bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: about 5 years ago

10.7717/peerj.10008

A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
Cited by: 3
Author(s): Zhenyu Zhao, Boxue He, Qidong Cai, Pengfei Zhang, Ping Xiong, Yuqian Zhang, Hui Xie, Xiang Wang
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.ppat.1009278

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
Cited by: 11
Author(s): Fredrik Barrenäs, Scott G. Hansen, G. Lynn Law, Connor B. Driscoll, Richard Green, Eric E. Smith, Jean Chang, Inah Golez, Taryn Urion, Xinxia Peng, Leanne S. Whitmore, Daniel J. Newhouse, Colette M. Hughes, David W. Morrow, Kurt T. Randall, Andrea N. Selseth, Julia C. Ford, Roxanne M. Gilbride, Bryan E. Randall, Emily Ainslie, Kelli Oswald, Rebecca Shoemaker, Randy Fast, William J. Bosche, Michael K. Axthelm, Yoshinori Fukazawa, George N. Pavlakis, Barbara K. Felber, Slim Fourati, Rafick Pierre Sékaly, Jeffrey D. Lifson, Jan Komorowski, Ewelina Kosmider, Danica Shao, Wenjun Song, Paul T. Edlefsen, Louis J. Picker, Michael Gale
Software Mentions: 9
Published: about 5 years ago

10.1186/s12885-021-08328-z

The tumor immune microenvironment and immune-related signature predict the chemotherapy response in patients with osteosarcoma
Cited by: 16
Author(s): Lijiang He, Hainan Yang, Jingshan Huang
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: about 13 years ago

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: almost 11 years ago

10.1155/2021/5510780

A Five-Gene Prognostic Nomogram Predicting Disease-Free Survival of Differentiated Thyroid Cancer
Cited by: 5
Author(s): Pan Ruchong, Hai-ping Tang, Xiang Wang
Software Mentions: 9
Published: about 5 years ago

10.18632/aging.203290

Expression mode and prognostic value of FXYD family members in colon cancer
Cited by: 8
Author(s): Ming Jin, Hui Zhang, Jun Yang, Zheng Zhao, Kaitai Liu
Software Mentions: 9
Published: about 5 years ago

10.1155/2021/9911184

Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis
Cited by: 7
Author(s): Fei Sun, Jian Zhou, Peiyu Pu, Chen Qiu, Jia rui Cao, Hao Peng
Software Mentions: 9
Published: over 5 years ago

10.1186/s12967-021-02770-0

Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis
Cited by: 9
Author(s): Hui Zhang, Chang Xu, Shi Chen, Junying Zhang, Ting Qian, Zhuo Wang, Rong Ma, Jianzhong Wu, Feng Jiang, Jifeng Feng
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.619242

The Identification and Validation of Two Heterogenous Subtypes and a Risk Signature Based on Ferroptosis in Hepatocellular Carcinoma
Cited by: 40
Author(s): Xinwei Han, Libo Wang, Long Liu, Taoyuan Lu, Dechao Jiao, Yuling Sun, Xinwei Han
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: about 5 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: about 6 years ago

10.3389/fonc.2020.602498

Metabolism-Associated Molecular Classification of Colorectal Cancer
Cited by: 13
Author(s): Meng Zhang, Haizhou Wang, Ruyi Peng, Fei Xu, Fan Wang, Qiu Zhao
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2020.626912

Molecular Subtypes and CD4+ Memory T Cell-Based Signature Associated With Clinical Outcomes in Gastric Cancer
Cited by: 15
Author(s): Zhikun Ning, Cegui Hu, Chao Huang, Jiang Liu, Taicheng Zhou, Zhen Zong
Software Mentions: 9
Published: over 5 years ago

10.15252/msb.20199389

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Cited by: 63
Author(s): Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, T. P. Speed, David M. Lin, Pengyi Yang, Jean Yee Hwa Yang
Software Mentions: 9
Published: over 6 years ago

10.15252/msb.20198849

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
Cited by: 24
Author(s): Antje Dittmann, Norman J. Kennedy, Nina L Soltero, Nader Morshed, Miyeko Mana, Ömer H. Yılmaz, Roger J. Davis, Forest M. White
Software Mentions: 9
Published: about 7 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: about 6 years ago

10.15252/msb.20177862

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
Cited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: about 8 years ago

10.1186/s12864-018-5166-z

RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data
Cited by: 17
Author(s): Amanda Ernlund, Robert J. Schneider, Kelly V. Ruggles
Software Mentions: 9
Published: almost 8 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: almost 5 years ago

10.7554/eLife.65537

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Cited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.54756

ATR expands embryonic stem cell fate potential in response to replication stress
Cited by: 34
Author(s): Sina Atashpaz, Sara Samadi Shams, Javier Martín‐González, Endre Sebestyén, Negar Arghavanifard, Andrea Gnocchi, Eliene Albers, Simone Minardi, Giovanni Fagà, Paolo Soffientini, E. Allievi, Valeria Cancila, Ángela Bachi, Óscar Fernández-Capetillo, Claudio Tripodo, Francesco Ferrari, Andrés J. López-Contreras, Vincenzo Costanzo
Software Mentions: 9
Published: over 6 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 12 years ago

10.1186/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: almost 9 years ago

10.1002/1878-0261.12595

Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltration
Cited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-021-84909-z

Omics data integration identifies ELOVL7 and MMD gene regions as novel loci for adalimumab response in patients with Crohn’s disease
Cited by: 8
Author(s): Mario Gorenjak, Mateja Zupin, Gregor Jezernik, Pavel Skok, Uroš Potočnik
Software Mentions: 9
Published: over 5 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12885-019-6235-7

lionessR: single sample network inference in R
Cited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: almost 7 years ago

10.1038/s41598-020-77201-z

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae
Cited by: 3
Author(s): José Córdoba-Caballero, Pedro Seoane, Fernando M. Jabato, James R. Perkins, Manuel Manchado, M. Gonzalo Claros
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12885-020-6638-5

Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis
Cited by: 33
Author(s): Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen, Haixing Jiang
Software Mentions: 9
Published: over 6 years ago

10.3389/fgene.2020.00785

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer
Cited by: 3
Author(s): Zihu Guo, Han Liang, Yingxue Fu, Ziyin Wu, Yaohua Ma, Yueping Liu, Haiqing Wang, Li Jiang, Shengnan Liang, Zhenzhong Wang, Furong Li, Wei Xiao, Jingbo Wang, Yonghua Wang
Software Mentions: 9
Published: about 6 years ago

10.1186/s12935-020-01230-x

A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis
Cited by: 19
Author(s): Yongzhi Wang, Zhonghua Yang
Software Mentions: 9
Published: over 6 years ago

10.1186/s12935-020-1113-6

Construction of a novel gene-based model for prognosis prediction of clear cell renal cell carcinoma
Cited by: 81
Author(s): Zedan Zhang, Enyu Lin, Hongkai Zhuang, Lu Xie, Xiaoqiang Feng, Jiumin Liu, Yuming Yu
Software Mentions: 9
Published: over 6 years ago

10.3390/cancers13061189

Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers
Cited by: 10
Author(s): Siddesh Southekal, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers13040917

Novel Gene Signatures Predictive of Patient Recurrence-Free Survival and Castration Resistance in Prostate Cancer
Cited by: 18
Author(s): Jun Ai, Baotong Zhang, Zhiqian Zhang, Hailiang Hu, Jiangtao Dong
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: almost 8 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: about 19 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: about 5 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 11 years ago

10.1371/journal.pone.0095224

Two-Stage, In Silico Deconvolution of the Lymphocyte Compartment of the Peripheral Whole Blood Transcriptome in the Context of Acute Kidney Allograft Rejection
Cited by: 18
Author(s): Casey P. Shannon, Robert Balshaw, Raymond T. Ng, J. Wilson-McManus, Paul Keown, Robert McMaster, Bruce M. McManus, David Landsberg, Nicole M. Isbel, Greg Knoll, Scott J. Tebbutt
Software Mentions: 9
Published: over 12 years ago

10.3389/fgene.2020.570325

Construction of a Nomogram Based on a Hypoxia-Related lncRNA Signature to Improve the Prediction of Gastric Cancer Prognosis
Cited by: 29
Author(s): Qian Chen, Lang Hu, Kaihua Chen
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: about 15 years ago

10.1038/s42003-021-01945-1

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression
Cited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.203455

Construction of an immune-related lncRNA signature as a novel prognosis biomarker for LUAD
Cited by: 9
Author(s): Hang Chen, Wei Shen, Saiqi Ni, Menglu Sang, Shibo Wu, Yinyu Mu, Kaitai Liu, Ni Li, Linwen Zhu, Guodong Xu
Software Mentions: 9
Published: about 5 years ago

10.3389/fphar.2021.746910

Spermine-Related DNA Hypermethylation and Elevated Expression of Genes for Collagen Formation are Susceptible Factors for Chemotherapy-Induced Hand-Foot Syndrome in Chinese Colorectal Cancer Patients
Cited by: 3
Author(s): Mingming Li, Jiani Chen, Shaoqun Liu, Xiaomeng Sun, Huilin Xu, Qianmin Gao, Xintao Chen, Chaowen Xi, Doudou Huang, Yi Deng, Feng zhang, Shouhong Gao, Shi Qiu, Xin Tao, Jingwen Zhai, Hua Wei, Houshan Yao, Wansheng Chen
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-019-55434-x

QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis
Cited by: 28
Author(s): Susan M. Corley, Niamh M. Troy, Anthony Bosco, Marc R. Wilkins
Software Mentions: 9
Published: over 6 years ago

10.1186/s13148-020-0824-9

Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population
Cited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0209656

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn’s disease patients
Cited by: 14
Author(s): Andrew Y. Li Yim, Jessica R. de Bruyn, Nicolette W. Duijvis, Catriona Sharp, Enrico Ferrero, Wouter J. de Jonge, Manon E. Wildenberg, Marcel M.A.M. Mannens, Christianne J. Buskens, Geert R. D’Haens, Peter Henneman, Anje A. te Velde
Software Mentions: 9
Published: over 7 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data
Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: over 6 years ago

10.3389/fmolb.2020.604252

Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related Genes
Cited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: almost 6 years ago

10.1186/s40425-018-0422-y

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 36
Author(s):
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: almost 12 years ago

10.3389/fgene.2020.576566

Systematic Profiling of Immune Risk Model to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 9
Author(s): Xingyu Liu, Jiarui Chen, Wei Lu, Zhao-Yi Zeng, Jiali Li, Xueping Jiang, Yanping Gao, Yan Gong, Qiuji Wu, Conghua Xie
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12943-020-01170-0

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer
Cited by: 600
Author(s): Bo Zhang, Qiong Wu, Ben Li, Defeng Wang, Lei Wang, You Zhou
Software Mentions: 9
Published: over 6 years ago

10.3389/fgene.2019.00880

LINC00460 Hypomethylation Promotes Metastasis in Colorectal Carcinoma
Cited by: 15
Author(s): Hui Zhang, Ya Lu, Jianzhong Wu, Jifeng Feng
Software Mentions: 9
Published: almost 7 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: over 6 years ago

10.1002/jia2.25148

Oral abstracts of the 22nd International AIDS Conference, 23-27 July 2018, Amsterdam, the Netherlands
Cited by: 9
Author(s):
Software Mentions: 9
Published: about 8 years ago

10.3390/biomedicines9040368

Single-Cell RNA Sequencing in Parkinson’s Disease
Cited by: 13
Author(s): Shi-Xun Ma, Su Bin Lim
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2020.00441

Prognostic Value of a Stemness Index-Associated Signature in Primary Lower-Grade Glioma
Cited by: 28
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Feibao Guo, Jinsheng Hong
Software Mentions: 9
Published: over 6 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: about 8 years ago

10.1155/2021/8864436

Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer
Cited by: 10
Author(s): Xuening Zhang, Xiaoguang Shi, Hao Zhao, Xiaocan Jia, Yongli Yang
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: over 13 years ago

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: almost 6 years ago

10.1172/jci.insight.140443

Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Cited by: 6
Author(s): Maria Llamazares Prada, Elisa Espinet, Vedrana Mijošek, Uwe Schwartz, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja P. Benz, Thomas Muley, Arne Warth, Claus Peter Heusel, Hauke Winter, Jonathan Landry, Felix J.F. Herth, Tinne Mertens, Harry Karmouty‐Quintana, Ina Koch, Vladimı́r Beneš, Jan O. Korbel, Sebastian M. Waszak, Andreas Trumpp, David Wyatt, Heiko Stahl, Christoph Plass, Renata Z. Jurkowska
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.711020

Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model
Cited by: 37
Author(s): Leilei Liang, Jing Yu, Jian Li, Ning Li, Jing Liu, Lin Xiu, Jia Zeng, Tiantian Wang, Lingying Wu
Software Mentions: 9
Published: almost 5 years ago

10.7554/eLife.58178

16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development
Cited by: 24
Author(s): Julien G. Roth, Kristin Muench, Aditya Asokan, Victoria M Mallett, Hongwei Gai, Yogendra Verma, Stephen G. Weber, Carol Charlton, Jonas L. Fowler, Kyle M. Loh, Ricardo E. Dolmetsch, Theo Palmer
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2020.578809

Identification and Verification on Prognostic Index of Lower-Grade Glioma Immune-Related LncRNAs
Cited by: 7
Author(s): Jing Wen, Youjun Wang, Lili Luo, Peng Lu, Caixia Chen, Jian Guo, Yunlong Ge, Wenjun Li, Xin Jin
Software Mentions: 9
Published: almost 6 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 6 years ago

10.1155/2021/6290261

Identification of a Tumor Microenvironment-Related Gene Signature Indicative of Disease Prognosis and Treatment Response in Colon Cancer
Cited by: 24
Author(s): Wenzheng Chen, Jianfeng Huang, Jianbo Xiong, Pengcheng Fu, Changyu Chen, Yi Liu, Zhengrong Li, Zhigang Jie, Yi Cao
Software Mentions: 9
Published: about 5 years ago

10.3389/fonc.2019.01243

Identification of Subtype-Specific Three-Gene Signature for Prognostic Prediction in Diffuse Type Gastric Cancer
Cited by: 12
Author(s): Bowen Bao, Chunlei Zheng, Bowen Yang, Yue Jin, Kezuo Hou, Zhi Li, Xueying Zheng, Shitong Yu, Xiaojie Zhang, Yibo Fan, Xiujuan Qu, Yunpeng Liu, Xiaofang Che
Software Mentions: 8
Published: almost 7 years ago

10.1186/s12950-020-00260-6

Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis
Cited by: 11
Author(s): Pedro A. Ruiz-Castro, Ulrike Kogel, Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, Bjoern Titz, Llenalia Garcia, Athanasios Kondylis, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-019-48746-5

Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Cited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: about 7 years ago

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: almost 6 years ago

10.3389/fgene.2019.00278

Identification of Prognostic Alternative Splicing Signature in Breast Carcinoma
Cited by: 25
Author(s): Dong Zhang, Yi Duan, Jinjing Cun, Qifeng Yang
Software Mentions: 8
Published: over 7 years ago

10.1186/s13148-020-00931-4

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma
Cited by: 7
Author(s): Rachel L. Clifford, Chen Xi Yang, Nick Fishbane, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Sean May, Marcos Castellanos-Uribe, Parameswaran Nair, Ma’en Obeidat, Michæl S. Kobor, Alan J. Knox, Tillie-Louise Hackett
Software Mentions: 8
Published: almost 6 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: over 11 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: about 5 years ago

10.7150/ijms.48244

Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis
Cited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: over 6 years ago

10.1186/s13148-016-0230-5

Peripheral blood methylation profiling of female Crohn’s disease patients
Cited by: 40
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Jing Hua Zhao, Wouter J. de Jonge, Geert R. D’Haens, Marcel M.A.M. Mannens, Adri N. Mul, Anje A. te Velde, Peter Henneman
Software Mentions: 8
Published: over 10 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: about 6 years ago

10.7150/ijms.51064

Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck Cancer
Cited by: 32
Author(s): Aimin Jiang, Mengdi Ren, Na Liu, Huan Gao, Jingjing Wang, Xiaoqiang Zheng, Xiao Fu, Xuan Liu, Zhiping Ruan, Tao Tian, Yu Yao
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 6 years ago

10.3389/fmolb.2021.661661

A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation
Cited by: 2
Author(s): Yicun Wang, Di Zhang, Xiaosong Hu
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0232271

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 6 years ago

10.3389/fnins.2021.613329

Integrated Transcriptional Profiling Analysis and Immune-Related Risk Model Construction for Intracranial Aneurysm Rupture
Cited by: 4
Author(s): Dezhi Shan, Xing Guo, Guozheng Yang, Zheng He, Rongrong Zhao, Hao Xue, Gang Li
Software Mentions: 8
Published: over 5 years ago

10.1016/j.molcel.2019.01.009

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
Cited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: over 7 years ago

10.1136/jitc-2020-000588

Monocyte-derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy
Cited by: 30
Author(s): Sjoerd Schetters, Elizabeth Rodríguez, Laura Kruijssen, Matheus H.W. Crommentuijn, Louis Boon, Jan Van den Bossche, Joke M. M. den Haan, Yvette van Kooyk
Software Mentions: 8
Published: about 6 years ago

10.1111/jcmm.15601

Novel gene signatures for prognosis prediction in ovarian cancer
Cited by: 25
Author(s): Mingyang Bao, Lihua Zhang, Yue‐Qing Hu
Software Mentions: 8
Published: about 6 years ago

10.7150/jca.49266

Establishment of the Prognostic Index Reflecting Tumor Immune Microenvironment of Lung Adenocarcinoma Based on Metabolism-Related Genes
Cited by: 13
Author(s): Jianguo Zhang, Jianzhong Zhang, Cheng Yuan, Yuan Luo, Yangyi Li, Panpan Dai, Wenjie Sun, Nannan Zhang, Jiangbo Ren, Mengjie Zhang, Yan Gong, Conghua Xie
Software Mentions: 8
Published: over 6 years ago

10.3233/JAD-170011

Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data
Cited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: about 9 years ago

10.3389/fendo.2020.561370

Adropin Stimulates Proliferation and Inhibits Adrenocortical Steroidogenesis in the Human Adrenal Carcinoma (HAC15) Cell Line
Cited by: 14
Author(s): Ewelina Stelcer, Paulina Milecka, Hanna Komarowska, Karol Jopek, Marianna Tyczewska, Marta Szyszka, Marta Leśniczak, Wiktoria Suchorska, Karlygash Bekova, Beata Szczepaniak, Marek Ruchała, Marek Karczewski, T Wierzbicki, Witold Szaflarski, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 8
Published: almost 6 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776