bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7717/peerj.11687

Construction and validation of a 15-gene ferroptosis signature in lung adenocarcinoma
Cited by: 5
Author(s): Guangxu Tu, Weilin Peng, Qidong Cai, Zhenyu Zhao, Ping Xiong, Boxue He, Pengfei Zhang, Shuai Shi, Yongguang Tao, Xiang Wang
Software Mentions: 9
Published: about 4 years ago

10.18632/aging.104064

Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors
Cited by: 29
Author(s): Kai Li, Hui Luo, Hui Luo, Xiao Zhu
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0084227

Automatic Context-Specific Subnetwork Discovery from Large Interaction Networks
Cited by: 10
Author(s): Ashis Saha, Aik Choon Tan, Jaewoo Kang
Software Mentions: 9
Published: over 11 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: about 13 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 6 years ago

10.3389/fcell.2021.654504

Role of CXCR4 as a Prognostic Biomarker Associated With the Tumor Immune Microenvironment in Gastric Cancer
Cited by: 5
Author(s): Yuyang Gu, Wenyue Gu, Rongrong Xie, Zhi Chen, Tongpeng Xu, Zhenghua Fei
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-016-1321-1

GEN3VA: aggregation and analysis of gene expression signatures from related studies
Cited by: 17
Author(s): Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter M.U. Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma’ayan
Software Mentions: 9
Published: over 8 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 5 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 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: about 4 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 4 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 7 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: almost 12 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 4 years ago

10.12688/f1000research.27868.3

WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
Cited by: 5
Author(s): Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Software Mentions: 9
Published: about 4 years ago

10.18632/aging.102847

Risk score based on expression of five novel genes predicts survival in soft tissue sarcoma
Cited by: 21
Author(s): Hao Gu, Zhang Chao, Jia Guo, Min Yang, Hongshan Zhong, Wei Jin, Yang Liu, Liping Gao, Renxiong Wei
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-020-3463-4

ORdensity: user-friendly R package to identify differentially expressed genes
Cited by: 0
Author(s): José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 9
Published: over 5 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 4 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: almost 8 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 9 years ago

10.18632/aging.203390

Comprehensive analysis of new prognostic signature based on ferroptosis-related genes in clear cell renal cell carcinoma
Cited by: 8
Author(s): Bin Zheng, Zhihong Niu, Shubin Si, Guiting Zhao, Jianwei Wang, Zhongshun Yao, Fajuan Cheng
Software Mentions: 9
Published: almost 4 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 5 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 4 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 14 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 6 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 4 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 4 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 6 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 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: over 10 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 4 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 4 years ago

10.12688/f1000research.2-264.v1

illuminaio: An open source IDAT parsing tool for Illumina microarrays
Cited by: 59
Author(s): Mike L. Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Software Mentions: 9
Published: over 11 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: over 7 years ago

10.1042/BSR20202898

Comprehensive analysis reveals a prognostic and therapeutic biomarker CD3D in the breast carcinoma microenvironment
Cited by: 13
Author(s): Zhipeng Zhu, Weipeng Ye, Xiaofang Wu, Sihao Lin, Jiuhua Xu, Lulu Li, Jiayi Li, Haibin Wang, Zhengjie Huang
Software Mentions: 9
Published: over 4 years ago

10.12688/f1000research.7563.2

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Cited by: 795
Author(s): Charlotte Soneson, Michael I. Love, Mark D. Robinson
Software Mentions: 9
Published: over 9 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: almost 4 years ago

10.1186/s12918-016-0349-1

DGCA: A comprehensive R package for Differential Gene Correlation Analysis
Cited by: 156
Author(s): Andrew McKenzie, Igor Katsyv, Won Min Song, Minghui Wang, Bin Zhang
Software Mentions: 9
Published: over 8 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 5 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: over 4 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 4 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 4 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 4 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 4 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 4 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 4 years ago

10.3389/fimmu.2019.02796

Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries
Cited by: 8
Author(s): Anastas Pashov, Velizar Shivarov, Maya Dimitrov Hadzhieva, V. Kostov, Dilyan Ferdinandov, Karen‐Marie Heintz, Shina Pashova, Milena Todorova, Tchavdar Vassilev, Thomas Kieber‐Emmons, Leonardo A. Meza‐Zepeda, Eivind Hovig
Software Mentions: 9
Published: over 5 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 5 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 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 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 5 years ago

10.1186/s13059-020-1935-5

Opportunities and challenges in long-read sequencing data analysis
Cited by: 1,295
Author(s): Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
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 11 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 5 years ago

10.1186/s13073-020-00786-7

A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Cited by: 11
Author(s): Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo, Teresa Manzo, Luigi Nezi, Ugo Cavallaro, Davide Cacchiarelli, Jörn Walter, Giuseppe Testa
Software Mentions: 9
Published: over 4 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 11 years ago

10.3389/fphar.2021.621359

Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: over 4 years ago

10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: about 4 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: almost 7 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: almost 4 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 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: about 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: about 5 years ago

10.1186/s13059-021-02286-2

Giotto: a toolbox for integrative analysis and visualization of spatial expression data
Cited by: 290
Author(s): Ruben Dries, Qi Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao, Rani E. George, Nico Pierson, Long Cai, Guo‐Cheng Yuan
Software Mentions: 9
Published: over 4 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 4 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: about 5 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: over 4 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: over 4 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: about 5 years ago

10.15252/msb.20209620

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
Cited by: 166
Author(s): Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef
Software Mentions: 9
Published: over 4 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 5 years ago

10.1186/s12864-018-5092-0

High-throughput proteomic profiling of the fish liver following bacterial infection
Cited by: 58
Author(s): Dwight R. Causey, Moritz A N Pohl, David Stead, Samuel Martín, Christopher J. Secombes, Daniel J. Macqueen
Software Mentions: 9
Published: almost 7 years ago

10.1186/s41065-021-00196-8

Dynamic co-expression modular network analysis in nonalcoholic fatty liver disease
Cited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: almost 4 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: almost 6 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: about 4 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: over 6 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 4 years ago

10.3389/fgene.2021.627508

Integrated Analysis of the Prognosis-Associated RNA-Binding Protein Genes and Candidate Drugs in Renal Papillary Cell Carcinoma
Cited by: 22
Author(s): Shuiping Jiang, Xiaohan Ren, Shouyong Liu, Zhongwen Lü, Aiming Xu, Chao Qin, Zengjun Wang
Software Mentions: 8
Published: over 4 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: almost 5 years ago

10.1002/cam4.2665

Genome‐wide screening of abberant methylated drivers combined with relative risk loci in bladder cancer
Cited by: 2
Author(s): Chuanjie Zhang, Kangjie Shen, Yuxiao Zheng, Feng Qi, Jun Luo
Software Mentions: 8
Published: over 5 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: almost 4 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 4 years ago

10.1242/dmm.040444

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Cited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 6 years ago

10.3390/cancers13051113

MPscore: A Novel Predictive and Prognostic Scoring for Progressive Meningioma
Cited by: 12
Author(s): Feili Liu, Jin Qian, Chenkai Ma
Software Mentions: 8
Published: over 4 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 5 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: almost 8 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 6 years ago

10.1016/j.cell.2019.08.003

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Cited by: 170
Author(s): Rosina Pryor, Povilas Norvaišas, Γεώργιος Μαρίνος, Lena Best, Louise B. Thingholm, Leonor M. Quintaneiro, Wouter De Haes, Daniela Esser, Silvio Waschina, Celia Lujan, Reuben L. Smith, Timothy A. Scott, Daniel Martínez-Martínez, Orla Woodward, Kevin Bryson, Matthias Laudes, Wolfgang Lieb, Riekelt H. Houtkooper, André Franke, Liesbet Temmerman, Ivana Bjedov, Helena M. Cochemé, Christoph Kaleta, Filipe Cabreiro
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-020-75541-4

Stromal microenvironment promoted infiltration in esophageal adenocarcinoma and squamous cell carcinoma: a multi-cohort gene-based analysis
Cited by: 6
Author(s): Jiali Li, Zhao-Yi Zeng, Xueping Jiang, Nannan Zhang, Yanping Gao, Yuan Luo, Wenjie Sun, Shuying Li, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-020-70596-9

Identification of potential diagnostic gene biomarkers in patients with osteoarthritis
Cited by: 13
Author(s): Xinling Wang, Yu Yang, Yong Huang, Zhu Ming-shuang, Rigao Chen, Zhanghui Liao, Shipeng Yang
Software Mentions: 8
Published: almost 5 years ago

10.1002/cam4.2493

Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidates
Cited by: 12
Author(s): Marco Antônio De Bastiani, Fábio Klamt
Software Mentions: 8
Published: almost 6 years ago

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: almost 4 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 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 10 years ago

10.1371/journal.pgen.1009744

The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila
Cited by: 25
Author(s): A. Lukacs, Andreas W. Thomae, P. Krueger, Tamás Schauer, Anuroop Venkateswaran Venkatasubramani, Natalia Y. Kochanova, Wasim Aftab, Rupam Choudhury, Ignasi Forné, Axel Imhof
Software Mentions: 8
Published: almost 4 years ago

10.3390/cancers13071561

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma
Cited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 4 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: over 4 years ago

10.3390/cancers13143621

HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements
Cited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: about 4 years ago

10.1186/s13059-019-1855-4

Common DNA sequence variation influences 3-dimensional conformation of the human genome
Cited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: over 5 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776