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: about 1 year ago
74 dependent packages
1,755,928 downloads total

Papers Mentioning affy 989

10.1186/1476-4598-6-13
Integrative analysis of a cancer somatic mutome
Cited by: 23
Author(s): Pilar Hernández, Xavier Solé, Joan Valls, Vı́ctor Moreno, Gabriel Capellá, Ander Urruticoechea, Miguel Ángel Pujana
Software Mentions: 2
Published: almost 18 years ago
10.1186/s13041-019-0436-5
Gene expression meta-analysis of Parkinson’s disease and its relationship with Alzheimer’s disease
Cited by: 43
Author(s): Jack Kelly, Rana Moyeed, Camille Carroll, Diego Albani, Xinzhong Li
Software Mentions: 2
Published: almost 6 years ago
10.3390/microorganisms8040562
Interactions among Redox Regulators and the CtrA Phosphorelay in Dinoroseobacter shibae and Rhodobacter capsulatus
Cited by: 6
Author(s): Sonja Koppenhöfer, Andrew S. Lang
Software Mentions: 2
Published: over 4 years ago
10.1186/s40168-018-0439-y
Microbiome–host systems interactions: protective effects of propionate upon the blood–brain barrier
Cited by: 279
Author(s): Lesley Hoyles, Tom Snelling, Umm-Kulthum Ismail Umlai, Jeremy K. Nicholson, Simon R. Carding, Robert C. Glen, Simon McArthur
Software Mentions: 2
Published: over 6 years ago
10.3389/fneur.2019.00297
Identification of Shared Genes Between Ischemic Stroke and Parkinson's Disease Using Genome-Wide Association Studies
Cited by: 14
Author(s): Wenjing Lang, Junjie Wang, Xiaofeng Ma, Nong Zhang, Li He, Pan Cui, Junwei Hao
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms19124106
Effects of Space Flight on Mouse Liver versus Kidney: Gene Pathway Analyses
Cited by: 17
Author(s): Timothy G. Hammond, Patricia Allen, Holly H. Birdsall
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms20092238
Transcriptomic Pattern of Genes Regulating Protein Response and Status of Mitochondrial Activity Are Related to Oocyte Maturational Competence—A Transcriptomic Study
Cited by: 8
Author(s): Błażej Chermuła, Maciej Brązert, Michal Ješeta, Katarzyna Ożegowska, Ievgeniia Kocherova, Maurycy Jankowski, Piotr Celichowski, Patrycja Sujka‐Kordowska, Aneta Konwerska, Hanna Piotrowska‐Kempisty, Joanna Budna‐Tukan, Paweł Antosik, Dorota Bukowska, Marie Machatková, Klaus‐Peter Brüssow, Mariusz T. Skowroński, Leszek Pawełczyk, M Bruska, Michał Nowicki, Bartosz Kempisty
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms20194891
Curcumin-Gene Expression Response in Hormone Dependent and Independent Metastatic Prostate Cancer Cells
Cited by: 23
Author(s): Shilpa Katta, Arun Srivastava, Rajesh L. Thangapazham, Inger L. Rosner, Jennifer Cullen, Hua Li, Shashwat Sharad
Software Mentions: 2
Published: about 5 years ago
10.3389/fnins.2014.00346
The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes
Cited by: 108
Author(s): Michael K. DeSalvo, Samantha J. Hindle, Zeid M. Rusan, Souvinh Orng, Mark Eddison, Kyle Halliwill, Roland J. Bainton
Software Mentions: 2
Published: about 10 years ago
10.1002/cam4.982
BEX3 contributes to cisplatin chemoresistance in nasopharyngeal carcinoma
Cited by: 16
Author(s): Wei Gao, John Zeng Hong Li, Si-Qi Chen, Ching‐Lung Chu, Jimmy Yu‐Wai Chan, Raymond King–Yin Tsang
Software Mentions: 2
Published: almost 8 years ago
10.3389/fonc.2021.631056
Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm
Cited by: 10
Author(s): Han-Ching Chan, Amrita Chattopadhyay, Eric Y. Chuang, Tzu-Pin Lu
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms21031070
Local and Systemic Humoral Response to Autologous Lineage-Negative Cells Intrathecal Administration in ALS Patients
Cited by: 10
Author(s): Bartłomiej Baumert, Anna Sobuś, Monika Gołąb-Janowska, Zofia Ulańczyk, Edyta Paczkowska, Karolina Łuczkowska, Alicja Zawiślak, Sławomir Milczarek, Bogumiła Osękowska, Agnieszka Meller, Karolina Machowska-Sempruch, Agnieszka Wełnicka, Krzysztof Safranow, Przemysław Nowacki, Bogusław Machaliński
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2105-14-340
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data
Cited by: 89
Author(s): Natalie L. Catlett, Anthony J Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O. Elliston, Dexter Pratt
Software Mentions: 2
Published: about 11 years ago
10.1186/s12935-018-0669-x
Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer
Cited by: 24
Author(s): Defeng Sun, Haoyi Jin, Jun Zhang, Xiaodong Tan
Software Mentions: 2
Published: about 6 years ago
10.1186/s40478-020-00984-9
Molecular identification of CNS NB-FOXR2, CNS EFT-CIC, CNS HGNET-MN1 and CNS HGNET-BCOR pediatric brain tumors using tumor-specific signature genes
Cited by: 26
Author(s): Maria Łastowska, Joanna Trubicka, Anna Sobocińska, Bartosz Wojtaś, Magdalena Niemira, Anna Szałkowska, Adam Krętowski, Agnieszka Karkucińska-Więckowska, Magdalena Kaleta, Maria Ejmont, Marta Perek-Polnik, Bożenna Dembowska–Bagińska, Wiesława Grajkowska, Ewa Matyja
Software Mentions: 2
Published: over 4 years ago
10.1186/s12935-018-0718-5
Analysis of dynamic molecular networks for pancreatic ductal adenocarcinoma progression
Cited by: 23
Author(s): Zongfu Pan, Lü Li, Qilu Fang, Yiwen Zhang, Xiaoping Hu, Yang‐Yang Qian, Ping Huang
Software Mentions: 2
Published: about 6 years ago
10.1186/s12935-020-1134-1
Construction of a circRNA-miRNA-mRNA network based on competitive endogenous RNA reveals the function of circRNAs in osteosarcoma
Cited by: 32
Author(s): Yu Qiu, Pu Chen, Yanchao Li, Baochuang Qi
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12935-018-0640-x
Identification of critical genes to predict recurrence and death in colon cancer: integrating gene expression and bioinformatics analysis
Cited by: 14
Author(s): Xuan Long, Zhigang Deng, Guoqiang Li, Ziwei Wang
Software Mentions: 2
Published: about 6 years ago
10.3389/fonc.2021.624421
Identification of a Six Gene Prognosis Signature for Papillary Thyroid Cancer Using Multi-Omics Methods and Bioinformatics Analysis
Cited by: 13
Author(s): He Ren, Xin Liu, Fuxin Li, Xianghui He, Na Zhao
Software Mentions: 2
Published: over 3 years ago
10.31557/APJCP.2020.21.9.2771
Network-Based Analysis Reveals Association of FOXE1 Gene Polymorphisms in Thyroid Cancer Patients; A Case-Control Study in Southeast of Iran
Cited by: 1
Author(s): Ahmad Mehrazin, Hossein Safarpour, Seyedeh Tahmineh Davoudi, Negin Parsamanesh, Farhad Saeedi, Ebrahim Miri‐Moghaddam
Software Mentions: 2
Published: over 4 years ago
10.1186/bcr3444
BreastMark: An Integrated Approach to Mining Publicly Available Transcriptomic Datasets Relating to Breast Cancer Outcome
Cited by: 121
Author(s): Stephen F. Madden, Colin Clarke, Patricia Gaule, Sinéad Aherne, Norma O’Donovan, Martin Clynes, John Crown, William M. Gallagher
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0097139
The Hepatoselective Glucokinase Activator PF-04991532 Ameliorates Hyperglycemia without Causing Hepatic Steatosis in Diabetic Rats
Cited by: 32
Author(s): Derek M. Erion, Amanda L. Lapworth, Paul A. Amor, Guoyun Bai, Nicholas B. Vera, Ronald W. Clark, Qi Yan, Y. Zhu, Trenton Ross, Julie J. Purkal, Matthew Gorgoglione, Guodong Zhang, Vinícius Bonato, Levenia Baker, Nicole Barucci, Theresa D’Aquila, Alan S. Robertson, Robert J. Aiello, Jiangli Yan, Jeff K. Trimmer, Timothy P. Rolph, Jeffrey A. Pfefferkorn
Software Mentions: 1
Published: over 10 years ago
10.3390/cells7120245
Exploring MicroRNA Biomarkers for Parkinson’s Disease from mRNA Expression Profiles
Cited by: 26
Author(s): Y-h. Taguchi, Hsiuying Wang
Software Mentions: 1
Published: almost 6 years ago
10.1186/1471-2105-11-183
A robust method for estimating gene expression states using Affymetrix microarray probe level data
Cited by: 29
Author(s): Megu Ohtaki, Keiko Otani, Keiko Hiyama, Naosuke Kamei, Kenichi Satoh, Eiso Hiyama
Software Mentions: 1
Published: over 14 years ago
10.1186/gb-2008-9-2-r26
Correction of technical bias in clinical microarray data improves concordance with known biological information
Cited by: 66
Author(s): Aron C. Eklund, Zoltán Szállási
Software Mentions: 1
Published: almost 17 years ago
10.1371/journal.pone.0151329
BET Bromodomain Proteins Brd2, Brd3 and Brd4 Selectively Regulate Metabolic Pathways in the Pancreatic β-Cell
Cited by: 62
Author(s): Jude T. Deeney, Anna C. Belkina, Orian S. Shirihai, Barbara E. Corkey, Gerald V. Denis
Software Mentions: 1
Published: over 8 years ago
10.1038/s41598-018-36671-y
Gene target discovery with network analysis in Toxoplasma gondii
Cited by: 9
Author(s): Andrés M. Alonso, María M. Corvi, Luis Diambra
Software Mentions: 1
Published: almost 6 years ago
10.1155/2017/5306790
Depletion of the Third Complement Component Ameliorates Age-Dependent Oxidative Stress and Positively Modulates Autophagic Activity in Aged Retinas in a Mouse Model
Cited by: 20
Author(s): Dorota Rogińska, Miłosz Kawa, Ewa Pius-Sadowska, Renata Lejkowska, Karolina Łuczkowska, Barbara Wiszniewska, Kai Kaarniranta, Jussi J. Paterno, Christian A. Schmidt, Bogusław Machaliński, Anna Machalińska
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pone.0072977
Integrated Analysis of Global mRNA and Protein Expression Data in HEK293 Cells Overexpressing PRL-1
Cited by: 12
Author(s): Carmen M. Dumaual, Boyd Steere, Chad D. Walls, Mu Wang, Zhong Yin Zhang, Stephen K. Randall
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0000216
Comparison of Protein and mRNA Expression Evolution in Humans and Chimpanzees
Cited by: 71
Author(s): Ning Fu, Ines A. Drinnenberg, Janet Kelso, Jiarui Wu, Svante Pääbo, Rong Zeng, Philipp Khaitovich
Software Mentions: 1
Published: almost 18 years ago
10.1186/1471-2164-10-253
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array
Cited by: 29
Author(s): Tristan E. Coram, Matthew L. Settles, Xianming Chen
Software Mentions: 1
Published: almost 16 years ago
10.1186/1752-0509-7-138
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells
Cited by: 14
Author(s): Yi Zhou, Alexei Vázquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar‐Joseph, Zoltán N. Oltvai
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0063494
An Ensemble Prognostic Model for Colorectal Cancer
Cited by: 13
Author(s): Biqing Li, Tao Huang, Jian Zhang, Ning Zhang, Guohua Huang, Lei Liu, Yu-Dong Cai
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0155408
Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL
Cited by: 18
Author(s): Sarah Stein, Ethan A. Mack, Kelly S. Rome, Kostandin V. Pajcini, Takuya Ohtani, Lanwei Xu, Yunlei Li, Jules P.P. Meijerink, Robert B. Faryabi, Warren S. Pear
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2105-7-23
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR
Cited by: 98
Author(s): Qin Li, Richard P. Beyer, Francesca N. Hudson, Nancy J. Linford, Daryl E. Morris, Kathleen F. Kerr
Software Mentions: 1
Published: almost 19 years ago
10.1186/s12964-017-0210-1
NFAT1-regulated IL6 signalling contributes to aggressive phenotypes of glioma
Cited by: 38
Author(s): Yang Jiang, Sheng Han, Wen Cheng, Zixun Wang, Anhua Wu
Software Mentions: 1
Published: about 7 years ago
10.1007/s00125-017-4460-7
Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes
Cited by: 11
Author(s): Niina Lietzén, Le Thi Thanh An, Maria K. Jaakkola, Henna Kallionpää, Sami Oikarinen, Juha Mykkänen, Mikael Knip, Riitta Veijola, Jorma Ilonen, Jorma Toppari, Heikki Hyöty, Riitta Lahesmaa, Laura L. Elo
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pgen.1000491
Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy
Cited by: 69
Author(s): Utpal P. Davé, Keiko Akagi, Rati Tripathi, Susan M. Cleveland, Mary Ann Thompson, Ming Yi, Robert M. Stephens, James R. Downing, Nancy A. Jenkins, Neal G. Copeland
Software Mentions: 1
Published: over 15 years ago
10.18632/aging.102966
CK1δ as a potential therapeutic target to treat bladder cancer
Cited by: 9
Author(s): Yu Chen Lin, Mei Chuan Chen, Tsung Han Hsieh, Jing Ping Liou, Chun Han Chen
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pgen.1000581
Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana
Cited by: 111
Author(s): Cheng Zou, Melissa D. Lehti-Shiu, Michael F. Thomashow, Shin Han Shiu
Software Mentions: 1
Published: over 15 years ago
10.1186/1752-0509-7-86
Identification of upstream regulators for prognostic expression signature genes in colorectal cancer
Cited by: 11
Author(s): Taejeong Bae, Kyoohyoung Rho, Jin Woo Choi, Katsuhisa Horimoto, Wankyu Kim, Sung Hoon Kim
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0040498
Concerted Perturbation Observed in a Hub Network in Alzheimer’s Disease
Cited by: 69
Author(s): Dapeng Liang, Guangchun Han, Xiao Feng, Jiya Sun, Yong Duan, Hongxing Lei
Software Mentions: 1
Published: over 12 years ago
10.1186/1687-4153-2012-2
Determination of minimal transcriptional signatures of compounds for target prediction
Cited by: 8
Author(s): Florian Nigsch, Janna Hutz, Ben Cornett, Douglas W. Selinger, Gregory McAllister, Somnath Bandyopadhyay, Joseph Loureiro, Jeremy L. Jenkins
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pgen.1002536
The miR-35-41 Family of MicroRNAs Regulates RNAi Sensitivity in Caenorhabditis elegans
Cited by: 37
Author(s): Katlin B. Massirer, Saida G. Perez, Vanessa Mondol, Amy E. Pasquinelli
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2105-11-32
The identification of informative genes from multiple datasets with increasing complexity
Cited by: 6
Author(s): Seyed Yahya Anvar, Peter A C ‘t Hoen, Allan Tucker
Software Mentions: 1
Published: almost 15 years ago
10.1371/journal.pone.0008898
Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation
Cited by: 298
Author(s): Juan Nunez-Iglesias, Chun Chi Liu, Todd E. Morgan, Caleb E. Finch, Xianghong Jasmine Zhou
Software Mentions: 1
Published: almost 15 years ago
10.1186/1471-2105-11-S11-S13
Revealing parasite influence in metabolic pathways in Apicomplexa infected patients
Cited by: 24
Author(s): Tao Xu, Jie Ping, Yao Yu, Fudong Yu, Yongtao Yu, Pei Hao, Xuan Li
Software Mentions: 1
Published: about 14 years ago
10.1038/s41598-019-52729-x
Mechanistic insights into autocrine and paracrine roles of endothelial GABA signaling in the embryonic forebrain
Cited by: 8
Author(s): Yong Kee Choi, Anju Vasudevan
Software Mentions: 1
Published: about 5 years ago
10.1186/s12967-019-1818-2
Bioinformatics-based discovery of the urinary BBOX1 mRNA as a potential biomarker of diabetic kidney disease
Cited by: 10
Author(s): Le-Ting Zhou, Lin‐Li Lv, Shen Qiu, Qian Yin, Zuo‐Lin Li, Tao-Tao Tang, Lei Ni, Yan Feng, Bin Wang, Kun-Ling Ma, Bi‐Cheng Liu
Software Mentions: 1
Published: almost 6 years ago
10.7150/ijms.35693
Transcriptome Profile of Human Fibroblasts in an <i>Ex Vivo</i> Culture
Cited by: 4
Author(s): Bogusław Machaliński, Dorota Rogińska, Kamila Szumilas, Alicja Zawiślak, Aleksandra Wilk, Iwona Stecewicz, Andrzej Brodkiewicz, Barbara Wiszniewska
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pgen.0020171
Functionality of Intergenic Transcription: An Evolutionary Comparison
Cited by: 76
Author(s): Philipp Khaitovich, Janet Kelso, Henriette Franz, Johann Visagie, Thomas Giger, Sabrina Joerchel, Ekkehard Petzold, Edward Green, Michael Lachmann, Svante Pääbo
Software Mentions: 1
Published: about 18 years ago
10.1186/s12967-020-02311-1
An integrated prognosis model of pharmacogenomic gene signature and clinical information for diffuse large B-cell lymphoma patients following CHOP-like chemotherapy
Cited by: 9
Author(s): Jinglei Hu, Jing Xu, Muqiao Yu, Yongchao Gao, Rong Liu, Hong‐Hao Zhou, Wei Zhang
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-57506-9
Extracellular NAD+ enhances PARP-dependent DNA repair capacity independently of CD73 activity
Cited by: 52
Author(s): Anna Wilk, Faisal Hayat, Richard P. Cunningham, Jianfeng Li, Silvia Garavaglia, Leila Zamani, Davide M. Ferraris, Peter Sýkora, Joel Andrews, Jennifer Clark, Amanda L. Davis, Laurent Chaloin, Menico Rizzi, Marie E. Migaud, Robert W. Sobol
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41598-020-59671-3
Homologous recombination deficiency status-based classification of high-grade serous ovarian carcinoma
Cited by: 120
Author(s): Hisamitsu Takaya, Hidekatsu Nakai, Shiro Takamatsu, Masaki Mandai, Noriomi Matsumura
Software Mentions: 1
Published: almost 5 years ago
10.1186/1471-2229-10-85
Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip(R) Soybean Genome Array: optimizing analysis by masking biased probes
Cited by: 17
Author(s): Shanshan Yang, Oswaldo Valdés‐López, Wayne Xu, Bruna Bucciarelli, John W. Gronwald, Georgina Hernández, Carroll P. Vance
Software Mentions: 1
Published: almost 15 years ago
10.3389/fnagi.2018.00178
Integrated Analysis and Identification of Novel Biomarkers in Parkinson’s Disease
Cited by: 33
Author(s): Jieshan Chi, Qizhi Xie, Jingjing Jia, Xiaoma Liu, Jingjing Sun, Yuanfei Deng, Yang Li
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pgen.1000781
Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification
Cited by: 38
Author(s): Kousuke Hanada, Takashi Kuromori, Fumiyoshi Myouga, Tetsuro Toyoda, Kazuo Shinozaki
Software Mentions: 1
Published: almost 15 years ago
10.1186/s12967-014-0319-6
Combined microRNA and ER expression: a new classifier for familial and sporadic breast cancer patients
Cited by: 9
Author(s): Katia Danza, Simona De Summa, Brunella Pilato, Massimo Carella, Orazio Palumbo, Ondina Popescu, Angelo Paradiso, Rosamaria Pinto, Stefania Tommasi
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0051259
GTSE1 Is a Microtubule Plus-End Tracking Protein That Regulates EB1-Dependent Cell Migration
Cited by: 50
Author(s): Massimilano Scolz, Per O. Widlund, Silvano Piazza, Débora Rosa Bublik, Simone Reber, Leticia Y. Peche, Yari Ciani, Nina C. Hubner, Mayumi Isokane, Martín Monte, Jan Ellenberg, Anthony A. Hyman, Claudio Schneider, Alexander W. Bird
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2229-8-21
Transcriptional profiling of Medicago truncatulameristematic root cells
Cited by: 41
Author(s): Peta Holmes, Nicolas Goffard, Georg F. Weiller, Barry G. Rolfe, Nijat Imin
Software Mentions: 1
Published: almost 17 years ago
10.3389/fbioe.2020.00256
Identification and Validation of Novel Long Non-coding RNA Biomarkers for Early Diagnosis of Oral Squamous Cell Carcinoma
Cited by: 19
Author(s): Yue Li, Xiaofang Cao, Hao Li
Software Mentions: 1
Published: over 4 years ago
10.3389/fcell.2021.685120
Analysis of Ferroptosis-Mediated Modification Patterns and Tumor Immune Microenvironment Characterization in Uveal Melanoma
Cited by: 15
Author(s): Y. Jin, Zhanwang Wang, Dong He, Yuxing Zhu, Lian Gong, Mengqing Xiao, Xingyu Chen, Ke Cao
Software Mentions: 1
Published: over 3 years ago
10.1186/s13073-018-0564-z
Integrative omics analyses broaden treatment targets in human cancer
Cited by: 14
Author(s): Sohini Sengupta, Sam Q. Sun, Kuan‐lin Huang, Clara Oh, Matthew H. Bailey, Rajees Varghese, Matthew A. Wyczalkowski, Jie Ning, Piyush Tripathi, Joshua F. McMichael, Kimberly Johnson, Cyriac Kandoth, John S. Welch, Cynthia Ma, Michael C. Wendl, Samuel H. Payne, David Fenyö, R. Reid Townsend, John F. DiPersio, Feng Chen, Ding Li
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0123194
Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients
Cited by: 8
Author(s): Valeria Musella, Maurizio Callari, Eleonora Di Buduo, Manuela Scuro, Matteo Dugo, Patrizia Miodini, Giampaolo Bianchini, Biagio Paolini, Luca Gianni, Maria Grazia Daidone, Vera Cappelletti
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2229-10-224
Transcriptome changes in grapevine (Vitis viniferaL.) cv. Malbec leaves induced by ultraviolet-B radiation
Cited by: 120
Author(s): Mariela Pontín, Patricia Píccoli, Rita Francisco, Rubén Bottini, J. M. Martínez-Zapater, Diego Lijavetzky
Software Mentions: 1
Published: about 14 years ago
10.1371/journal.pcbi.1003914
Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators
Cited by: 12
Author(s): Ryan Tasseff, Anjali Bheda-Malge, Teresa DiColandrea, Charles C. Bascom, Robert J. Isfort, Richard Gelinas
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0173847
Screening for interaction effects in gene expression data
Cited by: 5
Author(s): Peter J. Castaldi, Michael H. Cho, Liming Liang, Edwin K. Silverman, Craig P. Hersh, Kenneth Rice, Hugues Aschard
Software Mentions: 1
Published: over 7 years ago
10.4172/2476-1966.1000135
Transcriptional and Functional Plasticity Induced by Chronic Insulin Exposure in a Mast Cell-Like Basophilic Leukemia Cell Model
Cited by: 3
Author(s): Chad Jansen, Mark Speck, William E. Greineisen, Kristina Maaetoft-Udsen, Edward A. Cordasco, Lori M. N. Shimoda, Alexander J. Stokes, Helen Turner
Software Mentions: 1
Published: almost 8 years ago
10.3389/fcell.2020.586869
Knockdown of lncRNA MALAT1 Alleviates LPS-Induced Acute Lung Injury via Inhibiting Apoptosis Through the miR-194-5p/FOXP2 Axis
Cited by: 37
Author(s): Chuanchuan Nan, Ning Zhang, Katherine Cheung, Huadong Zhang, Wei Li, Chengying Hong, Huai-sheng Chen, Xueyan Liu, Nan Li, Lixin Cheng
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pcbi.1004744
MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression
Cited by: 57
Author(s): Steven W. Paugh, David R. Coss, Jie Bao, Lucas Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael R. Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik Bonten, William E. Evans
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pbio.1001448
Siglec-1 Is a Novel Dendritic Cell Receptor That Mediates HIV-1 Trans-Infection Through Recognition of Viral Membrane Gangliosides
Cited by: 200
Author(s): Nuria Izquierdo-Useros, Maier Lorizate, María C. Puertas, Maria T. Rodriguez-Plata, Nadine Zangger, Elina Erikson, María Pino, Itziar Erkizia, Bärbel Glass, Bonaventura Clotet, Oliver T. Keppler, Amalio Telenti, Hans‐Georg Kräusslich, Javier Martínez-Picado
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pbio.0040260
Gene Expression Analysis of Zebrafish Heart Regeneration
Cited by: 252
Author(s): Ching‐Ling Lien, Michael Schebesta, Shinji Makino, Gerhard Weber, Mark T. Keating
Software Mentions: 1
Published: over 18 years ago
10.3389/fendo.2017.00026
Transcriptome Profile of Rat Adrenal Evoked by Gonadectomy and Testosterone or Estradiol Replacement
Cited by: 30
Author(s): Karol Jopek, Piotr Celichowski, Marta Szyszka, Marianna Tyczewska, Paulina Milecka, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2164-10-474
The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines
Cited by: 29
Author(s): Paolo Fardin, Annalisa Barla, Sofia Mosci, Lorenzo Rosasco, Alessandro Verri, Luigi Varesio
Software Mentions: 1
Published: almost 16 years ago
10.1371/journal.pone.0006082
Early Cell Fate Decisions of Human Embryonic Stem Cells and Mouse Epiblast Stem Cells Are Controlled by the Same Signalling Pathways
Cited by: 244
Author(s): Ludovic Vallier, Thomas Touboul, Zhenzhi Chng, Minodora Brimpari, Nicholas R.F. Hannan, Enrique Millan, Lucy Smithers, Matthew Trotter, Peter J. Rugg‐Gunn, Anne Weber, Roger A. Pedersen
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pbio.2006443
The lysolipid transporter Mfsd2a regulates lipogenesis in the developing brain
Cited by: 69
Author(s): Jia Pei Chan, Bernice H. Wong, Cheen Fei Chin, Dwight L.A. Galam, Juat Chin Foo, Loo Chin Wong, Sujoy Ghosh, Markus R. Wenk, Amaury Cazenave-Gassiot, David L. Silver
Software Mentions: 1
Published: over 6 years ago
10.1186/s12891-015-0588-0
Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures
Cited by: 20
Author(s): Kayleigh Wong, Fangui Sun, Guy Trudel, Paola Sebastiani, Odette Laneuville
Software Mentions: 1
Published: over 9 years ago
10.1038/s41598-020-77774-9
Detection of urinary miRNAs for diagnosis of clear cell renal cell carcinoma
Cited by: 32
Author(s): Giovanni Cochetti, Luigi Cari, Giuseppe Nocentini, Vincenza Maulà, Chiara Suvieri, Rosy Cagnani, J.A. Rossi De Vermandois, Ettore Mearini
Software Mentions: 1
Published: almost 4 years ago
10.3389/fgene.2019.00803
Comprehensive Analysis of Therapy-Related Messenger RNAs and Long Noncoding RNAs as Novel Biomarkers for Advanced Colorectal Cancer
Cited by: 7
Author(s): Jibin Li, Shenglin Ma, Tao Lin, Yanxi Li, Shun Tai Yang, Wanchuan Zhang, Rui Zhang, Yongpeng Wang
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pone.0019895
Skin Barrier Homeostasis in Atopic Dermatitis: Feedback Regulation of Kallikrein Activity
Cited by: 29
Author(s): Reiko Tanaka, M. Ono, Heather A. Harrington
Software Mentions: 1
Published: over 13 years ago
10.1172/jci.insight.90723
The impact of environmental enrichment on the murine inflammatory immune response
Cited by: 31
Author(s): Samuel Brod, Thomas Gobbetti, Beatrice Gittens, M. Ono, Mauro Perretti, Fulvio D’Acquisto
Software Mentions: 1
Published: over 7 years ago
10.1186/s12920-019-0507-6
Comprehensive analysis of key genes and microRNAs in radioresistant nasopharyngeal carcinoma
Cited by: 12
Author(s): Ya Guo, Yang Zhang, Shu Juan Zhang, Nan Yang, Yun He
Software Mentions: 1
Published: over 5 years ago
10.1186/s12920-019-0514-7
GENT2: an updated gene expression database for normal and tumor tissues
Cited by: 220
Author(s): Seung Jin Park, Byoung-Ha Yoon, Seon‐Kyu Kim, Seon‐Young Kim
Software Mentions: 1
Published: over 5 years ago
10.1186/s12969-015-0047-3
Gene-expression analysis of adult-onset Still’s disease and systemic juvenile idiopathic arthritis is consistent with a continuum of a single disease entity
Cited by: 87
Author(s): Nanguneri Nirmala, Arndt Brachat, Eugen Feist, Norbert Blank, Christof Specker, Matthias Witt, Jan Zernicke, Alberto Martini, G. Junge
Software Mentions: 1
Published: about 9 years ago
10.1016/j.jaut.2015.12.004
Sonic Hedgehog regulates thymic epithelial cell differentiation
Cited by: 29
Author(s): José Ignacio Saldaña, Anisha Solanki, Ching‐In Lau, Hemant Sahni, Scott R. Ross, Anna L. Furmanski, M. Ono, Georg A. Holländer, Tessa Crompton
Software Mentions: 1
Published: over 8 years ago
10.1074/jbc.RA119.009699
A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria
Cited by: 6
Author(s): Helen L. Scott, Nicola Buckner, Francesc Fernández-Albert, Elisa Pedone, Lorena Postiglione, Gongyu Shi, Nicholas Denby Allen, Liang‐Fong Wong, Lorenzo Magini, Lucia Marucci, Gregory A. O’Sullivan, Sarah Cole, Justin Powell, Peter R. Maycox, James B. Uney
Software Mentions: 1
Published: almost 5 years ago
10.7150/jca.35901
Clinical Implications of Tumor-Infiltrating Immune Cells in Breast Cancer
Cited by: 92
Author(s): Shichao Zhang, Ziyi Hu, Ju Long, Guiming Zhu, Yun Wang, Yi Jia, Jing Zhou, Yu Ouyang, Zhu Zeng
Software Mentions: 1
Published: almost 6 years ago
10.7150/jca.31636
TBX2 Identified as a Potential Predictor of Bone Metastasis in Lung Adenocarcinoma via Integrated Bioinformatics Analyses and Verification of Functional Assay
Cited by: 7
Author(s): Huajian Yu, Fangyu Zhao, Jing Li, Kechao Zhu, Hechun Lin, Zheng Pan, Ming Zhu, Ming Yao, Mingxia Yan
Software Mentions: 1
Published: almost 5 years ago
10.1186/1755-8794-4-65
MicroRNA-34a modulates genes involved in cellular motility and oxidative phosphorylation in neural precursors derived from human umbilical cord mesenchymal stem cells
Cited by: 61
Author(s): Shing‐Jyh Chang, Shun-Long Weng, Jui-Yu Hsieh, Tao‐Yeuan Wang, Margaret Dah‐Tsyr Chang, Hsei‐Wei Wang
Software Mentions: 1
Published: about 13 years ago
10.1186/1755-8794-6-18
Cidofovir selectivity is based on the different response of normal and cancer cells to DNA damage
Cited by: 17
Author(s): Tim De Schutter, Gracíela Andrei, Dimitrios Topalis, Lieve Naesens, Robert Snoeck
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0001854
Using Ribosomal Protein Genes as Reference: A Tale of Caution
Cited by: 179
Author(s): Lieven Thorrez, Katrijn Van Deun, Léon-Charles Tranchevent, Leentje Van Lommel, Kristof Engelen, Kathleen Marchal, Yves Moreau, Iven Van Mechelen, Frans Schuit
Software Mentions: 1
Published: over 16 years ago
10.3390/ijms17111808
PPIC, EMP3 and CHI3L1 Are Novel Prognostic Markers for High Grade Glioma
Cited by: 32
Author(s): Yuanfeng Gao, Tao Zhu, Chen-Xue Mao, Zhixiong Liu, Zhibin Wang, Xiao‐Yuan Mao, Ling Li, Ji‐Ye Yin, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 1
Published: about 8 years ago
10.1186/s12881-020-00994-3
Identification of novel biomarkers in ischemic stroke: a genome-wide integrated analysis
Cited by: 17
Author(s): Qizhi Xie, Xiaoyun Zhang, Sai Peng, Jingjing Sun, Xiao Chen, Yuanfei Deng, Yang Li
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-213X-10-98
Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar
Cited by: 77
Author(s): Manoj Kumar Gupta, Damir J. Illich, Andrea Gaarz, Matthias Matzkies, Filomain Nguemo, Kurt Pfannkuche, Huamin Liang, Sabine Claßen, Michael Reppel, Joachim L. Schultze, Jürgen Hescheler, Tomo Šarić
Software Mentions: 1
Published: about 14 years ago
10.7150/jca.49702
Identification of novel biomarkers and candidate small-molecule drugs in cutaneous melanoma by comprehensive gene microarrays analysis
Cited by: 5
Author(s): Jilei Ma, Xin Cai, Kang Li, Songfeng Chen, Hongjian Liu
Software Mentions: 1
Published: almost 4 years ago
10.1186/1471-213X-7-60
A set of stage-specific gene transcripts identified in EK stage X and HH stage 3 chick embryos
Cited by: 20
Author(s): Bo Ram Lee, Heebal Kim, Tae Sub Park, Seok-Jae Moon, Seoae Cho, Taesung Park, Jeong Mook Lim, Jae Yong Han
Software Mentions: 1
Published: over 17 years ago
10.18632/oncotarget.22132
Regulatory role of NKG2D+ NK cells in intestinal lamina propria by secreting double-edged Th1 cytokines in ulcerative colitis
Cited by: 6
Author(s): Fan Wang, Pailan Peng, Xue Lin, Ying Chang, Jing Liu, Rui Zhou, Jiayan Nie, Weiguo Dong, Qiu Zhao, Jin Li
Software Mentions: 1
Published: about 7 years ago
10.1016/j.molcel.2013.12.020
Nitric Oxide Sensing in Plants Is Mediated by Proteolytic Control of Group VII ERF Transcription Factors
Cited by: 296
Author(s): Daniel J. Gibbs, Nurulhikma Md Isa, Mahsa Movahedi, Jorge Lozano‐Juste, Guillermina M. Mendiondo, Sophie Berckhan, Nora Marín-de la Rosa, Jorge Vicente, Cristina Sousa Correia, Simon P. Pearce, George W. Bassel, Bulut Hamali, Prabhavathi Talloji, Daniel F. A. Tomé, Alberto Coego, Jim Beynon, David Alabadı́, Andreas Bachmair, José León, Julie E. Gray, F. L. Theodoulou, Michael J. Holdsworth
Software Mentions: 1
Published: almost 11 years ago
10.1186/s12906-021-03257-7
Deciphering potential pharmacological mechanism of Sha-Shen-Mai-Dong decoction on primary Sjogren’s syndrome
Cited by: 2
Author(s): Yuepeng Jiang, Xiaoyan Zhao, Jie Yu, Qiao Wang, Chengping Wen, Lin Huang
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12943-015-0485-z
BALR-6 regulates cell growth and cell survival in B-lymphoblastic leukemia
Cited by: 28
Author(s): Norma I. Rodríguez-Malavé, Thilini R. Fernando, Parth Patel, Jorge R. Contreras, Jayanth Kumar Palanichamy, Tiffany Tran, Jaime Anguiano, Michael Davoren, Michael O. Alberti, KimAnh Trang Pioli, Salemiz Sandoval, Gay M. Crooks, Dinesh S. Rao
Software Mentions: 1
Published: about 9 years ago