bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.697043

A Ferroptosis-Related Gene Model Predicts Prognosis and Immune Microenvironment for Cutaneous Melanoma
Cited by: 12
Author(s): Congcong Xu, Hao Chen
Software Mentions: 5
Published: over 3 years ago

m6A RNA Methylation Regulators Participate in the Malignant Progression and Have Clinical Prognostic Value in Lung Adenocarcinoma
Cited by: 42
Author(s): Fangwei Li, Hong Wang, Huirong Huang, Li Zhang, Dan Wang, Yixin Wan
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0058572

Small Hydrophobic Protein of Human Metapneumovirus Does Not Affect Virus Replication and Host Gene Expression In Vitro
Cited by: 19
Author(s): Miranda de Graaf, Sander Herfst, Jamil Aarbiou, Peter C. Burgers, Fatiha Zaaraoui-Boutahar, M Bijl, Wilfred F. J. van IJcken, Eefje J. A. Schrauwen, Albert D. M. E. Osterhaus, Theo M. Luider, Bob J. Scholte, Ron A. M. Fouchier, Arno C. Andeweg
Software Mentions: 5
Published: almost 12 years ago

10.3389/fgene.2021.702102

Construction and Validation of an Immune-Based Prognostic Model for Pancreatic Adenocarcinoma Based on Public Databases
Cited by: 3
Author(s): Miaobin Mao, Hong-Jian Ling, Yu‐Ping Lin, Yanling Chen, Benhua Xu, Rong Zheng
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2020.608668

Prognosis-Predictive Signature and Nomogram Based on Autophagy-Related Long Non-coding RNAs for Hepatocellular Carcinoma
Cited by: 37
Author(s): Jie-Ping Yu, Yan Chen, Jiansheng Liu
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2021.706814

A Nomogram Integrating Ferroptosis- and Immune-Related Biomarkers for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 2
Author(s): Mengyu Chai, Xiuchun Li, Yaxin Zhang, Yemeng Tang, Pingping Shu, Lin Jia, Ke–Qing Shi, Liangxing Wang, Xiaoying Huang
Software Mentions: 5
Published: over 3 years ago

10.3389/fendo.2021.736286

Gene Signatures of NEUROGENIN3+ Endocrine Progenitor Cells in the Human Pancreas
Cited by: 2
Author(s): Hyo Jeong Yong, Gengqiang Xie, Chengyang Liu, Wei Wang, Ali Naji, Jerome Irianto, Yue J. Wang
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0174602

Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data
Cited by: 1
Author(s): Yunfeng Li, Jarrett Morrow, Benjamin A. Raby, Kelan G. Tantisira, Scott T. Weiss, Wei Huang, Weiliang Qiu
Software Mentions: 5
Published: over 7 years ago

10.1038/s41423-020-00574-8

Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia
Cited by: 48
Author(s): Adeline Crinier, Pierre‐Yves Dumas, Éric Bertrand, Christelle Pipéroglou, Laurine Gil, Arnaud Villacreces, Frédéric Vély, Zoran Ivanović, Pierre Milpied, Émilie Narni-Mancinelli, Éric Vivier
Software Mentions: 5
Published: about 4 years ago

10.3390/ijms20236098

RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics
Cited by: 5
Author(s): Amarinder Singh Thind, Kumar Parijat Tripathi, Mario Rosario Guarracino
Software Mentions: 5
Published: about 5 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

10.1111/cpr.12968

Systemic transcriptome comparison between early‐ And late‐onset pre‐eclampsia shows distinct pathology and novel biomarkers
Cited by: 15
Author(s): Fang Guo, Zhenan Bao, Hao Yang, Yixi Fu, Yaning Wang, Jianming Huang, Min Cheng, Xiaobo Li, Zhuo Shen, Li Li, Ping He, Andy Peng Xiang, Shuaiyu Wang, Hongbo Zhang
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0179726

Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors
Cited by: 166
Author(s): Nathan O. Siemers, James L. Holloway, Chang Han, Scott D. Chasalow, Petra Ross‐Macdonald, Charles F. Voliva, Joseph D. Szustakowski
Software Mentions: 5
Published: over 7 years ago

10.1016/j.celrep.2021.109119

Integrated OMICs unveil the bone-marrow microenvironment in human leukemia
Cited by: 13
Author(s): Diana Passaro, Manuel Garcia-Albornoz, Giovanni Diana, Probir Chakravarty, Linda Ariza‐McNaughton, Antoniana Batsivari, Clara Borràs-Eroles, Ander Abarrategi, Alexander Waclawiczek, Luigi Ombrato, Ilaria Malanchi, John G. Gribben, Dominique Bonnet
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0252508

Network pharmacology and molecular docking study on the mechanism of colorectal cancer treatment using Xiao-Chai-Hu-Tang
Cited by: 23
Author(s): Jingyun Jin, Bin Chen, Xiangyang Zhan, Zhiyi Zhou, Hui Liu, Yun Dong
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21030751

Effect of Bortezomib on Global Gene Expression in PC12-Derived Nerve Cells
Cited by: 10
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Bogusław Machaliński
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0053033

Differences in Transcription Patterns between Induced Pluripotent Stem Cells Produced from the Same Germ Layer Are Erased upon Differentiation
Cited by: 2
Author(s): Iryna Pirozhkova, Ana Barat, Petr Dmitriev, Elena Kim, Robert Thomas, Justine Guégan, Chrystèle Bilhou‐Nabera, Florence Busato, Jörg Tost, Gilles Carnac, Dalila Laoudj-Chenivesse, Marc Lipinski, Yegor S. Vassetzky
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12974-020-1706-y

Neonatal hypoxia-ischemia in rat elicits a region-specific neurotrophic response in SVZ microglia
Cited by: 14
Author(s): Urs Fisch, Catherine Brégère, Florian Geier, Laurie Chicha, Raphael Guzman
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.700607

Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 23
Author(s): Haihui Zhong, Jie Wang, Yaru Zhu, Yefeng Shen
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0171689

Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock
Cited by: 10
Author(s): Samanwoy Mukhopadhyay, Pravat Kumar Thatoi, AK Pandey, B. K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0017388

Azacytidine and Decitabine Induce Gene-Specific and Non-Random DNA Demethylation in Human Cancer Cell Lines
Cited by: 129
Author(s): Sabine Hagemann, Oliver Heil, Frank Lyko, Bodo Brueckner
Software Mentions: 5
Published: over 13 years ago

10.3389/fcell.2021.727935

Uncovering the Association Between m5C Regulator-Mediated Methylation Modification Patterns and Tumour Microenvironment Infiltration Characteristics in Hepatocellular Carcinoma
Cited by: 13
Author(s): Xinyu Gu, Haibo Zhou, Qingfei Chu, Qiuxian Zheng, Jing Wang, Haihong Zhu
Software Mentions: 5
Published: about 3 years ago

10.3389/fcell.2021.645482

Glycolysis Define Two Prognostic Subgroups of Lung Adenocarcinoma With Different Mutation Characteristics and Immune Infiltration Signatures
Cited by: 3
Author(s): Huo Chen, Mengyu Zhang, Rui Li, Tingting Liu, Jianping Li, Yi-Qing Qu
Software Mentions: 5
Published: over 3 years ago

10.1016/j.celrep.2021.109423

RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade
Cited by: 11
Author(s): Kun Tan, H. C. Song, Miles Wilkinson
Software Mentions: 5
Published: over 3 years ago

10.1016/j.celrep.2020.107843

Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation
Cited by: 194
Author(s): Karpagam Srinivasan, Brad A. Friedman, Ainhoa Etxeberría, Melanie A. Huntley, Marcel P. van der Brug, Oded Foreman, Jonathan S. Paw, Zora Modrušan, Thomas G. Beach, Geidy E. Serrano, David V. Hansen
Software Mentions: 5
Published: over 4 years ago

10.1016/j.celrep.2021.109101

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.665265

TP53 Mutational Status-Based Genomic Signature for Prognosis and Predicting Therapeutic Response in Pancreatic Cancer
Cited by: 4
Author(s): Feng Zhang, Wenhui Zhong, Honghao Li, Kaijun Huang, Min Yu, Yu-bin Liu
Software Mentions: 5
Published: over 3 years ago

10.1111/jcmm.15517

Carboxypeptidase A6 was identified and validated as a novel potential biomarker for predicting the occurrence of active ulcerative colitis
Cited by: 3
Author(s): Haizhou Wang, Meng Zhang, Mengna Zhang, Fan Wang, Jing Liu, Qiu Zhao
Software Mentions: 5
Published: over 4 years ago

10.1111/jcmm.15111

Novel miRNA markers for the diagnosis and prognosis of endometrial cancer
Cited by: 27
Author(s): Qian Wang, Kai Xu, Tong Yu, Xianning Dai, Teng Xu, Dazhi He, Jianchao Ying
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms21041512

Dynamics of the Transcriptome Response to Heat in the Moss, Physcomitrella patens
Cited by: 11
Author(s): Osama Elzanati, Saïd Mouzeyar, Jane Roche
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13058-017-0814-9

DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms
Cited by: 28
Author(s): David J. Lemler, Miranda L. Lynch, Lia Tesfay, Zhiyong Deng, Bibbin T. Paul, Xiaohong Wang, Poornima Hegde, David H. Manz, Suzy V. Torti, Frank M. Torti
Software Mentions: 5
Published: over 7 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-23195-8

Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Cited by: 13
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 5
Published: over 6 years ago

10.7150/jca.50868

Data mining analysis of the prognostic impact of N<sup>6</sup>-methyladenosine regulators in patients with endometrial adenocarcinoma
Cited by: 7
Author(s): Junyu Zhai, Shang Li, Yu Liu, Yanzhi Du
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0238764

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes
Cited by: 24
Author(s): Sahar Radwan, Darby Gilfillan, Bridget Eklund, Hend M. Radwan, Nagwan Galal El Menofy, Justin Lee, Marylee Kapuscinski, Zaid Abdo
Software Mentions: 5
Published: about 4 years ago

10.7150/jca.29958

TGFBI Promotes Tumor Growth and is Associated with Poor Prognosis in Oral Squamous Cell Carcinoma
Cited by: 16
Author(s): Bingjie Wang, Kun-Ping Chi, Ruling Shen, Saiwei Zheng, Yang Guo, Jianfeng Li, Jian Fei, Yuan He
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.molmet.2017.02.007

Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms22031111

Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type
Cited by: 9
Author(s): Sadegheh Haghshenas, Michael A. Levy, Jennifer Kerkhof, Erfan Aref‐Eshghi, Haley McConkey, Tugce B. Balci, Victoria Mok Siu, Cindy Skinner, Roger E. Stevenson, Bekim Sadiković, Charles E. Schwartz
Software Mentions: 5
Published: almost 4 years ago

10.1002/jcsm.12741

Meta‐analysis of genome‐wide DNA methylation and integrative omics of age in human skeletal muscle
Cited by: 29
Author(s): Sarah Voisin, Jacques Michaux, Shanie Landen, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Sofiya Gancheva, Meriem Ouni, Markus Jähnert, Kevin J. Ashton, Vernon G. Coffey, Jamie-Lee M Thompson, Thomas Doering, Anne Gabory, Claudine Junien, Robert Caïazzo, Hélène Verkindt, Violetta Raverdy, François Pattou, Philippe Froguel, Jeffrey M. Craig, Sara Blocquiaux, Martine Thomis, Adam P. Sharples, Annette Schürmann, Michael Roden, Steve Horvath, Nir Eynon
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-27027-7

Immunoprofiles of human Sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk
Cited by: 32
Author(s): Daniel P. Strange, Richard Green, Dietmar W. Siemann, Michael Gale, Saguna Verma
Software Mentions: 5
Published: over 6 years ago

10.1177/0748730418813785

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
Cited by: 47
Author(s): Jordan M. Singer, Jacob J. Hughey
Software Mentions: 5
Published: about 6 years ago

10.3389/fcell.2021.673295

Overexpression of PLXDC2 in Stromal Cell-Associated M2 Macrophages Is Related to EMT and the Progression of Gastric Cancer
Cited by: 15
Author(s): Yihan Guan, Yuzhang Du, Guanzheng Wang, Hongquan Gou, Yuezhen Xue, Jingsong Xu, Enhao Li, David W. Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 5
Published: over 3 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

10.1016/j.celrep.2018.03.046

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Cited by: 111
Author(s): Gregory P. Way, Francisco Sanchez‐Vega, Konnor La, Joshua Armenia, Walid K. Chatila, Augustin Luna, Chris Sander, Andrew D. Cherniack, Deqin Ma, Giovanni Ciriello, Nikolaus Schultz, Yolanda Sánchez, Casey S. Greene
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.648806

Construction of a Prognostic Immune-Related LncRNA Risk Model for Lung Adenocarcinoma
Cited by: 16
Author(s): Yue Li, Ruoyi Shen, Anqi Wang, Jian Zhao, Jieqi Zhou, Weijie Zhang, Ruochen Zhang, Jianjie Zhu, Zeyi Liu, Jian-An Huang
Software Mentions: 5
Published: over 3 years ago

10.1186/s13024-021-00481-0

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains
Cited by: 9
Author(s): Julio Barrera, Lingyun Song, Julia Gamache, Melanie E. Garrett, Alexias Safi, Young Won Yun, Ivana Premasinghe, Daniel J. Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison Ashley‐Koch, Gregory E. Crawford, Ornit Chiba‐Falek
Software Mentions: 5
Published: over 3 years ago

10.1172/jci.insight.142680

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Cited by: 33
Author(s): Kirsten E. Diggins, Elisavet Serti, Virginia S. Muir, Mario G. Rosasco, Tingting Lü, Elisa Balmas, Gerald T. Nepom, S. Alice Long, Peter S. Linsley
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.64478

Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo
Cited by: 7
Author(s): Darryl A. Wesener, Zachary Beller, Samantha L. Peters, Amir Rajabi, Gianluca Dimartino, Richard J. Giannone, Robert L. Hettich, Jeffrey I. Gordon
Software Mentions: 5
Published: over 3 years ago

10.3390/metabo8040078

Population-Level Analysis to Determine Parameters That Drive Variation in the Plasma Metabolite Profiles
Cited by: 2
Author(s): Mahmoud Al-Majdoub, Katharina Herzog, Bledar Daka, Martin Magnusson, Lennart Råstam, Ulf Lindblad, Peter Sartipy
Software Mentions: 5
Published: about 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

10.1186/s12885-020-07493-x

Identification of ALDH3A2 as a novel prognostic biomarker in gastric adenocarcinoma using integrated bioinformatics analysis
Cited by: 24
Author(s): Zhenhua Yin, Danni Wu, Jianping Shi, Xiao‐Hong Wei, Nuyun Jin, Xiaolan Lu, Xiaohan Ren
Software Mentions: 5
Published: about 4 years ago

10.1038/s41388-021-02005-y

Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma
Cited by: 19
Author(s): Chuanpeng Dong, Annamaria Cesarano, Giuseppe Bombaci, Jill L. Reiter, Christina Y. Yu, Yue Wang, Zhaoyang Jiang, Mohammad Abu Zaid, Kun Huang, Xiongbin Lu, Brian A Walker, Fabiana Perna, Yunlong Liu
Software Mentions: 5
Published: about 3 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

10.1371/journal.pone.0204236

In silico analysis of the Mus musculus uterine gene expression landscape during pregnancy identifies putative upstream regulators for labour
Cited by: 1
Author(s): Febilla Fernando, Souad Boussata, Aldo Jongejan, Joris A. M. van der Post, Gijs B. Afink, Carrie Ris‐Stalpers
Software Mentions: 5
Published: about 6 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

10.1155/2021/5588429

Crosstalk between RNA-Binding Proteins and Immune Microenvironment Revealed Two RBP Regulatory Patterns with Distinct Immunophenotypes in Periodontitis
Cited by: 0
Author(s): Xing Lü, Guanqun Meng, Tian Chen, Xiaoqi Zhang, Ding Bai, Hui Xu
Software Mentions: 5
Published: over 3 years ago

10.1155/2020/2514230

Deciphering N<sup>6</sup>-Methyladenosine-Related Genes Signature to Predict Survival in Lung Adenocarcinoma
Cited by: 26
Author(s): Jie Zhu, Min Wang, Daixing Hu
Software Mentions: 5
Published: almost 5 years ago

10.1155/2020/1980921

Identification of Differentially Expressed Genes and miRNAs Associated with Esophageal Squamous Cell Carcinoma by Integrated Analysis of Microarray Data
Cited by: 4
Author(s): Lemeng Zhang, Jianhua Chen, Tianli Cheng, Hua Yang, Changqie Pan, Haitao Li
Software Mentions: 5
Published: over 4 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

10.1155/2020/8832739

Identification of 5-Gene Signature Improves Lung Adenocarcinoma Prognostic Stratification Based on Differential Expression Invasion Genes of Molecular Subtypes
Cited by: 19
Author(s): Zhaoxu Zheng, Weijie Deng, Jiansheng Yang
Software Mentions: 5
Published: almost 4 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

10.3390/ijerph16040524

Age-Related Differences in miRNA Expression in Mexican-American Newborns and Children
Cited by: 6
Author(s): Karen Huen, Daneida Lizárraga, Katherine Kogut, Brenda Eskenazi, Nina Holland
Software Mentions: 5
Published: almost 6 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

10.3389/fgene.2021.616507

Molecular Subtypes Based on the Stemness Index Predict Prognosis in Glioma Patients
Cited by: 7
Author(s): Jun Tan, Hecheng Zhu, Guihua Tang, Hongwei Liu, Siyi Wanggou, Yudong Cao, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Ming Zhao, Chao Ren, Xingjun Jiang, Yin Wu
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2019.00855

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments
Cited by: 0
Author(s): Adele Ribeiro, Júlia Maria Pavan Soler, Roberto Hirata
Software Mentions: 5
Published: about 5 years ago

10.7150/ijms.49449

Identification and Validation of Six Autophagy-related Long Non-coding RNAs as Prognostic Signature in Colorectal Cancer
Cited by: 19
Author(s): Lin Cheng, Tong Han, Zheyu Zhang, Pan Yi, Chunhu Zhang, Sifang Zhang, Weijun Peng
Software Mentions: 5
Published: almost 4 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

10.3389/fgene.2020.591667

Effects of RNA Binding Proteins on the Prognosis and Malignant Progression in Prostate Cancer
Cited by: 13
Author(s): Xiaoliang Hua, Shengdong Ge, Juan Chen, Li Zhang, Sheng Tai, Chaozhao Liang
Software Mentions: 5
Published: about 4 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

10.1155/2020/7082408

Identification and Validation of an Individualized EMT-Related Prognostic Risk Score Formula in Gastric Adenocarcinoma Patients
Cited by: 13
Author(s): Deyu Zhang, Siran Zhou, Bing-Rong Liu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12885-021-08362-x

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Cited by: 2
Author(s): Bhavya Dhaka, Radhakrishnan Sabarinathan
Software Mentions: 5
Published: over 3 years ago

10.7150/ijms.39056

Identification of gene expression profiles and immune cell infiltration signatures between low and high tumor mutation burden groups in bladder cancer
Cited by: 33
Author(s): Zonglong Wu, Mu-Ru Wang, Qinggang Liu, Yaxiao Liu, Ke-Cheng Zhu, Lipeng Chen, Hongda Guo, Yan Li, Benkang Shi
Software Mentions: 5
Published: almost 5 years ago

10.3389/fgene.2021.625466

Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome
Cited by: 1
Author(s): Karissa Barthelson, Lachlan Baer, Yang Dong, Melanie L. Hand, Zac Pujic, Morgan Newman, Geoffrey J. Goodhill, Robert I. Richards, Stephen Pederson, Michael Lardelli
Software Mentions: 5
Published: over 3 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/fnins.2020.607215

Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer’s and Parkinson’s Brains With Digital Cytometry
Cited by: 5
Author(s): Marie Catherine Bordone, Nuno L. Barbosa‐Morais
Software Mentions: 5
Published: almost 4 years ago

10.1155/2020/3598417

Effect of BRCA1 on the Concurrent Chemoradiotherapy Resistance of Cervical Squamous Cell Carcinoma Based on Transcriptome Sequencing Analysis
Cited by: 13
Author(s): Xin Wen, Lingling Shui, Manhua Cui
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0044736

Brain Transcriptional and Epigenetic Associations with Autism
Cited by: 131
Author(s): Matthew R. Ginsberg, Robert A. Rubin, Tatiana Falcone, Angela H. Ting, Marvin R. Natowicz
Software Mentions: 5
Published: about 12 years ago

10.1038/s41598-021-87779-7

Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction
Cited by: 10
Author(s): Sanjiban Sekhar Roy, Y-h. Taguchi
Software Mentions: 5
Published: over 3 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

10.1038/s41598-021-90095-9

miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta
Cited by: 1
Author(s): Iram P. Rodríguez‐Sánchez, Daniel Rafael Saldaña-Torres, Olga Karina Villanueva-Segura, María Lourdes Garza‐Rodríguez, Mayra A. Gómez‐Govea, Ghongwei Liang, María de Lourdes Ramírez‐Ahuja, Margarita L. Martínez‐Fierro, Iván Delgado‐Enciso, Laura Elia Martínez-de-Villarreal, Yu Zhou, Adriana E. Flores-Suárez, Xi Chen, Diana Reséndez‐Pérez, Chenyu Zhang, Gustavo Ponce‐García
Software Mentions: 5
Published: over 3 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

10.1186/s12918-018-0671-x

Multi-omics integration reveals molecular networks and regulators of psoriasis
Cited by: 35
Author(s): Yuqi Zhao, Deepali Jhamb, Le Shu, Douglas Arneson, Deepak K. Rajpal, Xia Yang
Software Mentions: 5
Published: almost 6 years ago

10.1186/1752-0509-6-2

Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control
Cited by: 15
Author(s): Kevin M. D’Auria, Gina M. Donato, Mary C. Gray, Glynis L. Kolling, Cirle A. Warren, Lauren M Cave, Michael D. Solga, Joanne Lannigan, Jason A. Papin, Erik L. Hewlett
Software Mentions: 5
Published: almost 13 years ago

10.1038/s41598-021-82067-w

Calcium calmodulin kinase II activity is required for cartilage homeostasis in osteoarthritis
Cited by: 11
Author(s): Giovanna Nalesso, Anne‐Sophie Thorup, S. Eldridge, Armando M. De Palma, Amanpreet Kaur, Kiran Peddireddi, Kevin Blighe, Sharmila Rana, B. Stott, Tonia L. Vincent, B.L. Thomas, Jessica Bertrand, J. Sherwood, Antonella Fioravanti, Costantino Pitzalis, Francesco Dell’Accio
Software Mentions: 5
Published: over 3 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

10.18632/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

10.3389/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

10.3389/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

10.1038/s41598-021-81538-4

Clinical implications of intrinsic molecular subtypes of breast cancer for sentinel node status
Cited by: 12
Author(s): Maria Rossing, Christina Bligaard Pedersen, Tove Filtenborg Tvedskov, Ilse Vejborg, Maj Lis Møller Talman, Lars Rønn Olsen, Niels Kroman, Finn Cilius Nielsen, Maj Britt Jensen, Bent Ejlertsen
Software Mentions: 5
Published: almost 4 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

10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: over 10 years ago

10.1186/s13104-017-2455-6

Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks
Cited by: 12
Author(s): Anne Heidi Skogholt, Einar Ryeng, Sten Even Erlandsen, Frank Skorpen, Svanhild Margrethe Arentz Schønberg, Pål Sætrom
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.10462

Development and clinical validation of a 3-miRNA signature to predict prognosis of gastric cancer
Cited by: 8
Author(s): Wenqian Qi, Qian Zhang
Software Mentions: 5
Published: almost 4 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

10.18632/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

10.3389/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

10.1186/1756-0500-7-302

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression
Cited by: 9
Author(s): Alain Sewer, Sylvain Gubian, Ulrike Kogel, Emilija Veljkovic, Wanjiang Han, Arnd Hengstermann, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 5
Published: over 10 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: almost 6 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776