Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R.·2002·Nucleic Acids Research

DOI 10.1093/nar/30.1.207

Cited by (1,109)

Items 901–1,000 of 1,109

Identifying dysregulated pathways in cancers from pathway interaction networks
Ke-Qin Liu, Zhi-Ping Liu, Jin‐Kao Hao, Luonan Chen, Xing‐Ming Zhao · 2012 · BMC Bioinformatics
A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation
David Miguel Padua, Swapna Mahurkar‐Joshi, Ivy Ka Man Law, Christos Polytarchou, John P. Vu, Joseph R. Pisegna, David Shih, Dimitrios Iliopoulos, Charalabos Pothoulakis · 2016 · American Journal of Physiology-Gastrointestinal and Liver Physiology
Pharmacological inhibition of CSF1R by GW2580 reduces microglial proliferation and is protective against neuroinflammation and dopaminergic neurodegeneration
Neal, Matthew L., Fleming, Sheila M., Budge, Kevin M., Boyle, Alexa M., Kim, Chunki, Alam, Gelareh, Beier, Eric E., Wu, Long‐Jun, Richardson, Jason R. · 2020 · The FASEB Journal
DNA microarray technology for the microbiologist: an overview
Armin Ehrenreich · 2006 · Applied Microbiology and Biotechnology
Two New Clock Proteins, LWD1 and LWD2, Regulate Arabidopsis Photoperiodic Flowering
Jing-Fen Wu, Ying Wang, Shu‐Hsing Wu · 2008 · PLANT PHYSIOLOGY
Quantitative transcriptome, proteome, and sulfur metabolite profiling of theSaccharomyces cerevisiaeresponse to arsenite
Michael K. Thorsen, Gilles Lagniel, Erik Kristiansson, Christophe Junot, Olle Nerman, Jean Labarre, Markus J. Tamás · 2007 · Physiological Genomics
Genome‐wide transcriptome dissection of the rice root system: implications for developmental and physiological functions
Hinako Takehisa, Yutaka Sato, Motoko Igarashi, Tomomi Abiko, Baltazar A. Antonio, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Yoshiaki Inukai, Mikio Nakazono et al. · 2011 · The Plant Journal
Identification of targets for rational pharmacological therapy in childhood craniopharyngioma
Jacob M. Gump, Andrew M. Donson, Diane K. Birks, Vladimir M. Amani, Karun Kumar Rao, Andrea M. Griesinger, Bette Kay Kleinschmidt-DeMasters, James M. Johnston, Richard C. E. Anderson, Amy Rosenfeld et al. · 2015 · Acta Neuropathologica Communications
Early Telomerase Inactivation Accelerates Aging Independently of Telomere Length
Zhengwei Xie, Kyle A. Jay, Dana L. Smith, Yi Zhang, Zairan Liu, Jiashun Zheng, Ruilin Tian, Hao Li, Elizabeth Helen Blackburn · 2015 · Cell
Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes
Carlo Baejen, Jessica Andréani, Phillipp Torkler, Sofia Battaglia, Björn Schwalb, Michael Lidschreiber, Kerstin C. Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger et al. · 2017 · Molecular Cell
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Joanna Żyła, Michał Marczyk, Teresa Domaszewska, Stefan H. E. Kaufmann, Joanna Polańska, January Mikolaj Weiner · 2019 · Bioinformatics
Combined transcriptomic and physiological approaches reveal strong differences between short‐ and long‐term response of rice (Oryza sativa) to iron toxicity
Muriel Quinet, Delphine Vromman, André Clippe, Pierre Bertin, Hélène Lequeux, Inès Dufey, Stanley Lutts, Isabelle S. Lefèvre · 2012 · Plant Cell & Environment
Spatial control of adult stem cell fate using nanotopographic cues
Eun Hyun Ahn, Young-Hoon Kim, Kshitiz Gupta, Steven S. An, Junaid M. Afzal, Suengwon Lee, Moon Kyu Kwak, Kahp Yang Suh, Deok‐Ho Kim, Andre Levchenko · 2014 · Biomaterials
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes
Lilach Soreq, Nathan Salomonis, Michal Bronstein, David Greenberg, Zvi H. Israel, Hagai Bergman, Hermona Soreq · 2013 · Frontiers in Molecular Neuroscience
Array-Based Transcript Profiling and Limiting-Dilution Reverse Transcription-PCR Analysis Identify Additional Latent Genes in Kaposi's Sarcoma-Associated Herpesvirus
Sanjay J. Chandriani, Don Ganem · 2010 · Journal of Virology
A bHLH-Based Feedback Loop Restricts Vascular Cell Proliferation in Plants
Francisco Vera‐Sirera, Bert De Rybel, Cristina Úrbez, Evangelos Kouklas, Marta Pesquera, Juan Camilo Álvarez Mahecha, Eugenio G. Minguet, Hannele Tuominen, Juan Carbonell, Jan Willem Borst et al. · 2015 · Developmental Cell
An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers
Ana I. Robles, Eri Arai, Ewy A. Mathé, Hirokazu Okayama, Aaron J. Schetter, Derek W. Brown, David W. Petersen, Elise D. Bowman, Rintaro Noro, Judith A. Welsh et al. · 2015 · Journal of Thoracic Oncology
The human olfactory transcriptome
Tsviya Olender, Ifat Keydar, Jayant Marian Pinto, Pavlo Tatarskyy, Anna Alkelai, Ming‐Shan Chien, Simon Fishilevich, Diego Restrepo, Hiroaki Matsunami, Yoav Gilad et al. · 2016 · BMC Genomics
Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma
Yanyan Tang, Yi He, Lei Shi, Liting Yang, Jinpeng Wang, Yu Lian, Chunmei Fan, Ping Zhang, Can Jie Guo, Shanshan Zhang et al. · 2017 · Oncotarget
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT
Kevin C. Stein, Allison Kriel, Judith Frydman · 2019 · Molecular Cell
Bioinformatics toolbox for narrowing rodent quantitative trait loci
Keith DiPetrillo, Xiao‐Song Wang, Ioannis M. Stylianou, Beverly J. Paigen · 2005 · Trends in Genetics
Microarray analysis of the AHR system: Tissue-specific flexibility in signal and target genes
Markus Frericks, Marc Meissner, Charlotte Esser · 2007 · Toxicology and Applied Pharmacology
Boolean implication networks derived from large scale, whole genome microarray datasets
Debashis Sahoo, David L. Dill, Andrew J. Gentles, Robert John Tibshirani, Sylvia K. Plevritis · 2008 · Genome biology
Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses
Giulia Malacarne, Urška Vrhovšek, L. Zulini, Alessandro Cestaro, M. Stefanini, Fulvio Mattivi, Massimo Delledonne, Riccardo Velasco, Claudio Moser · 2011 · BMC Plant Biology
Database development in toxicogenomics: issues and efforts.
William B. Mattes, Syril D. Pettit, Susanna‐Assunta Sansone, Pierre R. Bushel, Michael D. Waters · 2004 · Environmental Health Perspectives
dmrff: identifying differentially methylated regions efficiently with power and control
Suderman, Matthew, Staley, James R, French, Robert, Arathimos, Ryan, Simpkin, Andrew, Tilling, Kate · 2018
A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis
Pei-Shan Chien, Hong Gil Nam, Yet‐Ran Chen · 2015 · Journal of Experimental Botany
The bromodomain protein BRD4 regulates the KEAP1/NRF2-dependent oxidative stress response
Michelle Hussong, Stefan T. Börno, Martin Kerick, Andrea Wunderlich, Aric M. Franz, Holger Sültmann, Bernd Timmermann, Hans Rudolf Lehrach, Monica Hirsch‐Kauffmann, Michal R. Schweiger · 2014 · Cell Death and Disease
Investigations on Transgenerational Epigenetic Response Down the Male Line in F2 Pigs
Martin Braunschweig, Vidhya Jagannathan, A. Gutzwiller, G. Bee · 2012 · PLoS ONE
Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence
Yury O. Núnez, Jay Truitt, Giorgio Gorini, Olga N. Ponomareva, Yuri A. Blednov, Robert Adron Harris, Roy Dayne Mayfield · 2013 · BMC Genomics
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease
Alexey Moskalev, Elizaveta Chernyagina, João Pedro de Magalhães, Diogo Barardo, Harikrishnan Thoppil, Mikhail Vyacheslavovich Shaposhnikov, Arie Budovsky, Vadim E. Fraifeld, Andrew Garazha, Vasily O. Tsvetkov et al. · 2015 · Aging
Global Adaptation to a Lipid Environment Triggers the Dormancy-Related Phenotype of Mycobacterium tuberculosis
Juan Germán Rodríguez, Adriana C. Hernández, Addy Cecilia Helguera‐Repetto, Diana A. Aguilar-Ayala, Rosalina Guadarrama-Medina, Juan Manuel Anzola, Jose Ricardo Bustos, María Mercedes Zambrano, Jorge A. González-y-Merchand, María J. García et al. · 2014 · mBio
The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region
Karyn Schmidt, Cailin E. Joyce, Frank A. Buquicchio, Adam S. Brown, Justin Ritz, Robert J. Distel, Charles H. Yoon, Carl D. Novina · 2016 · Cell Reports
klf2a couples mechanotransduction and zebrafish valve morphogenesis through fibronectin synthesis
Emily Steed, Nathalie Faggianelli, Stéphane Roth, Caroline Ramspacher, Jean‐Paul Concordet, Julien Vermot · 2016 · Nature Communications
Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection
Caitlin D. Bohannon, Ryan P. Powers, Lakshmipriyadarshini Satyabhama, Ang Cui, Christopher M. Tipton, Miri Michaeli, Ioanna Skountzou, Robert S. Mittler, Steven H. Kleinstein, Ramit Mehr et al. · 2016 · Nature Communications
Minor intron splicing is regulated by FUS and affected by ALS‐associated FUS mutants
Stefan Reber, Jolanda Stettler, Giuseppe Filosa, Martino Colombo, Daniel Jutzi, Silvia Carolina Lenzken, Christoph Schweingruber, Rémy Bruggmann, Angela Bachi, Silvia M.L. Barabino et al. · 2016 · The EMBO Journal
DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns
Ksenia Skvortsova, Etienne Masle‐Farquhar, Phuc‐Loi Luu, Jenny Z. Song, Wenjia Qu, Elena Zotenko, Cathryn M. Gould, Qian Du, Timothy J. Peters, Yolanda Colino‐Sanguino et al. · 2019 · Cancer Cell
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease
Jaclyn Taroni, Peter C. Grayson, Qiwen Hu, Sean F. Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene · 2019 · Cell Systems
Temporally Distinct Functions of the Cytokines IL-12 and IL-23 Drive Chronic Colon Inflammation in Response to Intestinal Barrier Impairment
Christina Eftychi, Robin Schwarzer, Katerina Vlantis, Laurens Wachsmuth, Marijana Basic, Prerana Wagle, Markus Friedrich Neurath, Christoph Becker, André Bleich, Manolis Pasparakis · 2019 · Immunity
Endothelialization of arterial vascular grafts by circulating monocytes
Randall J. Smith, Bita Nasiri, Julien Kann, Donald Albert Yergeau, Jonathan Bard, Daniel D. Swartz, Stelios T. Andreadis · 2020 · Nature Communications
Appyters: Turning Jupyter Notebooks into data-driven web apps
Daniel J. B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Sichao Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom et al. · 2021 · Patterns
SigCom LINCS: data and metadata search engine for a million gene expression signatures
John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz et al. · 2022 · Nucleic Acids Research
Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy
Judith Wienke, Lindy L. Visser, Waleed M. Kholosy, Kaylee M. Keller, Marta Barisa, Evon Poon, Sophie Munnings-Tomes, Courtney Himsworth, Elizabeth A. Calton, Ana Isabel Enríquez Rodríguez et al. · 2024 · Cancer Cell
BAFF Receptor Signaling Aids the Differentiation of Immature B Cells into Transitional B Cells following Tonic BCR Signaling
Sarah L. Rowland, Katelyn F. Leahy, Regina Halverson, Raul Martin Torres, Roberta Pelanda · 2010 · The Journal of Immunology
Submission of Microarray Data to Public Repositories
Catherine A. Ball, Alvis Brāzma, Helen C. Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John F Quackenbush, Martin Ringwald et al. · 2004 · PLoS Biology
Cluster analysis reveals differential transcript profiles associated with resistance training-induced human skeletal muscle hypertrophy
Thalacker-Mercer, Anna, Stec, Michael, Cui, Xiangqin, Cross, James, Windham, Samuel, Bamman, Marcas · 2013 · Physiological Genomics
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti
Francesco Pini, Nicole J. De Nisco, Lorenzo Ferri, Jon N Penterman, Antonella Fioravanti, Matteo Brilli, Alessio Mengoni, Marco Bazzicalupo, Patrick H. Viollier, Graham Charles Walker et al. · 2015 · PLoS Genetics
Non-growing Rhodopseudomonas palustris Increases the Hydrogen Gas Yield from Acetate by Shifting from the Glyoxylate Shunt to the Tricarboxylic Acid Cycle
James B. McKinlay, Yasuhiro Oda, Martin Rühl, Amanda L. Posto, Uwe Sauer, Caroline S. Harwood · 2013 · Journal of Biological Chemistry
A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses
Hugh D. Mitchell, Amie J. Eisfeld, Amy María Sims, Jason McDermott, Melissa M. Matzke, Bobbie‐Jo Webb‐Robertson, Susan C. Tilton, Nicolas Tchitchek, Laurence Josset, Chengjun Li et al. · 2013 · PLoS ONE
HIV‐exposed seronegative commercial sex workers show a quiescent phenotype in the CD4+ T cell compartment and reduced expression of HIV‐dependent host factors.
P. J. McLaren, T. Ball, C. Wachihi, W. Jaoko, D. J. Kelvin, A. Danesh, Joshua Kimani, Francis A. Plummer, K. Fowke · 2010 · Journal of Infectious Diseases
Microarray Analysis of Human Monocytes Infected with Francisella tularensis Identifies New Targets of Host Response Subversion
Jonathan P. Butchar, Thomas John Cremer, Corey Davis Clay, Mikhail A. Gavrilin, Mark Damian Wewers, Clay B. Marsh, Larry S. Schlesinger, Susheela Tridandapani · 2008 · PLoS ONE
Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments
Étienne Yergeau, Mélanie Arbour, Roland Brousseau, David Juck, John R. Lawrence, Luke Masson, Lyle G. Whyte, Charles W. Greer · 2009 · Applied and Environmental Microbiology
Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma
Asma Sindhoo Nangraj, Gurudeeban Selvaraj, Satyavani Kaliamurthi, Aman Chandra Kaushik, William Chi Shing Cho, Dong‐Qing Wei · 2020 · Frontiers in Pharmacology
Elucidating the fundamental fibrotic processes driving abdominal adhesion formation
Deshka S. Foster, Clement D. Marshall, Gunsagar Singh Gulati, Malini S. Chinta, Alan T. Nguyen, Ankit Salhotra, Ruth Ellen Jones, Austin R. Burcham, Tristan Lerbs, Lu Cui et al. · 2020 · Nature Communications
From Omics to Multi-Omics: A Review of Advantages and Tradeoffs
Hayes, C. Nelson, Nakahara, Hikaru, Ono, Atsushi, Tsuge, Masataka, Oka, Shiro · 2024 · Genes
Neuronal activity increases translocator protein (TSPO) levels
Notter, Tina, Schalbetter, Sina M., Clifton, Nicholas E., Mattei, Daniele, Richetto, Juliet, Thomas, Kerrie, Meyer, Urs, Hall, Jeremy · 2021 · Molecular Psychiatry
Quality Assessment of Affymetrix GeneChip Data
Steffen Heber, Beate Sick · 2006 · OMICS A Journal of Integrative Biology
Global Gene Expression Profiling of a Population Exposed to a Range of Benzene Levels
Cliona M. McHale, Luoping Zhang, Qing Lan B, Roel C.H. Vermeulen, Guilan Li, Alan Hubbard, Kristin E. Porter, Reuben Thomas, Christopher J. Portier, Min Shen et al. · 2010 · Environmental Health Perspectives
Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome
Cara Lunn Shirai, Brian S. White, Manorama Tripathi, ROBERTO C. TAPIA-CONYER, James N. Ley, Matthew Ndonwi, Sanghyun Peter Kim, Jin Shao, Alexa Carver, Borja Sáez et al. · 2017 · Nature Communications
Impact of Consuming Extra-Virgin Olive Oil or Nuts within a Mediterranean Diet on DNA Methylation in Peripheral White Blood Cells within the PREDIMED-Navarra Randomized Controlled Trial: A Role for Dietary Lipids
Ana Arpón, Fermin Ignacio Milagro, Cristina Razquín, Dolores Corella, Ramón Estruch, Montserrat Fitó, Amelia Martí, Miguel Ángel Martínez‐González, Emilio Ros, Jordi Salas‐Salvadó et al. · 2017 · Nutrients
Machine learning approaches and their current application in plant molecular biology: A systematic review
José Cleydson F. Silva, Ruan M. Teixeira, Fabyano Fonseca e Silva, Sérgio Hermínio Brommonschenkel, Elizabeth P. B. Fontes · 2019 · Plant Science
Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications
Pascal Jézéquel, Olivier Kerdraon, Hubert Hondermarck, Catherine Guérin‐Charbonnel, Hamza Lasla, Wilfried Gouraud, Jean-Luc Re Canon, Andrea Gombos, Florence Dalenc, Suzette Delaloge et al. · 2019 · Breast Cancer Research
Robust hepatitis E virus infection and transcriptional response in human hepatocytes
Daniel Tödt, Martina Friesland, Nora Moeller, Dimas Praditya, Volker Kinast, Yannick Brüggemann, Leonard Knegendorf, Thomas L. Burkard, Joerg Steinmann, Rani Burm et al. · 2020 · Proceedings of the National Academy of Sciences
FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers
Xingyi Li, Ju Xiang, Jianxin Wang, Jinyan Li, Fang‐Xiang Wu, Min Li · 2020 · IEEE Transactions on Computational Biology and Bioinformatics
Transcriptome analysis of synaptoneurosomes identifies neuroplasticity genes overexpressed in incipient Alzheimer's disease
Williams, Celia, Mehrian Shai, Ruty, Wu, Yongchun, Hsu, Ya-Hsuan, Sitzer, Traci, Spann, Bryan, McCleary, Carol, Mo, Yi, Miller, Carol A. · 2009 · PLoS ONE
Aggressive Fibromatosis (Desmoid Tumor) Is Derived from Mesenchymal Progenitor Cells
Colleen Wu, Saied Nik-Amini, Puviindran Nadesan, William L. Stanford, Benjamin Aaron Alman · 2010 · Cancer Research
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
Bart Buitenhuis, Christine Maria Røntved, Stefan McKinnon Edwards, K.L. Ingvartsen, Peter Sørensen · 2011 · BMC Genomics
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics
Warnat-Herresthal, Stefanie, Perrakis, Konstantinos, Taschler, Bernd, Becker, Matthias, Baßler, Kevin, Beyer, Marc, Günther, Patrick, Schulte-Schrepping, Jonas, Seep, Lea, Klee, Kathrin et al. · 2020 · iScience
Increased CYFIP1 dosage alters cellular and dendritic morphology and dysregulates mTor
Oguro-Ando, A, Rosensweig, C, Herman, E, Nishimura, Y, Werling, D, Bill, B R, Berg, J M, Gao, F, Coppola, G, Abrahams, B S et al. · 2015 · Molecular Psychiatry
Insights into Eyestalk Ablation Mechanism to Induce Ovarian Maturation in the Black Tiger Shrimp
Umaporn Uawisetwathana, Rungnapa Leelatanawit, Amornpan Klanchui, Juthatip Prommoon, Sirawut Klinbunga, Nitsara Karoonuthaisiri · 2011 · PLoS ONE
Gene expression profiling of peripheral blood cells for early detection of breast cancer
Jørgen Aarøe, Torbjørn Lindahl, Vanessa Dumeaux, Solve Sæbø, Derek Tobin, Nina Hagen, Per Skaane, Anders Lönneborg, Praveen Sharma, Anne‐Lise Børresen‐Dale · 2010 · Breast Cancer Research
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa
Dorit Cohen, Undine Mechold, Hadas Nevenzal, Yafit Yarmiyhu, Trevor E. Randall, Denice C. Bay, Jacquelyn D. Rich, Matthew R. Parsek, Volkhard Kaever, Joe Jonathan Harrison et al. · 2015 · Proceedings of the National Academy of Sciences
Circulating cell-free DNA-based epigenetic assay can detect early breast cancer
Natsue Uehiro, Fumiaki Sato, Fengling Pu, Sunao Tanaka, Masahiro Kawashima, Kosuke Kawaguchi, Masahiro Sugimoto, Shigehira Saji, Masakazu Toi · 2016 · Breast Cancer Research
Asynchronous and pathological windows of implantation: two causes of recurrent implantation failure†
Patricia Sebastián-León, Nicolás Garrido, Jose Remohi SR, António Pellicer, Patricia Díaz-Gimeno · 2018 · Human Reproduction
Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming
Nicole R. Stone, Casey A. Gifford, Reuben Thomas, Karishma J. B. Pratt, Kaitlen M Samse, Tamer Mohamed, Ethan M. Radzinsky, Amelia Schricker, Lin Ye, Pengzhi Yu et al. · 2019 · Cell stem cell
LAG3 (LAG-3, CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma
Niklas Klümper, Damian Johannes Ralser, Emma Bawden, Jenny Landsberg, Romina Zarbl, Glen Kristiansen, Marieta Ioana Toma, Manuel Ritter, Michael Hölzel, Jörg Ellinger et al. · 2020 · Journal for ImmunoTherapy of Cancer
The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells
Igor L. Bado, Weijie Zhang, Jingyuan Hu, Zhan Xu, Hai Wang, Poonam Sarkar, Lucian Li, Ying‐Wooi Wan, Jun Liu, William Wu et al. · 2021 · Developmental Cell
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development
Andrew J. Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna Anand et al. · 2021 · Cell
Functional gene expression differences between inbred alcohol-preferring and –non-preferring rats in five brain regions
Mark W. Kimpel, Wendy N. Strother, Jeanette N. McClintick, Lucinda G. Carr, Tiebing Liang, Howard J. Edenberg, William J. McBride · 2007 · Alcohol
Protein Translation and Cell Death: The Role of Rare tRNAs in Biofilm Formation and in Activating Dormant Phage Killer Genes
Rodolfo García‐Contreras, Xue‐Song Zhang, Younghoon Kim, Thomas Keith Wood · 2008 · PLoS ONE
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
Mark G. Carter, Alexei A. Sharov, Vincent VanBuren, Dawood Babu Dudekula, Condie Edwin Carmack, Charlie N. Nelson, Minoru S.H. Ko · 2005 · Genome biology
Functional genomics and proteomics: charting a multidimensional map of the yeast cell
Gary D. Bader, Adrian M Heilbut, Brenda Andrews, Mike Tyers, Timothy R. Hughes, Charles M. Boone · 2003 · Trends in Cell Biology
Histone Deacetylase Inhibitors in the Treatment of Muscular Dystrophies: Epigenetic Drugs for Genetic Diseases
Silvia Consalvi, Valentina Saccone, Lorenzo Giordani, Giulia Minetti, Chiara Mozzetta, Prem Puri · 2011 · Molecular Medicine
Lae1 regulates expression of multiple secondary metabolite gene clusters in Fusarium verticillioides
Robert A. E. Butchko, Daren W. Brown, Mark Busman, Bettina Tudzynski, Philipp Wiemann · 2012 · Fungal Genetics and Biology
Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes
Leif Väremo, Camilla Charlotte Scheele, Christa Broholm, Adil Mardinoğlu, Caroline Kampf, Anna Asplund, Intawat Nookaew, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen · 2015 · Cell Reports
Global miRNA expression analysis of serous and clear cell ovarian carcinomas identifies differentially expressed miRNAs including miR-200c-3p as a prognostic marker
Bente Vilming Elgaaen, Ole Kristoffer Olstad, Kari Bente Foss Haug, Berit Sletbakk Brusletto, Leiv Sandvik, Anne Cathrine Staff, Kaare M. Gautvik, Ben Davidson · 2014 · BMC Cancer
Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types
Craig P. Giacomini, Steven Sun, Sushama Varma, Alan Hunter Shain, Marilyn M. Giacomini, Jay Michael S. Balagtas, Robert T. Sweeney, Everett Lai, Catherine Del Vecchio Fitz, Andrew D. Forster et al. · 2013 · PLoS Genetics
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans
Joel N. Meyer, Windy A. Boyd, Gregory Albert Azzam, Astrid C. Haugen, Jonathan H. Freedman, Bennett Van Houten · 2007 · Genome biology
Noncanonical thyroid hormone signaling mediates cardiometabolic effects in vivo
Georg Sebastian Hönes, Helena Rakov, John G. Logan, Xiao-Hui Liao, Eugenie Werbenko, Andrea S. Pollard, Stine Marie Præstholm, Majken Storm Siersbæk, Eddy Rijntjes, Janina Gassen et al. · 2017 · Proceedings of the National Academy of Sciences
Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
E. Magda Price, Wendy P. Robinson · 2018 · Frontiers in Genetics
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment
Jiahui Zheng, Min Huan Wu, Haiyan Wang, Shasha Li, Xin Wang, Yan Li, Dong Wang, Shao Li · 2018 · Cancers
Commensal microbiota drive the functional diversification of colon macrophages
Byunghyun Kang, Luigi J. Alvarado, Teayong Kim, Michael L. Lehmann, Hyeseon Cho, Jianping He, Peng Li, Bo‐Hyun Kim, André Larochelle, Brian Lee Kelsall · 2019 · Mucosal Immunology
Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis
Sarka Benesova, Mikael Kubista, Lukáš Valihrach · 2021 · Diagnostics
Extracellular matrix educates an immunoregulatory tumor macrophage phenotype found in ovarian cancer metastasis
E. H. Puttock, Eleanor J. Tyler, Michela Manni, Eleni Maniati, Charlotte Butterworth, Marcos Burger Ramos, Eleonora Peerani, Priyanka Hirani, V. Gauthier, Ying Liu et al. · 2023 · Nature Communications
Foundation models in bioinformatics
Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang · 2025 · National Science Review
Isolation of Novel Multipotent Neural Crest-Derived Stem Cells from Adult Human Inferior Turbinate
Stefan Hauser, Darius Widera, Firas Qunneis, Janine Müller, Christin Zander, Johannes F. W. Greiner, Christina Strauss, Patrick Lüningschrör, Peter Heimann, Hartmut Schwarze et al. · 2011 · Stem Cells and Development
BIOINFORMATICS AND ITS APPLICATIONS IN PLANT BIOLOGY
Seung Y. Rhee, Julie A. Dickerson, Dong He Xu · 2006 · Annual Review of Plant Biology
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA sequencing in a porcine model
Kogelman, Lisette J A, Cirera, Susanna, Zhernakova, Daria V, Fredholm, Merete, Franke, Lude, Kadarmideen, Haja N · 2014 · BMC Medical Genomics
Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer’s disease
Xu, Jielin, Mao, Chengsheng, Hou, Yuan, Luo, Yuan, Binder, Jessica L., Zhou, Yadi, Bekris, Lynn M., Shin, Jiyoung, Hu, Ming, Wang, Fei et al. · 2022 · Cell Reports
Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact
Lei Li, Yuhong Wei, Christine To, Chang‐Qi Zhu, Jiefei Tong, Nhu‐An Pham, Paul P. Taylor, Vladimir Ignatchenko, Alexandr Ignatchenko, Wen Zhang et al. · 2014 · Nature Communications