bioconductor: sva | Projects | Ecosyste.ms: Papers

10.1186/s41065-021-00201-0

Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis
Cited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: about 3 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: over 3 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: about 4 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: about 6 years ago

10.1002/1878-0261.12389

Using microarray‐based subtyping methods for breast cancer in the era of high‐throughput RNA sequencing
Cited by: 6
Author(s): Christina Bligaard Pedersen, Finn C. Nielsen, Maria Rossing, Lars Rønn Olsen
Software Mentions: 7
Published: about 6 years ago

10.3389/fcell.2021.659080

ANXA1 as a Prognostic and Immune Microenvironmental Marker for Gliomas Based on Transcriptomic Analysis and Experimental Validation
Cited by: 8
Author(s): Zhongxiao Lin, Ming‐Shien Wen, Enxing Yu, Xiao Yan Lin, Hua Wang, Jiayu Chen, Chaojie Yao, Hengli Zhang, Junnan Ru, Kankai Wang, Ying Zhang, Lijie Huang, Qichuan Zhuge, Shuxu Yang
Software Mentions: 7
Published: over 3 years ago

10.18632/aging.102571

Identification of molecular correlations of RBM8A with autophagy in Alzheimer's disease
Cited by: 40
Author(s): Donghua Zou, Rongjie Li, Xiaohua Huang, Guoying Chen, Ying Liu, Youshi Meng, Yimei Wang, Yuan Wu, Ying Mao
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13229-017-0119-y

Exaggerated CpH methylation in the autism-affected brain
Cited by: 30
Author(s): Shannon Ellis, Saloni Gupta, Anna Moes, Andrew B. West, Dan E. Arking
Software Mentions: 7
Published: almost 8 years ago

10.1136/gutjnl-2019-318343

A blood-based prognostic biomarker in IBD
Cited by: 125
Author(s): Daniele Biasci, James C. Lee, Nurulamin M Noor, Diana R Pombal, Monica Hou, Nina Lewis, Tariq Ahmad, Ailsa Hart, Miles Parkes, Eoín McKinney, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.588411

Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Cited by: 6
Author(s): Elisa Crisci, Marco Moroldo, Thien‐Phong Vu Manh, Ammara Mohammad, Laurent Jourdren, Céline Urien, Edwige Bouguyon, Elise Bordet, Claudia Bevilacqua, Mickaël Bourge, Jérémy Pezant, Alexis Pléau, Olivier Boulesteix, Isabelle Schwartz, Nicolas Bertho, Elisabetta Giuffra
Software Mentions: 7
Published: almost 4 years ago

10.3389/fmolb.2021.656145

Identification and Exploration of Novel Macrophage M2-Related Biomarkers and Potential Therapeutic Agents in Endometriosis
Cited by: 10
Author(s): Zhongqi Cui, Ramesh Singh Bhandari, Lei Qin, Mingzhi Lu, Lei Zhang, Mengmei Zhang, Fenyong Sun, Lijin Feng, Shasha Zhao
Software Mentions: 7
Published: over 3 years ago

10.3389/fcell.2021.665364

Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment
Cited by: 11
Author(s): Yuanyuan Zhang, Feng Yang, Xiaohong Peng, Xiaoyü Li, Na Luo, Wenjun Zhu, Min Fu, Qianxia Li, Guangyuan Hu
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: about 4 years ago

10.7554/eLife.31977

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci
Cited by: 101
Author(s): Matthias Thurner, Martijn van de Bunt, Jason Torres, Anubha Mahajan, Vibe Nylander, Amanda J. Bennett, Kyle J. Gaulton, Amy Barrett, Carla Burrows, Christopher G. Bell, Robert Lowe, Stephan Beck, Vardhman K. Rakyan, Anna L. Gloyn, Mark I. McCarthy
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41435-020-00118-0

Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation
Cited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-020-03734-9

MADA: a web service for analysing DNA methylation array data
Cited by: 1
Author(s): Xinyu Hu, Li Tang, Linconghua Wang, Fang‐Xiang Wu, Min Li
Software Mentions: 7
Published: about 4 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: almost 7 years ago

10.1155/2020/2415374

Identifying 4 Novel lncRNAs as Potential Biomarkers for Acute Rejection and Graft Loss of Renal Allograft
Cited by: 7
Author(s): Zedan Zhang, Yanlin Tang, Hongkai Zhuang, Enyu Lin, Lu Xie, Xiaoqiang Feng, Jiayi Zeng, Yanjun Liu, Jiumin Liu, Yuming Yu
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.60223

Analysis of the immune response to sciatic nerve injury identifies efferocytosis as a key mechanism of nerve debridement
Cited by: 64
Author(s): Ashley L. Kalinski, Choya Yoon, Lucas D. Huffman, Patrick C. Duncker, Rafi Kohen, Ryan Passino, Hannah Hafner, Craig Johnson, Riki Kawaguchi, Kevin S. Carbajal, Juan Sebastián Jara, Edmund R. Hollis, Daniel H. Geschwind, Benjamin M. Segal, Roman J. Giger
Software Mentions: 7
Published: almost 4 years ago

10.3389/fonc.2021.734873

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

10.1038/s41598-021-81952-8

Gene co-expression network analysis reveals immune cell infiltration as a favorable prognostic marker in non-uterine leiomyosarcoma
Cited by: 12
Author(s): Mohammad Darzi, Saeid Gorgin, Keivan Majidzadeh‐A, Rezvan Esmaeili
Software Mentions: 7
Published: almost 4 years ago

10.7150/thno.54134

Single-cell melanoma transcriptomes depicting functional versatility and clinical implications of STIM1 in the tumor microenvironment
Cited by: 2
Author(s): Henry Sung Ching Wong, Wei Chiao Chang
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: over 6 years ago

10.3389/fonc.2020.580263

A Prognostic Microenvironment-Related Immune Signature via ESTIMATE (PROMISE Model) Predicts Overall Survival of Patients With Glioma
Cited by: 23
Author(s): Huaide Qiu, Yongqiang Li, Shupeng Cheng, Jiahui Li, Chuan He, Jianan Li
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12940-021-00754-7

Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes
Cited by: 11
Author(s): Anne K. Bozack, Philippe Boileau, Linqing Wei, Alan Hubbard, Fenna C.M. Sillé, Catterina Ferreccio, Johanna Acevedo, Lifang Hou, Vesna Ilievski, Craig Steinmaus, Martyn T. Smith, Ana Navas-Acién, Mary V. Gamble, Andrés Cárdenas
Software Mentions: 7
Published: over 3 years ago

10.1186/s13195-020-00709-z

TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
Cited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-020-75573-w

Development of a novel immune-related genes prognostic signature for osteosarcoma
Cited by: 17
Author(s): Zhi-Xi Wu, Yajun Deng, Guangzhi Zhang, Enhui Ren, Wenhua Yuan, Qiqi Xie
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0215565

A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection
Cited by: 6
Author(s): Ron Ammar, Pitchumani Sivakumar, Gábor Járai, John Ryan Thompson
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0227760

A graph-based algorithm for RNA-seq data normalization
Cited by: 2
Author(s): Diem-Trang Tran, Aditya Bhaskara, Balagurunathan Kuberan, Matthew Might
Software Mentions: 7
Published: almost 5 years ago

10.20892/j.issn.2095-3941.2020.0402

The m6A methylation landscape stratifies hepatocellular carcinoma into 3 subtypes with distinct metabolic characteristics
Cited by: 17
Author(s): Xiaotian Shen, Beiyuan Hu, Jing Xu, Wei Qin, Yan Fu, Shun Wang, Qiongzhu Dong, Lun–Xiu Qin
Software Mentions: 7
Published: almost 5 years ago

10.1111/acel.13344

Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans
Cited by: 62
Author(s): Ricardo Iván Martínez-Zamudio, Hannah K Dewald, Themistoklis Vasilopoulos, Lisa Gittens-Williams, Patricia Fitzgerald-Bocarsly, Utz Herbig
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0159138

Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
Cited by: 26
Author(s): Payam Delfani, Linda Dexlin Mellby, Malin Nordström, Andreas Holmér, Mattias Ohlsson, Carl Borrebaeck, Christer Wingren
Software Mentions: 7
Published: over 8 years ago

10.3389/fnagi.2021.605970

Immune Profiling of Parkinson’s Disease Revealed Its Association With a Subset of Infiltrating Cells and Signature Genes
Cited by: 12
Author(s): Xi Zhang, Zhihua Shao, Sutong Xu, Qiulu Liu, Chenming Liu, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 7
Published: almost 4 years ago

10.3389/fonc.2021.671892

A Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Epithelial Ovarian Cancer
Cited by: 9
Author(s): Yan Qiu, Min Pan, Xuemei Chen
Software Mentions: 7
Published: over 3 years ago

10.3389/fcell.2021.659294

Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy
Cited by: 5
Author(s): Peng Zhou, Yuchao Lu, Xiufen Yang, Jin‐Zhou Xu, Chen‐Qian Liu, Qi‐Dong Xia, Junlin Lu, Shaogang Wang, Jia Hu
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2020.595757

Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis
Cited by: 4
Author(s): Jinlong Wu, Qisheng Lin, Shu Li, Xinghua Shao, Xuying Zhu, Minfang Zhang, Wenyan Zhou, Zhaohui Ni
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-64794-8

Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes
Cited by: 12
Author(s): Hanna Engqvist, Toshima Z. Parris, Jana Biermann, Elisabeth Werner Rönnerman, Peter Larsson, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.11968

Development and validation of a novel survival model for acute myeloid leukemia based on autophagy-related genes
Cited by: 7
Author(s): Li Huang, Lier Lin, Xing Fu, Can Meng
Software Mentions: 7
Published: over 3 years ago

10.1111/jcmm.15877

RAD51AP1 promotes progression of ovarian cancer via TGF‐β/Smad signalling pathway
Cited by: 17
Author(s): Hongyu Zhao, Yan Gao, Qi Chen, Jie Li, Meng Ren, Xiaoting Zhao, Wentao Yue
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.ppat.1006767

Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection
Cited by: 50
Author(s): Ashton T. Belew, Caroline Junqueira, Gabriela F. Rodrigues-Luiz, Bruna M. Valente, Antônio Edson Rocha Oliveira, Rafael B. Polidoro, Luciana W. Zuccherato, Daniella Castanheira Bartholomeu, Sérgio Schenkman, Ricardo T. Gazzinelli, Barbara A. Burleigh, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 7
Published: almost 7 years ago

10.1002/jcsm.12556

An epigenetic clock for human skeletal muscle
Cited by: 58
Author(s): Sarah Voisin, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Kevin J. Ashton, Vernon G. Coffey, Thomas Doering, Jamie-Lee M Thompson, Christian Benedict, Jonathan Cedernaes, Maléne E. Lindholm, Jeffrey M. Craig, David S. Rowlands, Adam P. Sharples, Steve Horvath, Nir Eynon
Software Mentions: 7
Published: almost 5 years ago

10.15252/msb.20199156

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver
Cited by: 19
Author(s): Vanessa Dubois, Céline Gheeraert, Wouter Vankrunkelsven, Julie Dubois-Chevalier, Hélène Dehondt, Marie Bobowski-Gérard, Manjula Vinod, Francesco Paolo Zummo, Fabian Güiza, Maheul Ploton, Emilie Dorchies, Laurent Pineau, Alexis Boulinguiez, Emmanuelle Vallez, Eloïse Woitrain, Eric Baugé, Fanny Lalloyer, Christian Duhem, Nabil Rabhi, Ronald E. van Kesteren, Cheng Ming Chiang, Steve Lancel, Hélène Duez, Jean-Sébastien Annicotte, Réjane Paumelle, Ilse Vanhorebeek, Greet Van den Berghe, Bart Staels, Philippe Lefèbvre, Jérôme Eeckhoute
Software Mentions: 6
Published: over 4 years ago

10.3389/fcell.2021.648856

Comprehensive Characterization of Cachexia-Inducing Factors in Diffuse Large B-Cell Lymphoma Reveals a Molecular Subtype and a Prognosis-Related Signature
Cited by: 5
Author(s): Zhixing Kuang, Xun Li, Rongqiang Liu, Shaoxing Chen, Jiannan Tu
Software Mentions: 6
Published: over 3 years ago

10.1186/s13229-020-00402-w

Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm
Cited by: 23
Author(s): Hudson P. Santos, Arjun Bhattacharya, Robert M. Joseph, Lisa Smeester, Karl Kuban, Carmen J. Marsit, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 6
Published: almost 4 years ago

10.18632/aging.202638

Identification of key genes in coronary artery disease: an integrative approach based on weighted gene co-expression network analysis and their correlation with immune infiltration
Cited by: 10
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-016-3199-8

Identification of novel targets of diabetic nephropathy and PEDF peptide treatment using RNA-seq
Cited by: 29
Author(s): Ana Rubín, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
Software Mentions: 6
Published: about 8 years ago

10.1186/s12864-019-5553-0

Comparing DNA methylation profiles in saliva and intestinal mucosa
Cited by: 13
Author(s): Nerissa L. Hearn, Aaron S. Coleman, Vincent Ho, Christine L Chiu, Joanne M. Lind
Software Mentions: 6
Published: over 5 years ago

10.1186/s12967-020-02597-1

Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass
Cited by: 8
Author(s): Bishnupriya Chhatriya, Moumita Mukherjee, Sukanta Ray, Barsha Saha, Somdatta Lahiri, Sandip Halder, Indranil Ghosh, Sujan Khamrui, Kshaunish Das, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra, Srikanta Goswami
Software Mentions: 6
Published: about 4 years ago

10.3390/life11020115

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: almost 4 years ago

10.1002/cam4.3890

Normal tissue adjacent to tumor expression profile analysis developed and validated a prognostic model based on Hippo‐related genes in hepatocellular carcinoma
Cited by: 10
Author(s): Qingbo Pan, Fanbo Qin, Hanyu Yuan, Baoning He, Ni Yang, Yitong Zhang, Hong Ren, Yi Arial Zeng
Software Mentions: 6
Published: over 3 years ago

10.18632/aging.202478

Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature
Cited by: 7
Author(s): Yan Qin, Jiehua Deng, Lihua Zhang, Jiaxing Yuan, Huawei Yang, Qiuyun Li
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-014-0503-2

Functional normalization of 450k methylation array data improves replication in large cancer studies
Cited by: 640
Author(s): Jean Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W. Zanke, Thomas J. Hudson, Elana J. Fertig, Celia M.T. Greenwood, Kasper D. Hansen
Software Mentions: 6
Published: about 10 years ago

10.3389/fimmu.2021.671201

Identification and Validation of the Signatures of Infiltrating Immune Cells in the Eutopic Endometrium Endometria of Women With Endometriosis
Cited by: 22
Author(s): Xinglong Wu, Jin-Jiao Chen, Huiling Zhou, Yu Wu, Fei Lin, Jing Shi, Hong-Zhen Wu, Hai-Qun Xiao, Wei Wang
Software Mentions: 6
Published: about 3 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 7 years ago

10.1186/s12935-020-01552-w

Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population
Cited by: 7
Author(s): Qiang Zhao, Jian Xue, Bo Hong, Wubin Qian, Tiezhu Liu, Bin Fan, Jie Cai, Yunpeng Ji, Jia Liu, Yong Yang, Qi-Xiang Li, Sheng Guo, Ning Zhang
Software Mentions: 6
Published: about 4 years ago

10.1186/s13148-019-0755-5

Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood
Cited by: 79
Author(s): Roy Lardenoije, Janou A. Y. Roubroeks, Ehsan Pishva, Markus Leber, Holger Wagner, Artemis Iatrou, Adam R. Smith, Rebecca G. Smith, Lars Eijssen, Luca Kleineidam, Amit Kawalia, Per Hoffmann, Tobias Luck, Steffi G. Riedel‐Heller, Frank Jessen, Wolfgang Maier, Michael Wagner, René Hurlemann, Günter Kenis, Muhammad Ali, Antonio del Sol, Diego Mastroeni, Elaine Delvaux, Paul D. Coleman, Jonathan Mill, Bart P. F. Rutten, Katie Lunnon, Alfredo Ramı́rez, Daniël L.A. van den Hove
Software Mentions: 6
Published: almost 5 years ago

10.3390/cells8080921

Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
Cited by: 12
Author(s): João Victor da Silva Guerra, Bruna Maria de Sá Pereira, Jéssica Gonçalves Vieira da Cruz, Nicole de Miranda Scherer, Carolina Furtado, Rafaela Montalvão de Azevedo, Paulo Sérgio Lopes de Oliveira, Paulo Faria, Mariana Boroni, Beatriz de Camargo, Mariana Maschietto
Software Mentions: 6
Published: over 5 years ago

10.1016/j.cels.2018.08.001

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Cited by: 77
Author(s): Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, Markus Ralser
Software Mentions: 6
Published: about 6 years ago

10.3389/fcell.2021.622021

Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease
Cited by: 6
Author(s): Qiuhong Wu, Yang Liu, Yan Xie, Shixiong Wei, Yi Liu
Software Mentions: 6
Published: over 3 years ago

10.3390/genes12091339

Integrated Bioinformatics Analysis Reveals Marker Genes and Potential Therapeutic Targets for Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Aoqi Li, Jin He, Zhe Zhang, Shuhui Jiang, Yun Gao, Yuchun Pan, Huanan Wang, Lenan Zhuang
Software Mentions: 6
Published: about 3 years ago

10.1155/2021/6635526

Construction and Validation of a Ferroptosis-Related Prognostic Model for Gastric Cancer
Cited by: 33
Author(s): Xiaotao Jiang, Qiaofeng Yan, Linling Xie, Shiqi Xu, Kailin Jiang, Jiahua Huang, Yi Wen, Yanhua Yan, Junhui Zheng, Shiyun Tang, Kechao Nie, Zhihua Zheng, Jinglin Pan, Peng Liu, Yuancheng Huang, Xingrui Yan, Yushan Zou, Xuan Chen, Fengbin Liu, Peiwu Li, Kunhai Zhuang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-86319-7

Screening of osteoarthritis diagnostic markers based on immune-related genes and immune infiltration
Cited by: 15
Author(s): Wenhua Yuan, Qiqi Xie, Ke-Ping Wang, Wei Shen, Xiaofei Feng, Zheng Liu, Jin-Tao Shi, Xiaobo Zhang, Kai Zhang, Yajun Deng, Hai-Yu Zhou
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2020.578933

Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes
Cited by: 7
Author(s): Yuanyuan Zhang, Shuai Ma, Moran Wang, Wei Shi, Yu Hu
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0252096

Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos
Cited by: 9
Author(s): María Belén Rabaglino, Alan M. O’Doherty, Jan Bojsen-Møller Secher, Patrick Lonergan, Poul Hyttel, Trudee Fair, Haja N. Kadarmideen
Software Mentions: 6
Published: over 3 years ago

10.1111/febs.15578

Genome‐wide postnatal changes in immunity following fetal inflammatory response
Cited by: 0
Author(s): DC Costa, Núria Bonet, Amanda Solé, José Manuel González de Aledo-Castillo, Eduard Sabidó, Ferrán Casals, Carlota Rovira, Alfons Nadal, J. L. Marı́n, Teresa Cobo, Robert Castelo
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2019.01056

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One
Cited by: 5
Author(s): Eduardo R. Fukutani, Pablo Ivan Pereira Ramos, José Irahe Kasprzykowski, Lucas Gentil Azevedo, Moreno Magalhães de Souza Rodrigues, João Victor Lima, Helton Fábio Santos de Araújo, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: about 5 years ago

10.1186/s12885-019-6101-7

A large cohort study identifying a novel prognosis prediction model for lung adenocarcinoma through machine learning strategies
Cited by: 43
Author(s): Yin Li, Di Ge, Jie Gu, Fan Xu, Qinqing Zhu
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2020.626555

Development and Validation of an Immune-Related Gene-Pair Model of High-Grade Serous Ovarian Cancer After Platinum-Based Chemotherapy
Cited by: 0
Author(s): Jiaxing Lin, Xiao Xu, Dan Sun, Tianren Li
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0243807

Optimised generation of iPSC-derived macrophages and dendritic cells that are functionally and transcriptionally similar to their primary counterparts
Cited by: 17
Author(s): Susan J. Monkley, Jayendra Kumar Krishnaswamy, Melker Göransson, Maryam Clausen, Johan Meuller, Kristofer Thörn, Ryan Hicks, Stephen Delaney, Louise Stjernborg
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2020.544610

Identification of Four Immune Subtypes in Bladder Cancer Based on Immune Gene Sets
Cited by: 25
Author(s): Chaozhi Tang, Jiakang Ma, Xiuli Liu, Zhengchun Liu
Software Mentions: 6
Published: about 4 years ago

10.1186/s13148-016-0241-2

Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
Cited by: 11
Author(s): Emma Cazaly, Russell Thomson, James R. Marthick, Adele F. Holloway, Jac Charlesworth, Joanne L. Dickinson
Software Mentions: 6
Published: over 8 years ago

10.3389/fonc.2021.622752

Tumor Immunometabolism Characterization in Ovarian Cancer With Prognostic and Therapeutic Implications
Cited by: 9
Author(s): Miner Yang, Gaowen Chen, Kunjie Gao, Yifeng Wang
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.632934

RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma
Cited by: 19
Author(s): Yimin Pan, Kai Xiao, Yue Li, Yuzhe Li, Qing Liu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0239495

Sources of variation in cell-type RNA-Seq profiles
Cited by: 16
Author(s): Johan Gustafsson, Felix Held, Jonathan L. Robinson, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-020-69330-2

A novel predictive model incorporating immune-related gene signatures for overall survival in melanoma patients
Cited by: 14
Author(s): Mengting Liao, Furong Zeng, Li Yao, Qian Gao, Mingzhu Yin, Guangtong Deng, Xiang Chen
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-75505-8

Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart
Cited by: 12
Author(s): Vishantie Dostal, Silas D. Wood, Cody T Thomas, Yu Han, Edward Lau, Maggie P. Y. Lam
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2021.653474

Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis
Cited by: 6
Author(s): Yaozhong Liu, Na Liu, Fan Bai, Qiming Liu
Software Mentions: 6
Published: over 3 years ago

10.3389/fnins.2019.00392

Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease
Cited by: 19
Author(s): Lavida R. K. Brooks, George I. Mias
Software Mentions: 6
Published: over 5 years ago

10.1038/srep26947

Variation in serum biomarkers with sex and female hormonal status: implications for clinical tests
Cited by: 29
Author(s): Jordan M. Ramsey, Jason D. Cooper, Brenda W. J. H. Penninx, Sabine Bahn
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pcbi.1006701

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Cited by: 271
Author(s): Mohamed Mounir, Marta Lucchetta, Tiago Henrique Da T.C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008769

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Cited by: 1
Author(s): Song He, Xinyu Song, Xisheng Yang, Jianyang Yu, Yao Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pbio.2006687

Quantitative assessment of cell population diversity in single-cell landscapes
Cited by: 40
Author(s): Qi Liu, Charles A. Herring, Quanhu Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, Ken S. Lau
Software Mentions: 6
Published: about 6 years ago

10.3389/fcell.2021.724837

Integrative Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis
Cited by: 14
Author(s): Huanhuan Zhao, Shaokang Pan, Jiayu Duan, Fengxun Liu, Guangpu Li, Dongwei Li, Zhangsuo Liu
Software Mentions: 6
Published: about 3 years ago

10.3389/fgene.2021.618277

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Cited by: 7
Author(s): Mateusz Garbulowski, Karolina Smolińska, Klev Diamanti, Gang Pan, Khurram Maqbool, Lars Feuk, Jan Komorowski
Software Mentions: 6
Published: over 3 years ago

10.18632/aging.103350

A novel molecular-clinicopathologic nomogram to improve prognosis prediction of hepatocellular carcinoma
Cited by: 3
Author(s): Zhongjing Zhang, Wanqing Weng, Weiguo Huang, Boda Wu, Yi Zhou, Jie Zhang, Tuo Deng, Yan Wen, Jiecheng Zhang, Jian‐Yang Ao, Qiyu Zhang, Ke‐Qing Shi
Software Mentions: 6
Published: over 4 years ago

10.1080/21655979.2020.1847398

Development of cancer prognostic signature based on pan-cancer proteomics
Cited by: 6
Author(s): Weiguo Huang, Jianhui Chen, Wanqing Weng, Yukai Xiang, Hongqi Shi, Yunfeng Shan
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13040-021-00261-y

A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma
Cited by: 6
Author(s): Qian Yan, Wenjiang Zheng, Boqing Wang, Baoqian Ye, Huiyan Luo, Xinqian Yang, Ping Zhang, Xiongwen Wang
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.8961

Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets
Cited by: 41
Author(s): Meijing Wu, Xianwen Shang, Yue Sun, Jing Wu, Guoyan Liu
Software Mentions: 6
Published: over 4 years ago

10.3389/fmolb.2021.644557

Reconstruction and Analysis of the Immune-Related LINC00987/A2M Axis in Lung Adenocarcinoma
Cited by: 8
Author(s): Jiakang Ma, Xinhua Lin, Xueting Wang, Qing-Qing Min, Tonglian Wang, Chaozhi Tang
Software Mentions: 6
Published: over 3 years ago

10.3389/fnagi.2021.602781

Exploring the Key Genes and Identification of Potential Diagnosis Biomarkers in Alzheimer’s Disease Using Bioinformatics Analysis
Cited by: 20
Author(s): Wuhan Yu, Weihua Yu, Yan Yang, Yang Lü
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2021.644220

Prognostic Signatures of Metabolic Genes and Metabolism-Related Long Non-coding RNAs Accurately Predict Overall Survival for Osteosarcoma Patients
Cited by: 8
Author(s): Chang Gong, Rong Tang, Yawei Shi, Liu Tai-cong, Kaisheng Zhou, Nan Wu, Haihong Zhang
Software Mentions: 6
Published: over 3 years ago

10.1186/s13148-020-00944-z

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: about 4 years ago

10.7150/jca.55570

Upregulating <i>KTN1</i> promotes Hepatocellular Carcinoma progression
Cited by: 1
Author(s): Jian Pan, Naixia Chao, Yao‐Yao Zhang, Tianyi Huang, Chengxiao Chen, Qiuhong Qin, Jinhong Guo, Rongshi Huang, Guopei Luo
Software Mentions: 6
Published: almost 4 years ago

10.1172/jci.insight.143654

A longitudinal and transancestral analysis of DNA methylation patterns and disease activity in lupus patients
Cited by: 34
Author(s): Patrick Coit, Lourdes Ortíz-Fernández, Edith A. Lewis, W. Joseph McCune, Kathleen Maksimowicz-McKinnon, Amr H. Sawalha
Software Mentions: 6
Published: about 4 years ago

10.15252/msb.20156520

Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
Cited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: over 8 years ago

10.1200/PO.17.00241

Transcriptional Subtyping and CD8 Immunohistochemistry Identifies Patients With Stage II and III Colorectal Cancer With Poor Prognosis Who Benefit From Adjuvant Chemotherapy
Cited by: 40
Author(s): Wendy L. Allen, Philip D. Dunne, Simon S. McDade, Enya Scanlon, Maurice B. Loughrey, Helen Coleman, Christopher McCann, Kristy McLaughlin, Zsuzsanna Németh, Najeeb Syed, Puthen V. Jithesh, Ken Arthur, Richard H. Wilson, Vicky M. Coyle, Darragh G. McArt, Graeme I. Murray, Leslie Samuel, Paolo Nuciforo, José Jimenez, Guillem Argilés, Rodrigo Dienstmann, J. Tabernero, Lucia Picariello, Luca Messerini, Stefania Nobili, Enrico Mini, Kieran Sheahan, Elizabeth J. Ryan, Patrick G. Johnston, Sandra Van Schaeybroeck, Mark Lawler, Daniel B. Longley
Software Mentions: 6
Published: about 6 years ago

10.1128/mSphere.00843-20

Pseudomonas aeruginosa Volatilome Characteristics and Adaptations in Chronic Cystic Fibrosis Lung Infections
Cited by: 10
Author(s): Thomas J. Davis, Ava V. Karanjia, Charity N. Bhebhe, Sarah B. West, Matthew Richardson, Heather D. Bean
Software Mentions: 6
Published: about 4 years ago

10.1186/s12920-019-0519-2

A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies
Cited by: 7
Author(s): Joshua Mannheimer, Dawn L. Duval, Ashok Prasad, Daniel L. Gustafson
Software Mentions: 5
Published: over 5 years ago

10.1186/s12920-020-0670-9

Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals
Cited by: 9
Author(s): Nerissa L. Hearn, Christine L Chiu, Joanne M. Lind
Software Mentions: 5
Published: almost 5 years ago

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