signature to improve the prediction of cervical cancer prognosis
Cited by: 9
Author(s): Qian Chen, Bingqing Qiu, Xianmin Zeng, Lang Hu, Dongping Huang, Kaihua Chen, Xiaoqiang Qiu
Software Mentions: 3
Published: over 5 years ago

10.1016/j.celrep.2019.04.076

Integrin-Mediated Macrophage Adhesion Promotes Lymphovascular Dissemination in Breast Cancer
Cited by: 38
Author(s): Rachel Evans, Fabián Flores-Borja, Sina Nassiri, Elena Miranda, Katherine Lawler, Anita Grigoriadis, James Monypenny, Cheryl Gillet, Julie Owen, Peter M. Gordon, Victoria Male, Anthony Cheung, Farzana Noor, Paul R. Barber, Rebecca Marlow, Erika Francesch-Domenech, Gilbert O. Fruhwirth, Mario Leonardo Squadrito, Borivoj Vojnovic, Andrew Tutt, Frederic Festy, Michele De Palma, Tony Ng
Software Mentions: 3
Published: over 7 years ago

10.1038/s41419-018-0342-2

Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells
Cited by: 30
Author(s): Shariq Ansari, Ashwini Kumar Sharma, Himanshu Soni, Doaa M. Ali, Björn Tews, Rainer König, Hansjörg Eibl, Martin R. Berger
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0010348

Multidimensional Gene Set Analysis of Genomic Data
Cited by: 71
Author(s): David Montaner, Joaquı́n Dopazo
Software Mentions: 3
Published: over 16 years ago

10.3389/fnins.2020.591196

Anticonvulsants and Chromatin-Genes Expression: A Systems Biology Investigation
Cited by: 1
Author(s): Thayne Woycinck Kowalski, João Luiz Ellera Gomes, Mariléa Furtado Feira, Ágata de Vargas Dupont, Mariana Recamonde‐Mendoza, Fernanda Sales Luiz Vianna
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0215495

CiiiDER: A tool for predicting and analysing transcription factor binding sites
Cited by: 120
Author(s): Linden J. Gearing, Helen E. Cumming, R. A. Chapman, Alexander M. Finkel, Isaac Woodhouse, Kevin Luu, Jodee Gould, Samuel C. Forster, Paul J. Hertzog
Software Mentions: 3
Published: about 7 years ago

10.1186/s12967-021-02708-6

HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia
Cited by: 1
Author(s): Chao Guo, Ya-yue Gao, Qianqian Ju, Chunxia Zhang, Ming Gong, Zhenling Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s12967-019-1932-1

RETRACTED ARTICLE: Overexpression of microRNA-195-5p reduces cisplatin resistance and angiogenesis in ovarian cancer by inhibiting the PSAT1-dependent GSK3β/β-catenin signaling pathway
Cited by: 53
Author(s): Jun Dai, Rujia Wei, Peihai Zhang, Beihua Kong
Software Mentions: 3
Published: over 7 years ago

10.1111/1759-7714.13497

Integrated analysis of <scp>miRNAs</scp> and <scp>DNA</scp> methylation identifies <scp>miR‐132‐3p</scp> as a tumor suppressor in lung adenocarcinoma
Cited by: 7
Author(s): Yun Su, Amol Shetty, Feng Jiang
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0089187

Miz1 Deficiency in the Mammary Gland Causes a Lactation Defect by Attenuated Stat5 Expression and Phosphorylation
Cited by: 7
Author(s): Adrián Sanz-Moreno, David Fuhrmann, Elmar Wolf, Björn von Eyß, Martin Eilers, Hans–Peter Elsässer
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-018-21937-2

The immune contexture of hepatocellular carcinoma predicts clinical outcome
Cited by: 82
Author(s): Friedrich Foerster, Moritz Hess, Aslihan Gerhold‐Ay, Jens U. Marquardt, Diana Becker, Peter R. Galle, Detlef Schuppan, Harald Binder, Ernesto Bockamp
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-44882-0

Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Cited by: 15
Author(s): Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutškov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0131103

The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis
Cited by: 13
Author(s): Kim L. Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Takeshi Kurata, Michael W. Bevan, Michael Lenhard
Software Mentions: 3
Published: about 11 years ago

10.1186/s12957-020-01921-9

Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms
Cited by: 8
Author(s): Sihan Chen, Guodong Cao, Wei Wu, Yida Lu, Xueling He, Lei Yang, Ke Chen, Bo Chen, Mao Ming Xiong
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2021.620740

Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People
Cited by: 5
Author(s): Zhenhua Lu, Ling‐Bing Meng, Zhen Sun, Xiaolei Shi, Weiwei Shao, Yangyang Zheng, Xinglei Yao, Jianguo Song
Software Mentions: 3
Published: over 5 years ago

10.3389/fmolb.2020.565173

IGFLR1 as a Novel Prognostic Biomarker in Clear Cell Renal Cell Cancer Correlating With Immune Infiltrates
Cited by: 8
Author(s): Wenjing Song, You-Cheng Shao, Xin He, Peng Gong, Yan Yang, Shu‐Chun Huang, Yifan Zeng, Lei Wei, Jingwei Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-44661-x

The ion channels and transporters gene expression profile indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma
Cited by: 18
Author(s): Alberto Magi, Marika Masselli, Cesare Sala, Angela Guerriero, Pasquale Laise, Benedetta Puccini, Luigi Rigacci, C Breschi, Olivia Crociani, Serena Pillozzi, Annarosa Arcangeli
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/ery062

Thermopriming triggers splicing memory in Arabidopsis
Cited by: 91
Author(s): Lexiang Yu, Natalia Serrano, Ge Gao, Mohamed A. M. Atia, Morad M. Mokhtar, Yong Woo, Jérémie Bazin, Alaguraj Veluchamy, Moussa Benhamed, Martín Crespi, Chris Gehring, Anireddy S. N. Reddy, Magdy M. Mahfouz
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-23609-7

Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma
Cited by: 13
Author(s): Jessica E. Sagers, Adam S. Brown, Saša Vasilijić, Rebecca Lewis, Mehmet İlhan Şahin, Lukas D. Landegger, Roy H. Perlis, Isaac S. Kohane, D. Bradley Welling, Chirag Patel, Konstantina M. Stanković
Software Mentions: 3
Published: over 8 years ago

10.1186/s12967-020-02366-0

Development and validation of a hypoxia-immune-based microenvironment gene signature for risk stratification in gastric cancer
Cited by: 59
Author(s): Yifan Liu, Jianhua Wu, Weiwei Huang, Shao‐Wen Weng, Baochun Wang, Yiming Chen, Hao Wang
Software Mentions: 3
Published: over 6 years ago

10.1002/2211-5463.12181

The gene expression of numerous SLC transporters is altered in the immortalized hypothalamic cell line N25/2 following amino acid starvation
Cited by: 19
Author(s): Sofie V. Hellsten, Emilia Lekholm, Tauseef Ahmad, Robert Fredriksson
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2020.500064

A Machine Learning Approach to Predicting Autism Risk Genes: Validation of Known Genes and Discovery of New Candidates
Cited by: 22
Author(s): Ying Lin, Shiva Afshar, Anjali M. Rajadhyaksha, James B. Potash, Shizhong Han
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2020.585980

Discovery and Validation of a Metastasis-Related Prognostic and Diagnostic Biomarker for Melanoma Based on Single Cell and Gene Expression Datasets
Cited by: 16
Author(s): Qi Wan, Chengxiu Liu, Chang Liu, Weiqin Liu, Xiaoran Wang, Zhichong Wang
Software Mentions: 3
Published: almost 6 years ago

10.1093/jxb/eraa264

The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels
Cited by: 4
Author(s): Bo Zhang, Bernadette Sztojka, Carolin Seyfferth, Sacha Escamez, Pál Miskolczi, Maxime Chantreau, L. Bako, Nicolas Delhomme, András Gorzsás, Rishikesh P. Bhalerao, Hannele Tuominen
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2019.00932

Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis
Cited by: 25
Author(s): Aftab Alam, Nikhat Imam, Mohd Murshad Ahmed, Safiya Tazyeen, Naaial Tamkeen, Anam Farooqui, Md. Zubbair Malik, Romana Ishrat
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1000154

Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis
Cited by: 227
Author(s): Andrew McDonagh, Natalie D. Fedorova, Jonathan Crabtree, Yu Yan, Heenam Stanley Kim, Dan Chen, Omar Loss, Timothy C. Cairns, Gustavo H. Goldman, Darius Armstrong‐James, Ken Haynes, Hubertus Haas, Markus Schrettl, Gregory S. May, William C. Nierman, Elaine Bignell
Software Mentions: 3
Published: about 18 years ago

10.1186/s12866-020-02020-1

Berberine alters gut microbial function through modulation of bile acids
Cited by: 10
Author(s): Patricia G. Wolf, Saravanan Devendran, Heidi L. Doden, Lindsey K. Ly, Tyler Moore, Hiroyuki Takei, Hiroshi Nittono, Tsuyoshi Murai, Takao Kurosawa, George E. Chlipala, Stefan J. Green, Genta Kakiyama, Purna C. Kashyap, Vance J. McCracken, H. Rex Gaskins, Patrick M. Gillevet, Jason M. Ridlon
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-30587-3

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Cited by: 2
Author(s): Brett W. Engelmann, Chiaowen Joyce Hsiao, John Blischak, Yannick Fourne, Zia Khan, Michael J. Ford, Yoav Gilad
Software Mentions: 3
Published: about 8 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776