bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7717/peerj.11422

The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
Cited by: 5
Author(s): Lei Tian, Huandi Zhou, Guohui Wang, Wen Yan Wang, Yuehong Li, Xiaoying Xue
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: over 3 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

10.12688/wellcomeopenres.11253.2

A genomic atlas of human adrenal and gonad development
Cited by: 46
Author(s): Ignacio del Valle, Federica Buonocore, Andrew Duncan, Lin Lin, Martino Barenco, Rahul Parnaik, Sonia Shah, Michael Hubank, Dianne Gerrelli, John C. Achermann
Software Mentions: 5
Published: about 7 years ago

10.3390/genes11080868

Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia
Cited by: 52
Author(s): Yuanrong Cheng, Yangfeng Su, Shoubi Wang, Yurun Liu, Lin Jin, Qi Wan, Ying Liu, Chaoyang Li, Xuan Sang, Yang Liu, Chang Liu, Zhichong Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
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

10.1186/s13059-015-0844-5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Cited by: 1,843
Author(s): Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian H. Gersuk, Alex K. Shalek, Chloe K. Slichter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter S. Linsley, Raphaël Gottardo
Software Mentions: 5
Published: about 9 years ago

10.1186/s12882-018-0944-z

Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data
Cited by: 3
Author(s): Yingbo Guo, Weijie Gao, Danyang Wang, Weijing Liu, Zhongjie Liu
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.634697

A Combined Two-mRNA Signature Associated With PD-L1 and Tumor Mutational Burden for Prognosis of Lung Adenocarcinoma
Cited by: 12
Author(s): Congkuan Song, Zhi‐Quan Wu, Qingwen Wang, Yujin Wang, Zixin Guo, Sheng Li, Weidong Hu
Software Mentions: 5
Published: almost 4 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

10.1371/journal.pone.0038365

Detection of Simultaneous Group Effects in MicroRNA Expression and Related Target Gene Sets
Cited by: 21
Author(s): Stephan Artmann, Klaus Jung, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 5
Published: over 12 years ago

10.3389/fcell.2021.723721

Identification of the Immune-Related Genes in Tumor Microenvironment That Associated With the Recurrence of Head and Neck Squamous Cell Carcinoma
Cited by: 6
Author(s): Chengcheng Liu, Wenwen Qi, Nianqiao Gong, Fenlu Zhu, Ran Xu, Zhaogang Teng, Fanxing Xu, Ya‐Zhen Qin, Mingqiu Zhao, Xiaoming Li, Ming Xia
Software Mentions: 5
Published: over 3 years ago

10.3389/fnins.2021.620899

Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer’s Disease Using Post-mortem Brain Tissue Samples
Cited by: 21
Author(s): Qingqin Li, Diana Cai
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0240943

Three-gene prognostic biomarkers for seminoma identified by weighted gene co-expression network analysis
Cited by: 2
Author(s): Hualin Chen, Gang Chen, Yang Pan, Xiaoxiang Jin
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-74748-9

Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
Cited by: 6
Author(s): Harry M. Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A. Gethings, Johannes P.C. Vissers, Jonathan G. Lees, Christine A. Orengo, Linda Partridge, Konstantinos Thalassinos
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0067907

Gene-Metabolite Expression in Blood Can Discriminate Allergen-Induced Isolated Early from Dual Asthmatic Responses
Cited by: 18
Author(s): Amrit Singh, Masatsugu Yamamoto, Sarah Kam, Jian Ruan, Gail M. Gauvreau, Paul M. O'Byrne, J. Mark FitzGerald, R. Robert Schellenberg, Louis‐Philippe Boulet, Gabriella Wojewodka, Cynthia Kanagaratham, Juan B. De Sanctis, Danuta Radzioch, Scott J. Tebbutt
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0247669

Immune gene expression networks in sepsis: A network biology approach
Cited by: 13
Author(s): Kyung Soo Kim, Dong Wook Jekarl, Jaeeun Yoo, Seungok Lee, Myungshin Kim, Yonggoo Kim
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12957-021-02367-3

Comprehensive analysis of angiogenesis subtype of squamous cell carcinoma
Cited by: 3
Author(s): Fanglu Qin, Sheng-hua Lin, Kun Deng, Junqi Qin, Zhanyu Xu, Liqiang Yuan, Jiangbo Wei, Yu Sun, Tiaozhan Zheng, Shikang Li
Software Mentions: 5
Published: about 3 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

10.1186/s11689-020-09316-3

Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Bonnie Alberry, Christina A Castellani, Shiva M. Singh
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0208982

Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) RNAi is associated with cell cycle inhibition, apoptosis, DNA damage response and drug sensitivity in breast cancer
Cited by: 11
Author(s): Şahika Cıngır Köker, Ermira Jahja, Huma Shehwana, Ayşe Gökçe Keşküş, Özlen Konu
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-74705-6

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
Cited by: 5
Author(s): Marta Lucchetta, Marco Pellegrini
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-016-1097-7

Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
Cited by: 64
Author(s): Andrée Delahaye‐Duriez, Prashant K. Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno‐Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafał M. Kamiński, Enrico Petretto, Michael R. Johnson
Software Mentions: 5
Published: about 8 years ago

10.3390/ijms21239169

Development and Validation of a Novel 11-Gene Prognostic Model for Serous Ovarian Carcinomas Based on Lipid Metabolism Expression Profile
Cited by: 28
Author(s): Mingjun Zheng, Heather Mullikin, Anna Hester, Bastian Czogalla, H Heidegger, Theresa� Vilsmaier, Aurelia Vattai, Anca Chelariu-Raicu, Udo Jeschke, Fabian Trillsch, Sven Mahner, Till Kaltofen
Software Mentions: 5
Published: about 4 years ago

10.7717/peerj.11342

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
Cited by: 6
Author(s): Qingqing Wang, Xiaoyan Yu, Zhewen Zheng, Fengxia Chen, Ningning Yang, Youwen Zhou
Software Mentions: 5
Published: over 3 years ago

10.3390/microarrays3040212

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Cited by: 1
Author(s): Andrew R. Dalby, Ian Bailey
Software Mentions: 5
Published: about 10 years ago

10.3389/fnut.2021.675935

Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue
Cited by: 1
Author(s): Marianthi Kalafati, Michael Lenz, Gökhan Ertaylan, Ilja C. W. Arts, Chris T. Evelo, Marleen M.J. van Greevenbroek, Ellen E. Blaak, Michiel E. Adriaens, Martina Kutmon
Software Mentions: 5
Published: over 3 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2021.668595

Prognostic and Predicted Significance of FENDRR in Colon and Rectum Adenocarcinoma
Cited by: 2
Author(s): Fan Yang, Siyu Sun, Fei Yang
Software Mentions: 5
Published: about 3 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

10.1038/s41598-020-72988-3

Machine learning approach to integrated endometrial transcriptomic datasets reveals biomarkers predicting uterine receptivity in cattle at seven days after estrous
Cited by: 10
Author(s): María Belén Rabaglino, Haja N. Kadarmideen
Software Mentions: 5
Published: about 4 years ago

10.3390/ijms22073735

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders
Cited by: 6
Author(s): Guillaume Velasco, Damien Ulveling, Sophie Rondeau, Pauline Marzin, Motoko Unoki, Valérie Cormier‐Daire, Claire Francastel
Software Mentions: 5
Published: over 3 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/gb-2007-8-9-r190

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data
Cited by: 29
Author(s): Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P. King, Paul Britton
Software Mentions: 5
Published: almost 18 years ago

10.1186/s13148-016-0266-6

DNA methylation and smoking in Korean adults: epigenome-wide association study
Cited by: 48
Author(s): Mi Kyeong Lee, Yoonki Hong, Sun‐Young Kim, Stephanie J. London, Woo Jin Kim
Software Mentions: 5
Published: about 8 years ago

10.3389/fmolb.2020.566491

Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma
Cited by: 15
Author(s): Muqi Li, Minni Liang, Tian Lan, Xiwen Wu, Wenlin Xie, Tielong Wang, Z Chen, Shunli Shen, Baogang Peng
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0103207

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
Cited by: 195
Author(s): Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry F. Bartlett, Naomi R. Wray, Qiongyi Zhao
Software Mentions: 5
Published: over 10 years ago

10.3390/genes12060876

High SGO2 Expression Predicts Poor Overall Survival: A Potential Therapeutic Target for Hepatocellular Carcinoma
Cited by: 3
Author(s): Min Deng, Shaohua Li, Jie Mei, Wenping Lin, Jingwen Zou, Wei Wei, Rong Guo
Software Mentions: 5
Published: over 3 years ago

10.1186/s13148-018-0580-2

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis
Cited by: 26
Author(s): Youdinghuan Chen, David A. Armstrong, Lucas A. Salas, Haley F. Hazlett, Amanda B. Nymon, John A. Dessaint, Daniel Aridgides, Diane Mellinger, Xiaoying Li, Brock C. Christensen, Alix Ashare
Software Mentions: 5
Published: about 6 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

10.1038/srep29251

Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data
Cited by: 21
Author(s): Tin Nguyen, Diana Diaz, Rebecca Tagett, Sorin Drăghici
Software Mentions: 5
Published: over 8 years ago

10.1002/cam4.3959

IBSP, a potential recurrence biomarker, promotes the progression of colorectal cancer via Fyn/β‐catenin signaling pathway
Cited by: 8
Author(s): Cheng Yan, Ying Qin, Mengmeng Dai, Liping Liu, Yicheng Ni, Qiao Sun, Lulu Li, Yaoyao Zhou, Cheng Qiu, Yuyang Jiang
Software Mentions: 5
Published: over 3 years ago

10.1002/cam4.3353

Construction of a lipid metabolism‐related and immune‐associated prognostic signature for hepatocellular carcinoma
Cited by: 37
Author(s): Bo Hu, Xiaobo Yang, Xinting Sang
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms22179650

Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics
Cited by: 15
Author(s): Miranda L. Gardner, Michael A. Freitas
Software Mentions: 5
Published: about 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

10.1371/journal.pone.0041066

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis
Cited by: 25
Author(s): Federico Carlos Blanco, Marcelo Soria, María Verónica Bianco, Fabiana Bigi
Software Mentions: 5
Published: over 12 years ago

10.26508/lsa.202000864

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories
Cited by: 12
Author(s): Sophie G Kellaway, Peter Keane, Benjamin Edginton-White, Kakkad Regha, Ella Kennett, Constanze Bonifer
Software Mentions: 5
Published: almost 4 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: over 4 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

10.1038/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

10.1038/srep31669

Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells
Cited by: 3
Author(s): Mariam El-Ashmawy, Melissa Coquelin, Krishna Luitel, Kimberly Batten, Jerry W. Shay
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms22168611

Identification of a DNA Methylation Episignature in the 22q11.2 Deletion Syndrome
Cited by: 10
Author(s): Kathleen Rooney, Michael A. Levy, Sadegheh Haghshenas, Jennifer Kerkhof, Daniela Rogaia, Maria Giovanna Tedesco, Valentina Imperatore, Amedea Mencarelli, Gabriella Maria Squeo, Eleonora Di Venere, Giuseppe Di Cara, Alberto Verrotti, Giuseppe Merla, Matthew L. Tedder, Barbara R. DuPont, Bekim Sadiković, Paolo Prontera
Software Mentions: 5
Published: over 3 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

10.1038/srep31479

Pancreas-enriched miRNAs are altered in the circulation of subjects with diabetes: a pilot cross-sectional study
Cited by: 131
Author(s): Attila A. Seyhan, Yury O. Nunez Lopez, Hui Xie, Fanchao Yi, Clayton E. Mathews, Magdalena Pasarica, Richard E. Pratley
Software Mentions: 5
Published: over 8 years ago

10.1186/s13148-019-0637-x

Association of leukocyte DNA methylation changes with dietary folate and alcohol intake in the EPIC study
Cited by: 20
Author(s): Flavie Perrier, Vivian Viallon, Srikant Ambatipudi, Akram Ghantous, Cyrille Cuenin, Héctor Hernández-Vargas, Véronique Chajès, Laura Baglietto, Marco Matejcic, Hortensia Moreno-Macías, Tilman Kühn, Heiner Boeing, Anna Karakatsani, Αναστασία Κοτανίδου, Antonia Trichopoulou, Sabina Sieri, Salvatore Panico, Francesca Fasanelli, Martijn E.T. Dollé, N. Charlotte Onland‐Moret, Ivonne Sluijs, Elisabete Weiderpass, J. Ramón Quiŕos, Antonio Agudo, José María Huerta, Eva Ardanaz, Miren Dorronsoro, Tammy Y.N. Tong, Konstantinos K. Tsilidis, Elio Riboli, Marc J. Gunter, Zdenko Herceg, Pietro Ferrari, Isabelle Romieu
Software Mentions: 5
Published: over 5 years ago

10.1186/s41016-021-00235-3

The increasing expression of GPX7 related to the malignant clinical features leading to poor prognosis of glioma patients
Cited by: 5
Author(s): Jiawei Yao, Xin Chen, Zhendong Liu, Ruotian Zhang, Cheng Zhang, Quan Yang, Penglei Yao, Qiuyi Jiang, Jianing Wu, Shen Zhao
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0024351

Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Cited by: 63
Author(s): Nancy Mah, Ying Wang, Mei-Chih Liao, Alessandro Prigione, Justyna Józefczuk, Björn Lichtner, Katharina Wolfrum, Manuela Haltmeier, Max Flöttmann, Martin H. Schaefer, Alexander Hahn, Ralf Mrowka, Edda Klipp, Miguel A. Andrade‐Navarro, James Adjaye
Software Mentions: 5
Published: over 13 years ago

10.3389/fcell.2021.696878

Classification of Osteosarcoma Based on Immunogenomic Profiling
Cited by: 14
Author(s): Xinwen Wang, Liangming Wang, Weifeng Xu, Xinwu Wang, Dianshan Ke, Jiumao Lin, Wanzun Lin, Xiaochun Bai
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.11012

Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations
Cited by: 13
Author(s): André Junggebauer, Tamara R. Hartke, Daniel Ramos, Ina Schaefer, Damayanti Buchori, Purnama Hidayat, Stefan Scheu, Jochen Drescher
Software Mentions: 5
Published: almost 4 years ago

10.3389/fonc.2020.01119

Identification of RNA: 5-Methylcytosine Methyltransferases-Related Signature for Predicting Prognosis in Glioma
Cited by: 23
Author(s): Peng Wang, Minxian Wu, Zewei Tu, Chuming Tao, Qing Hu, Kuangxun Li, Xingen Zhu, Kai Huang
Software Mentions: 5
Published: over 4 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

10.3389/fonc.2021.663556

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer
Cited by: 14
Author(s): Yang Liu, Hefen Sun, Xuan Li, Qiqi Liu, Yuanyuan Zhao, Liangdong Li, Baojin Xu, Yifeng Hou, Wei Jin
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2021.592107

Identification of Expression Patterns and Potential Prognostic Significance of m5C-Related Regulators in Head and Neck Squamous Cell Carcinoma
Cited by: 11
Author(s): Zhaolong Han, Biao Yang, Yu Wang, Xiuxia Zeng, Zhen Tian
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1009140

Drosophila Caliban preserves intestinal homeostasis and lifespan through regulating mitochondrial dynamics and redox state in enterocytes
Cited by: 12
Author(s): Zhaoxia Dai, Dong Liu, Xiao Du, Ying Ge, Deborah A. Hursh, Xiaolin Bi
Software Mentions: 5
Published: about 4 years ago

10.1186/s12935-021-01823-0

A signature of seven immune‐related genes predicts overall survival in male gastric cancer patients
Cited by: 10
Author(s): Xin Xu, Yida Lu, Youliang Wu, Mingliang Wang, Xiaodong Wang, Huizhen Wang, Bo Chen, Yongxiang Li
Software Mentions: 5
Published: almost 4 years ago

10.3389/fonc.2020.553045

m6A Reader HNRNPA2B1 Promotes Esophageal Cancer Progression via Up-Regulation of ACLY and ACC1
Cited by: 62
Author(s): Huimin Guo, Bei Wang, Kaiyue Xu, Ling Nie, Yao Fu, Zhangding Wang, Qiang Wang, Shouyu Wang, Xiaoping Zou
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-016-0951-7

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer
Cited by: 18
Author(s): Mengyun Wu, Xiaofei Zhang, Dao‐Qing Dai, Le Ou-Yang, Yuan Zhu, Hong Yan
Software Mentions: 5
Published: almost 9 years ago

10.3389/fonc.2021.615234

Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma
Cited by: 5
Author(s): Weicheng Duan, Kang Wang, Yijie Duan, Xiuyi Chen, Xufeng Chu, Ping Hu, Bo Xiong
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1006222

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans
Cited by: 68
Author(s): Agnieszka Gacek‐Matthews, Harald Berger, Takahiko Sasaki, Kathrin Wittstein, Clemens Gruber, Zachary A. Lewis, Joseph Strauss
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-020-6739-1

The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster
Cited by: 17
Author(s): Ben Harrison, Lu Wang, Erika Gajda, Elise V. Hoffman, Brian Y. Chung, Scott D. Pletcher, Daniel Raftery, Daniel Promislow
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.721252

Antioxidant Gene Signature Impacts the Immune Infiltration and Predicts the Prognosis of Kidney Renal Clear Cell Carcinoma
Cited by: 11
Author(s): Xueting Ren, Li Ma, Nan Wang, Ruina Zhou, Jianhua Wu, Xin Xie, Hao Zhang, Di Liu, Xiuli Ma, Chengxue Dang, Huafeng Kang, Zhangjian Zhou
Software Mentions: 5
Published: over 3 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.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

10.3389/fonc.2021.710767

N6-Methylandenosine-Related lncRNAs Predict Prognosis and Immunotherapy Response in Bladder Cancer
Cited by: 20
Author(s): Yuying Zhang, Baoyi Zhu, Minghui He, Yi Cai, Xiaoling Ying, Chonghe Jiang, Weidong Ji, Jing Zeng
Software Mentions: 5
Published: over 3 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

10.1186/1471-2164-9-124

Can subtle changes in gene expression be consistently detected with different microarray platforms?
Cited by: 48
Author(s): Paola Pedotti, Peter A C ‘t Hoen, Erno Vreugdenhil, Geert J. Schenk, Rolf H. A. M. Vossen, Yavuz Ariyürek, Mattias de Hollander, Rowan Kuiper, G.J.B. van Ommen, Johan T. den Dunnen, Judith M. Boer, Renée X. de Menezes
Software Mentions: 5
Published: over 16 years ago

10.18632/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

10.1371/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

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: over 7 years ago

10.3389/fonc.2021.700062

Identification of a Hypoxia-Related Molecular Classification and Hypoxic Tumor Microenvironment Signature for Predicting the Prognosis of Patients with Triple-Negative Breast Cancer
Cited by: 16
Author(s): Xiaoli Sun, Huan Luo, Chen Han, Yu Zhang, Cunli Yan
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-015-1546-9

Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)
Cited by: 31
Author(s): Andriy Kovalchuk, Tommaso Raffaello, Emad Jaber, Susanna Keriö, Rajendra P. Ghimire, W. Walter Lorenz, Jeffrey F. D. Dean, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-14-263

Ontology based molecular signatures for immune cell types via gene expression analysis
Cited by: 12
Author(s): Terrence F. Meehan, Nicole Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl
Software Mentions: 5
Published: over 11 years ago

10.1186/s12859-021-04046-2

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Cited by: 0
Author(s): Heeju Noh, Hua Ziyi, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-2164-12-326

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Cited by: 19
Author(s): Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, A.M. Mosquera, E. A. Gonzalez, Juan José Lozano, Matthew Ingham, Juliane C. Dohm, María Noguera, Robert Kofler, José Antonio del Rı́o, Mònica Bayés, Heinz Himmelbauer, Lauro Sumoy
Software Mentions: 5
Published: over 13 years ago

10.3389/fonc.2021.621430

Identification of Hub Genes Associated With Melanoma Development by Comprehensive Bioinformatics Analysis
Cited by: 8
Author(s): Jie Jiang, Chong Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Xinli Zhan
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-07225-2

Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice
Cited by: 25
Author(s): Pabodha Hettige, Uzma Tahir, Kiisa C. Nishikawa, Matthew J. Gage
Software Mentions: 5
Published: about 4 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-015-1532-2

Pathway reporter genes define molecular phenotypes of human cells
Cited by: 24
Author(s): Jitao David Zhang, Erich Küng, Franziska Boess, Ulrich Certa, Martin Ebeling
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-019-2697-5

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
Cited by: 5
Author(s): Karl Stamm, Aoy Tomita‐Mitchell, Serdar Bozdag
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2020.522831

Systematic Analyses of the Differentially Expressed Alternative Splicing Events in Gastric Cancer and Its Clinical Significance
Cited by: 2
Author(s): Changwei Lin, Bowen Yu, Mao Zhang, Yifei Chen, Liang Li, Delong Zhao
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0103514

Identification of a Novel Luminal Molecular Subtype of Breast Cancer
Cited by: 14
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 5
Published: over 10 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2021.637733

Low Expression of ADCY4 Predicts Worse Survival of Lung Squamous Cell Carcinoma Based on Integrated Analysis and Immunohistochemical Verification
Cited by: 3
Author(s): Zhicong Liu, Lixin Ru, Zhenchao Ma
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2020.586019

Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis
Cited by: 19
Author(s): Quanwei Zhou, Xuejun Yan, Weidong Liu, Yin Wu, Hongjuan Xu, Damei Cheng, Xingjun Jiang, Chao Ren
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

10.1186/1471-2164-11-32

Integrative analysis of the heat shock response in Aspergillus fumigatus
Cited by: 76
Author(s): Daniela Albrecht, Reinhard Guthke, Axel A. Brakhage, Olaf Kniemeyer
Software Mentions: 5
Published: almost 15 years ago

10.1186/1471-2105-14-174

PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: over 11 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776