Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: affy

https://packages.ecosyste.ms/registries/bioconductor.org/packages/affy

Methods for Affymetrix Oligonucleotide Arrays
1 version
Latest release: 7 months ago
74 dependent packages
1,755,928 downloads total

Papers Mentioning affy 989

10.1186/1471-2105-12-464
From hybridization theory to microarray data analysis: performance evaluation
Cited by: 4
Author(s): Fabrice Berger, Enrico Carlon
Software Mentions: 8
Published: over 12 years ago
10.7717/peerj.7816
CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosis
Cited by: 11
Author(s): Xuefeng Gu, Hongbo Li, Ling Sha, Man Yuan, Chao Shi, Wei Zhao
Software Mentions: 8
Published: over 4 years ago
10.1186/1471-2105-12-467
Empirical comparison of cross-platform normalization methods for gene expression data
Cited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: over 12 years ago
10.7717/peerj.11233
Identification of a ferroptosis-related gene signature (FRGS) for predicting clinical outcome in lung adenocarcinoma
Cited by: 11
Author(s): Sheng Wang, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 8
Published: about 3 years ago
10.3389/fnins.2021.682247
Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer’s Disease
Cited by: 8
Author(s): Hui Li, Rui Wang, Xuqi Guo, Yugang Jiang
Software Mentions: 7
Published: almost 3 years ago
10.1186/1752-0509-6-63
Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease
Cited by: 121
Author(s): Michael C. Oldham, Peter Langfelder, Steve Horvath
Software Mentions: 7
Published: over 12 years ago
10.1186/s12967-016-0906-9
Centrosome associated genes pattern for risk sub-stratification in multiple myeloma
Cited by: 13
Author(s): Fedor Kryukov, Pavel Němec, Lenka Radová, Elena V. Kryukova, Samuel Adeyinka Okubote, Jiří Minařík, Zdena Štefániková, Luděk Pour, Roman Hájek
Software Mentions: 7
Published: almost 8 years ago
10.3390/ijms19102903
Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma
Cited by: 27
Author(s): Philip Dao Trong, Saskia Rösch, Heimo Mairbäurl, Stefan Pusch, Andreas Unterberg, Christel Herold‐Mende, Rolf Warta
Software Mentions: 7
Published: over 5 years ago
10.3389/fmolb.2020.598583
SARS-CoV-2 Proteins Exploit Host’s Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways
Cited by: 29
Author(s): A. A. Khan, Abul B.M.M.K. Islam
Software Mentions: 7
Published: over 3 years ago
10.3389/fimmu.2019.02616
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination
Cited by: 12
Author(s): Lavida R. K. Rogers, Gustavo de los Campos, George I. Mias
Software Mentions: 7
Published: over 4 years ago
10.1002/cam4.343
The transcriptomic profile of ovarian cancer grading
Cited by: 2
Author(s): Cindy Q. Yao, Francis Nguyen, Syed Haider, Maud H.W. Starmans, Philippe Lambin, Paul C. Boutros
Software Mentions: 7
Published: over 9 years ago
10.1186/1471-2164-9-S1-S5
Transcription network construction for large-scale microarray datasets using a high-performance computing approach
Cited by: 14
Author(s): Mengxia Zhu, Qishi Wu
Software Mentions: 7
Published: over 16 years ago
10.7150/thno.52717
m<sup>6</sup>A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer
Cited by: 135
Author(s): Wei Chong, Liang Shang, Jin Liu, Zhen Fang, Fengying Du, Hao Wu, Liu Yang, Zhe Wang, Chen Yang, Shengtao Jia, Liming Chen, Leping Li, Hao Chen
Software Mentions: 7
Published: over 3 years ago
10.1186/1471-2164-11-349
Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Cited by: 70
Author(s): RM Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel‐Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
Software Mentions: 7
Published: almost 14 years ago
10.3389/fgene.2019.00971
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool
Cited by: 15
Author(s): André Nicolau Aquime Gonçalves, Melissa Lever, Pedro Russo, Bruno Gomes-Correia, Alysson H. Urbanski, Gabriele Pollara, Mahdad Noursadeghi, Vinicius Maracaja‐Coutinho, Helder I. Nakaya
Software Mentions: 7
Published: over 4 years ago
10.1038/s41598-019-44491-x
The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: almost 5 years ago
10.1038/s41598-017-05927-4
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity
Cited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: almost 7 years ago
10.3389/fnagi.2021.605970
Immune Profiling of Parkinson’s Disease Revealed Its Association With a Subset of Infiltrating Cells and Signature Genes
Cited by: 12
Author(s): Xi Zhang, Zhihua Shao, Sutong Xu, Qiulu Liu, Chenming Liu, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 7
Published: over 3 years ago
10.12688/f1000research.6030.2
AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
Cited by: 3
Author(s): Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
Software Mentions: 7
Published: over 8 years ago
10.1371/journal.pone.0196836
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: about 6 years ago
10.1111/jcmm.15877
RAD51AP1 promotes progression of ovarian cancer via TGF‐β/Smad signalling pathway
Cited by: 17
Author(s): Hongyu Zhao, Yan Gao, Qi Chen, Jie Li, Meng Ren, Xiaoting Zhao, Wentao Yue
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-017-4167-7
SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles
Cited by: 30
Author(s): David Lopez, Dennis Montoya, Michael Ambrose, Larry Lam, Leah Briscoe, Claire Adams, Robert L. Modlin, Matteo Pellegrini
Software Mentions: 7
Published: over 6 years ago
10.1111/jcmm.16321
Characterization of an endoplasmic reticulum stress‐related signature to evaluate immune features and predict prognosis in glioma
Cited by: 29
Author(s): Qing Zhang, Gefei Guan, Cheng Peng, Wen Cheng, Lianhe Yang, Anhua Wu
Software Mentions: 7
Published: about 3 years ago
10.1016/j.csbj.2021.04.056
A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression
Cited by: 3
Author(s): Sergey Ivanov, Dmitry Filimonov, O. Tarasova
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pone.0097678
Evaluation of Toxicogenomics Approaches for Assessing the Risk of Nongenotoxic Carcinogenicity in Rat Liver
Cited by: 16
Author(s): Johannes Eichner, Clemens Wrzodek, Michael Roemer, Heidrun Ellinger‐Ziegelbauer, Andreas Zell
Software Mentions: 7
Published: about 10 years ago
10.1186/1471-2164-14-445
The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India
Cited by: 20
Author(s): R. Kimberley Cook, James R. Hennell, Samiuela Lee, Cheang Khoo, Maria Carles, Vincent J. Higgins, Suresh Govindaraghavan, Nikolaus J. Sucher
Software Mentions: 7
Published: almost 11 years ago
10.18632/aging.102200
Identification and validation of four hub genes involved in the plaque deterioration of atherosclerosis
Cited by: 12
Author(s): Peipei Chen, Yuexin Chen, Wei Wu, Lianfeng Chen, Xufei Yang, Shuyang Zhang
Software Mentions: 7
Published: over 4 years ago
10.1136/gutjnl-2019-318343
A blood-based prognostic biomarker in IBD
Cited by: 125
Author(s): Daniele Biasci, James C. Lee, Nurulamin M Noor, Diana R Pombal, Monica Hou, Nina Lewis, Tariq Ahmad, Ailsa Hart, Miles Parkes, Eoín McKinney, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 7
Published: about 5 years ago
10.18632/aging.202417
Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis
Cited by: 13
Author(s): Linlin Yang, Yunxia Cui, Xiao Sun, Yudong Wang
Software Mentions: 7
Published: over 3 years ago
10.7150/jca.58076
An integrative microenvironment approach for laryngeal carcinoma: the role of immune/methylation/autophagy signatures on disease clinical prognosis and single-cell genotypes
Cited by: 18
Author(s): Xueran Kang, Yisheng Chen, Bin Yi, Yan Xin, Chenyan Jiang, Bin Chen, Lixing Lu, Yuxing Sun, Ruihan Shi
Software Mentions: 7
Published: over 3 years ago
10.1186/1471-2105-9-46
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Cited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: over 16 years ago
10.1186/s12859-017-1619-7
Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia
Cited by: 4
Author(s): Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 7
Published: about 7 years ago
10.18632/aging.101912
The widespread increase in inter-individual variability of gene expression in the human brain with age
Cited by: 19
Author(s): Veronika R. Kedlian, Handan Melike Dönertaş, Janet M. Thornton
Software Mentions: 7
Published: about 5 years ago
10.3389/fcell.2021.659294
Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy
Cited by: 5
Author(s): Peng Zhou, Yuchao Lu, Xiufen Yang, Jin‐Zhou Xu, Chen‐Qian Liu, Qi‐Dong Xia, Junlin Lu, Shaogang Wang, Jia Hu
Software Mentions: 7
Published: about 3 years ago
10.3390/genes11070802
Convergence of Prognostic Gene Signatures Suggests Underlying Mechanisms of Human Prostate Cancer Progression
Cited by: 6
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Shea P. Connell, Daniel Brewer, Christopher S. Cooper
Software Mentions: 6
Published: almost 4 years ago
10.1186/gb-2005-6-9-r76
Cited by: 122
Author(s): Stephen Henderson, David B. Guiliano, Nadège Presneau, Sean R. McLean, Richard Frow, Sonja Vujovic, John Anderson, Neil J. Sebire, Jeremy Whelan, Nick Athanasou, Adrienne M. Flanagan, Chris Boshoff
Software Mentions: 6
Published: over 19 years ago
10.1186/1471-2105-15-170
Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences
Cited by: 24
Author(s): Natalie S. Fox, Maud H.W. Starmans, Syed Haider, Philippe Lambin, Paul C. Boutros
Software Mentions: 6
Published: almost 10 years ago
10.3389/fphys.2018.01778
Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis
Cited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: over 5 years ago
10.3389/fonc.2020.557638
Tumor-Infiltrating Immune Cell Signature Predicts the Prognosis and Chemosensitivity of Patients With Pancreatic Ductal Adenocarcinoma
Cited by: 21
Author(s): Yinghong Gao, Shipeng Chen, Somayeh Vafaei, Xiaoli Zhong
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0052299
Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity
Cited by: 22
Author(s): Petr Novák, Martha R. Stampfer, José L. Muñoz-Rodríguez, James C. Garbe, Mathias Ehrich, Bernard W. Futscher, Taylor J. Jensen
Software Mentions: 6
Published: over 11 years ago
10.3389/fphar.2016.00142
Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension
Cited by: 22
Author(s): Shota Sasagawa, Yuhei Nishimura, Hirofumi Sawada, Eric Erquan Zhang, Shiko Okabe, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Yoshihide Mitani, Kazuo Maruyama, Toshio Tanaka
Software Mentions: 6
Published: almost 8 years ago
10.1371/journal.pone.0134011
A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: over 9 years ago
10.3389/fonc.2021.630706
The Immune-Related Gene HCST as a Novel Biomarker for the Diagnosis and Prognosis of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yongying Zhou, Xiao Wang, Weibing Zhang, Huiyong Liu, Daoquan Liu, Ping Chen, Dongmei Xu, Jianmin Liu, Yan Li, Guang Zeng, Mingzhou Li, Zhonghua Wu, Yingao Zhang, Xinghuan Wang, Michael E. DiSanto, Xinhua Zhang
Software Mentions: 6
Published: about 3 years ago
10.1186/1743-422X-11-126
Reactive astrogliosis in response to hemorrhagic fever virus: microarray profile of Junin virus-infected human astrocytes
Cited by: 8
Author(s): Olga A. Kolokoltsova, Nadezhda E. Yun, Slobodan Paessler
Software Mentions: 6
Published: almost 10 years ago
10.3389/fonc.2021.665870
Prognostic and Predictive Value of Immune-Related Gene Pair Signature in Primary Lower-Grade Glioma Patients
Cited by: 2
Author(s): Kunjian Lei, Jingying Li, Zewei Tu, Feng Liu, Minhua Ye, Minxian Wu, Yue Zhu, Min Luo, Lin Li, Chuming Tao, Kai Huang, Xingen Zhu
Software Mentions: 6
Published: almost 3 years ago
10.15252/msb.20167435
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
Cited by: 51
Author(s): Seth A. Ament, Jocelynn Pearl, Jeffrey P. Cantle, Robert M. Bragg, Peter J. Skene, Sydney R. Coffey, Dani E Bergey, Vanessa C. Wheeler, Marcy E. MacDonald, Nitin S. Baliga, Jim Rosinski, Leroy Hood, Jeffrey B. Carroll, Nathan D. Price
Software Mentions: 6
Published: about 6 years ago
10.3389/fonc.2021.597536
Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets
Cited by: 7
Author(s): Mehran Piran, Neda Sepahi, Afagh Moattari, A. M. Rahimi, Ali Ghanbariasad
Software Mentions: 6
Published: almost 3 years ago
10.1186/s12859-015-0610-4
Factors affecting the accuracy of a class prediction model in gene expression data
Cited by: 17
Author(s): Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 6
Published: almost 9 years ago
10.1186/s12967-020-02689-y
Three hematologic/immune system-specific expressed genes are considered as the potential biomarkers for the diagnosis of early rheumatoid arthritis through bioinformatics analysis
Cited by: 60
Author(s): Qi Cheng, Xin Chen, Huaxiang Wu, Yan Du
Software Mentions: 6
Published: over 3 years ago
10.3390/jpm9020021
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: about 5 years ago
10.18632/aging.103433
SLC7A2 serves as a potential biomarker and therapeutic target for ovarian cancer
Cited by: 16
Author(s): Tianshui Sun, Fangfang Bi, Zhuonan Liu, Qing Yang
Software Mentions: 6
Published: almost 4 years ago
10.3389/fnins.2019.00392
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease
Cited by: 19
Author(s): Lavida R. K. Brooks, George I. Mias
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pone.0155802
Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis
Cited by: 6
Author(s): Bernard Fongang, Andrzej Kudlicki
Software Mentions: 6
Published: about 8 years ago
10.1371/journal.pone.0012657
A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses
Cited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: over 13 years ago
10.1371/journal.pone.0037714
Dynamic Gene Expression in the Human Cerebral Cortex Distinguishes Children from Adults
Cited by: 32
Author(s): Kirstin N. Sterner, Amy Weckle, Harry T. Chugani, Adi L. Tarca, Chet C. Sherwood, Patrick R. Hof, Christopher W. Kuzawa, Amy M. Boddy, Asad Abbas, Ryan L. Raaum, Lucie Grégoire, Leonard Lipovich, Lawrence I. Grossman, Monica Uddin, Morris Goodman, Derek E. Wildman
Software Mentions: 6
Published: almost 12 years ago
10.7717/peerj.8505
Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pone.0208132
Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus
Cited by: 67
Author(s): Adam C. Labonte, Brian Kegerreis, Nicholas S. Geraci, Prathyusha Bachali, Sushma Madamanchi, Robert Robl, Michelle D. Catalina, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 6
Published: over 5 years ago
10.7554/eLife.11491
Localized JNK signaling regulates organ size during development
Cited by: 37
Author(s): Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A. Jeremy Willsey, Philip A. Beachy, Tian Xu
Software Mentions: 6
Published: about 8 years ago
10.3389/fgene.2021.571231
Identification and Analysis of Potential Key Genes Associated With Hepatocellular Carcinoma Based on Integrated Bioinformatics Methods
Cited by: 21
Author(s): Zhuolin Li, Yao Lin, Bizhen Cheng, Qiaoxin Zhang, Yingmu Cai
Software Mentions: 6
Published: about 3 years ago
10.3389/fgene.2016.00031
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe
Cited by: 17
Author(s): Stefano Berto, Alvaro Perdomo‐Sabogal, Daniel Gerighausen, Jing Qin, Katja Nowick
Software Mentions: 6
Published: about 8 years ago
10.3389/fgene.2021.618277
Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Cited by: 7
Author(s): Mateusz Garbulowski, Karolina Smolińska, Klev Diamanti, Gang Pan, Khurram Maqbool, Lars Feuk, Jan Komorowski
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pone.0019024
Functional Genomics Unique to Week 20 Post Wounding in the Deep Cone/Fat Dome of the Duroc/Yorkshire Porcine Model of Fibroproliferative Scarring
Cited by: 21
Author(s): Loren H. Engrav, Christopher K. Tuggle, Kathleen F. Kerr, Kehao Zhu, Surawej Numhom, Oliver Couture, Richard P. Beyer, Anne M. Hocking, Gretchen J. Carrougher, Maria Luiza Christóvão Ramos, Matthew B. Klein, Nicole S. Gibran
Software Mentions: 6
Published: about 13 years ago
10.1186/s40246-021-00313-8
Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis
Cited by: 3
Author(s): Guodong Zhu, Xun‐Jie Cao, Yaping Li, Jiaxin Li, Zi-Jian Leng, Lisha Xie, Xu‐Guang Guo
Software Mentions: 6
Published: about 3 years ago
10.3389/fcell.2021.561086
Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes
Cited by: 6
Author(s): Elisabeth Findeiss, Sigrid C. Schwarz, Valentin Evsyukov, Thomas W. Rösler, Matthias Höllerhage, Tasnim Chakroun, Niko-Petteri Nykänen, Yimin Shen, Wolfgang Wurst, Michael Köhl, Jörg Tost, Günter U. Höglinger
Software Mentions: 6
Published: about 3 years ago
10.3390/jcm8101524
Rethinking Lupus Nephritis Classification on a Molecular Level
Cited by: 16
Author(s): Salem Almaani, Stephenie D. Prokopec, Jianying Zhang, Lianbo Yu, Carmen Ávila-Casado, Joan E. Wither, James W. Scholey, Valeria Albertón, Ana Malvar, Samir Parikh, Paul C. Boutros, Brad H. Rovin, Heather N. Reich
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-018-19451-6
Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma
Cited by: 20
Author(s): Nina P. Connolly, Amol C. Shetty, Jesse A. Stokum, Ina Hoeschele, Marni B. Siegel, C. Ryan Miller, Anthony J. Kim, Cheng‐Ying Ho, Eduardo Dávila, J. Marc Simard, Scott E. Devine, John H. Rossmeisl, Eric C. Holland, Jeffrey A. Winkles, Graeme F. Woodworth
Software Mentions: 6
Published: over 6 years ago
10.1186/1471-2164-15-1053
Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity
Cited by: 10
Author(s): Ren Sun, Lauren C. Chong, Trent T. Simmons, Kathleen E. Houlahan, Stephenie D. Prokopec, John D. Watson, Ivy D. Moffat, Sanna Lensu, Jere Lindén, Christine P’ng, Allan B. Okey, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 6
Published: over 9 years ago
10.1111/jcmm.14999
A stroma‐related lncRNA panel for predicting recurrence and adjuvant chemotherapy benefit in patients with early‐stage colon cancer
Cited by: 13
Author(s): Rui Zhou, Huiying Sun, Songbai Zheng, Jingwen Zhang, Dongqiang Zeng, Jianhua Wu, Zhenhua Huang, Xiaoxiang Rong, Jianping Bin, Yulin Liao, Min Shi, Wangjun Liao
Software Mentions: 6
Published: over 4 years ago
10.1186/s12864-018-4782-y
Gene expression profiling in the developing secondary palate in the absence of Tbx1 function
Cited by: 2
Author(s): Maria Zoupa, Guilherme M. Xavier, Stephanie Bryan, Ioannis Theologidis, Matthew Arno, Martyn T. Cobourne
Software Mentions: 6
Published: almost 6 years ago
10.1111/jcmm.14938
A risk signature with four autophagy‐related genes for predicting survival of glioblastoma multiforme
Cited by: 47
Author(s): Yulin Wang, Wenjin Zhao, Zhe Xiao, Gefei Guan, Xin Liu, Minghua Zhuang
Software Mentions: 6
Published: over 4 years ago
10.12688/f1000research.25713.2
VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
Cited by: 1
Author(s): Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.102746
Identification of an immune-related risk signature for predicting prognosis in clear cell renal cell carcinoma
Cited by: 34
Author(s): Xiaoliang Hua, Juan Chen, Yang Su, Chaozhao Liang
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-018-33498-5
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer
Cited by: 28
Author(s): Raquel L. Costa, Mariana Boroni, Marcelo A. Soares
Software Mentions: 6
Published: over 5 years ago
10.7150/ijbs.61441
Multi-omics Analysis of Ferroptosis Regulation Patterns and Characterization of Tumor Microenvironment in Patients with Oral Squamous Cell Carcinoma
Cited by: 17
Author(s): Wenchao Gu, Mai Kim, Lei Wang, Zongcheng Yang, Takahito Nakajima, Yoshito Tsushima
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0187091
DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network
Cited by: 43
Author(s): Divya Mistry, Roger P. Wise, Julie A. Dickerson
Software Mentions: 6
Published: over 6 years ago
10.1200/PO.17.00241
Transcriptional Subtyping and CD8 Immunohistochemistry Identifies Patients With Stage II and III Colorectal Cancer With Poor Prognosis Who Benefit From Adjuvant Chemotherapy
Cited by: 40
Author(s): Wendy L. Allen, Philip D. Dunne, Simon S. McDade, Enya Scanlon, Maurice B. Loughrey, Helen Coleman, Christopher McCann, Kristy McLaughlin, Zsuzsanna Németh, Najeeb Syed, Puthen V. Jithesh, Ken Arthur, Richard H. Wilson, Vicky M. Coyle, Darragh G. McArt, Graeme I. Murray, Leslie Samuel, Paolo Nuciforo, José Jimenez, Guillem Argilés, Rodrigo Dienstmann, J. Tabernero, Lucia Picariello, Luca Messerini, Stefania Nobili, Enrico Mini, Kieran Sheahan, Elizabeth J. Ryan, Patrick G. Johnston, Sandra Van Schaeybroeck, Mark Lawler, Daniel B. Longley
Software Mentions: 6
Published: over 5 years ago
10.1186/s13148-018-0463-6
Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia
Cited by: 60
Author(s): Katherine Leavey, Samantha L. Wilson, Shannon Bainbridge, Wendy P. Robinson, Brian Cox
Software Mentions: 6
Published: about 6 years ago
10.1371/journal.pntd.0009633
Identification of potential biomarkers in dengue via integrated bioinformatic analysis
Cited by: 5
Author(s): Lisha Xie, Xin Yin, Jie Bi, Hongyu Luo, Xun‐Jie Cao, Yu-Wen Ma, Ye-Ling Liu, Jianwen Su, Geng-Ling Lin, Xu‐Guang Guo
Software Mentions: 6
Published: almost 3 years ago
10.1186/s12864-015-1840-6
Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin
Cited by: 38
Author(s): Jamie Lee, Stephenie D. Prokopec, John D. Watson, Ren Sun, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 6
Published: over 8 years ago
10.1371/journal.pone.0015581
Therapeutic Implications of GIPC1 Silencing in Cancer
Cited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: over 13 years ago
10.1371/journal.pone.0210467
Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets
Cited by: 0
Author(s): Katerina Taškova, Jean-Fred Fontaine, Ralf Mrowka, Miguel A. Andrade‐Navarro
Software Mentions: 6
Published: over 5 years ago
10.3390/cancers11101610
The Epithelial to Mesenchymal Transition Promotes Glutamine Independence by Suppressing GLS2 Expression
Cited by: 27
Author(s): Esmeralda Ramirez-Peña, James M. Arnold, Vinita Shivakumar, Robiya Joseph, Geraldine V. Vijay, Petra den Hollander, Neeraja Bhangre, Paul Allegakoen, Rishika Prasad, Zachary Conley, José M. Matés, Javier Márquez, Jeffrey T. Chang, Suhas Vasaikar, Rama Soundararajan, Arun Sreekumar, Sendurai A. Mani
Software Mentions: 6
Published: over 4 years ago
10.1186/gm496
A robust prognostic signature for hormone-positive node-negative breast cancer
Cited by: 18
Author(s): Obi L. Griffith, François Pépin, Oana Enache, Laura M. Heiser, Eric A. Collisson, Paul T. Spellman, Joe W. Gray
Software Mentions: 6
Published: over 11 years ago
10.1371/journal.pgen.1004994
Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
Cited by: 147
Author(s): Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts
Software Mentions: 6
Published: over 9 years ago
10.3390/cancers12113380
Cancer-Associated Angiogenesis: The Endothelial Cell as a Checkpoint for Immunological Patrolling
Cited by: 69
Author(s): Antonio Giovanni Solimando, Simona De Summa, Angelo Vacca, Doménico Ribatti
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0107801
A Robust and Accurate Method for Feature Selection and Prioritization from Multi-Class OMICs Data
Cited by: 31
Author(s): Vittorio Fortino, Pia Anneli Sofia Kinaret, Nanna Fyhrquist, Harri Alenius, Dario Greco
Software Mentions: 6
Published: over 9 years ago
10.1371/journal.pcbi.1000193
Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm
Cited by: 236
Author(s): Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao
Software Mentions: 6
Published: over 15 years ago
10.1371/journal.pcbi.1002350
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
Cited by: 66
Author(s): Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jiànróng Lǐ, Tanguy Y. Seiwert, Ezra E.W. Cohen, H. Rosie Xing, Yves A. Lussier
Software Mentions: 6
Published: over 12 years ago
10.7150/ijms.46456
Lipid Metabolism is the common pathologic mechanism between Type 2 Diabetes Mellitus and Parkinson's disease
Cited by: 6
Author(s): Xi Zhang, Yu Fan, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 6
Published: over 4 years ago
10.1534/g3.117.300125
Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen
Cited by: 4
Author(s): Priyanka Surana, Ruo Xu, Greg Fuerst, Antony V. E. Chapman, Dan Nettleton, Roger P. Wise
Software Mentions: 5
Published: over 6 years ago
10.1186/s12885-016-2178-4
Genetic and cellular studies highlight that A Disintegrin and Metalloproteinase 19 is a protective biomarker in human prostate cancer
Cited by: 13
Author(s): Gerard F. Hoyne, Caoline Rudnicka, Qing‐Xiang Amy Sang, Mark D. Roycik, Sarah Howarth, Peter J. Leedman, Markus P. Schlaich, Patrick A. Candy, Vance B. Matthews
Software Mentions: 5
Published: about 8 years ago
10.18632/aging.202635
Transcriptome profiling reveals target in primary myelofibrosis together with structural biology study on novel natural inhibitors regarding JAK2
Cited by: 7
Author(s): Weihang Li, Bin Yuan, Yingjing Zhao, Tianxing Lu, Shilei Zhang, Ziyi Ding, Dong Wang, Sheng Zhong, Guangxun Gao, Ming Yan
Software Mentions: 5
Published: about 3 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: over 17 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: about 11 years ago
10.3389/fonc.2014.00251
Hidden Treasures in “Ancient” Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue
Cited by: 14
Author(s): Konstantinos Kerkentzes, Vincenzo Lagani, Ioannis Tsamardinos, Mogens Vyberg, Oluf Dimitri Røe
Software Mentions: 5
Published: over 9 years ago
10.1152/ajpendo.00473.2013
Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice
Cited by: 289
Author(s): Meritxell Rosell, Myrsini Kaforou, Andrea Frontini, Anthony Okolo, Yi‐Wah Chan, Evanthia Nikolopoulou, Steven Millership, Matthew Fenech, David A. MacIntyre, J. Turner, Jonathan D. Moore, E. K. Blackburn, William J. Gullick, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 5
Published: about 10 years ago
10.1186/s12885-020-07493-x
Identification of ALDH3A2 as a novel prognostic biomarker in gastric adenocarcinoma using integrated bioinformatics analysis
Cited by: 24
Author(s): Zhenhua Yin, Danni Wu, Jianping Shi, Xiao‐Hong Wei, Nuyun Jin, Xiaolan Lu, Xiaohan Ren
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0004481
Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: over 15 years ago
10.1186/1741-7007-7-70
Genetical genomic determinants of alcohol consumption in rats and humans
Cited by: 136
Author(s): Boris Tabakoff, Laura Saba, Morton P. Printz, Pam Flodman, Colin A. Hodgkinson, David Goldman, George F. Koob, H. G. Richardson, Katerina Kechris, Richard L. Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, M Dongier, Katherine M. Conigrave, John B. Whitfield, John B. Saunders, Bridget F. Grant, Paula L. Hoffman
Software Mentions: 5
Published: over 14 years ago
10.1016/j.molp.2020.07.010
The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense
Cited by: 25
Author(s): Roland E. Schwarzenbacher, Grace Wardell, Joost H. M. Stassen, Emily Guest, Peijun Zhang, Estrella Luna, Jurriaan Ton
Software Mentions: 5
Published: over 3 years ago