Molecular signatures database (MSigDB) 3.0

Liberzon, Arthur, Subramanian, Aravind, Pinchback, Reid, Thorvaldsdóttir, Helga, Tamayo, Pablo, Mesirov, Jill P.·2011·Bioinformatics

DOI 10.1093/bioinformatics/btr260

Cited by (1,039)

Items 801–900 of 1,039

Footprint-based functional analysis of multiomic data
Dugourd, Aurelien, Saez-Rodriguez, Julio · 2019 · Current Opinion in Systems Biology
Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes
Andrew R. DiNardo, Tomoki Nishiguchi, Emily Margaret Mace, Kimal Rajapakshe, Godwin Mtetwa, Alexander W. Kay, Gugu P. Maphalala, William Evan Secor, Rojelio Mejía, Jordan Scott Orange et al. · 2018 · The Journal of Immunology
Association of peripheral blood DNA methylation level with Alzheimer’s disease progression
Qingqin S. Li, Aparna Vasanthakumar, J. Wade Davis, Kenneth B. Idler, Kwangsik T. Nho, Jeffrey F. Waring, Andrew J. Saykin, Alzheimer’s Disease Neuroimaging Initiative · 2021 · Clinical Epigenetics
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer
Sarah M. Groves, Geena V. Ildefonso, Caitlin O. McAtee, Patricia Midori Murobushi Ozawa, Abbie S. Ireland, Philip E. Stauffer, Perry T. Wasdin, Xiaomeng Huang, Yi Qiao, Jing Shan Lim et al. · 2022 · Cell Systems
Collagen Hydrogel Containing Polyethylenimine‐Gold Nanoparticles for Drug Release and Enhanced Beating Properties of Engineered Cardiac Tissues
Kaveh Roshanbinfar, Maria M. Koleśnik-Gray, Miriam Angeloni, Stefan Schrüfer, Maren Fiedler, Dirk Wolfram Schubert, Fulvia Ferrazzi, Vojislav Krstić, Felix Benedikt Engel · 2023 · Advanced Healthcare Materials
In vivo interaction screening reveals liver-derived constraints to metastasis
Costanza Borrelli, Morgan Roberts, Davide Eletto, Marie‐Didiée Hussherr, Hassan Fazilaty, Tomáš Valenta, Atefeh Lafzi, Jonas A. Kretz, Elena Guido Vinzoni, Andromachi Karakatsani et al. · 2024 · Nature
MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC
Elena Fiorini, Antonia Malinova, Daniel Schreyer, Davide Pasini, Michele Bevere, Giorgia Alessio, Diego Rosa, Sabrina L. D’Agosto, Luca Azzolin, Salvatore Milite et al. · 2025 · Nature
Maintenance of CD4 T cell fitness through regulation of Foxo1
Ryan H. Newton, Sharad Shrestha, Jenna M. Sullivan, Kathleen B. Yates, Ewoud Bernardus Compeer, Noga Ron‐Harel, Bruce R. Blazar, Steven J. Bensinger, W. Nicholas Haining, Michael Loran Dustin et al. · 2018 · Nature Immunology
Epithelial endoplasmic reticulum stress orchestrates a protective IgA response
Joep Grootjans, Niklas Krupka, Shuhei Hosomi, Juan David Matute, Thomas Hanley, Svetlana Saveljeva, Thomas Gensollen, Jarom Heijmans, Hai Li, Julien P. Limenitakis et al. · 2019 · Science
The new identified biomarkers determine sensitivity to immune check-point blockade therapies in melanoma
Hao Chen, Meng Yang, Qinghua Wang, Fengju Song, Xiangchun Li, Kexin Chen · 2019 · OncoImmunology
A germ cell‐specific ageing pattern in otherwise healthy men
Sandra Laurentino, Jann‐Frederik Cremers, Bernhard Horsthemke, Frank Tüttelmann, Karen Czeloth, Michael Zitzmann, Eva Pohl, Sven Rahmann, Christopher Schröder, Sven Berres et al. · 2020 · Aging Cell
Activation of the MAPK pathway mediates resistance to PI3K inhibitors in chronic lymphocytic leukemia
Ishwarya Murali, Siddha N. Kasar, Aishath S. Naeem, Svitlana Tyekucheva, Jasneet Kaur Khalsa, Emily M. Thrash, Gilad Itchaki, Dimitri G. Livitz, Ignaty Leshchiner, Shuai Dong et al. · 2021 · Blood
DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity
Qian Du, Grady C. Smith, Phuc‐Loi Luu, James M. Ferguson, Nicola J. Armstrong, Catherine Elizabeth Caldon, Elyssa M. Campbell, Shalima S. Nair, Elena Zotenko, Cathryn M. Gould et al. · 2021 · Cell Reports
The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease
Bendl, Jaroslav, Hauberg, Mads E., Girdhar, Kiran, Im, Eunju, Vicari, James M., Rahman, Samir, Fernando, Michael B., Townsley, Kayla G., Dong, Pengfei, Misir, Ruth et al. · 2022 · Nature Neuroscience
Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers
John W. Phillips, Yang Pan, Brandon L. Tsai, Zhijie Xie, Levon Demirdjian, Wen Xiao, Harry Taegyun Yang, Yida Zhang, Chia Ho Lin, Donghui Cheng et al. · 2020 · Proceedings of the National Academy of Sciences
A Network-Based Analysis Reveals the Mechanism Underlying Vitamin D in Suppressing Cytokine Storm and Virus in SARS-CoV-2 Infection
Firoz Ahmed · 2020 · Frontiers in Immunology
Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer
Adam C. Mueller, Miles Piper, Andrew E. Goodspeed, Shiv Bhuvane, Jason S. Williams, Shilpa Bhatia, Andy V. Phan, Benjamin Van Court, Kathryn L. Zolman, Brisa Peña et al. · 2021 · Cancer Research
Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma
John A. DeSisto, John Thomas Lucas, Ke Xu, Andrew M. Donson, Tong Lin, Bridget L. Sanford, Gang Wu, Quynh T. Tran, Dale J. Hedges, Chih‐Yang Hsu et al. · 2021 · Nature Communications
Safety, pharmacokinetic, pharmacodynamic and clinical activity of molibresib for the treatment of nuclear protein of the testis carcinoma and other cancers: Results of a Phase I / II open‐label, dose escalation study
Sophie Cousin, Jean‐Yves Blay, Irene Braña, Johann Sebastian De Bono, Christophe Le Tourneau, Víctor Moreno, José Manuel Trigo, Christine L. Hann, Arun Azad, Seock‐Ah Im et al. · 2021 · International Journal of Cancer
Vaccinology in the era of high-throughput biology
Helder Imoto Nakaya, Bali Pulendran · 2015 · Philosophical Transactions of the Royal Society B Biological Sciences
Bacterial Siderophores That Evade or Overwhelm Lipocalin 2 Induce Hypoxia Inducible Factor 1α and Proinflammatory Cytokine Secretion in Cultured Respiratory Epithelial Cells
Victoria I. Holden, Steven Lenio, Rork D. Kuick, Sadeesh Kumar Ramakrishnan, Yatrik Madhukar Shah, Michael A. Bachman · 2014 · Infection and Immunity
SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity
Matthew A. Care, Mario Cocco, Jon P. Laye, Nicholas Barnes, Yuanxue Huang, Ming Wang, Sharon Barrans, Ming‐Qing Du, Andrew Jack, David R. Westhead et al. · 2014 · Nucleic Acids Research
Metastasis-associated protein 1 (MTA1) is transferred by exosomes and contributes to the regulation of hypoxia and estrogen signaling in breast cancer cells
Bethany N. Hannafon, Amy L. Gin, Yi-Fan Xu, Matthew Bruns, Cameron L. Calloway, Wei‐Qun Ding · 2019 · Cell Communication and Signaling
Meta-analysis of genome-wide association studies and functional assays decipher susceptibility genes for gastric cancer in Chinese populations
Caiwang Yan, Meng Zhu, Yanbing Ding, Ming Yang, Mengyun Wang, Gang Li, Chuanli Ren, Tongtong Huang, Wenjun Yang, Bangshun He et al. · 2019 · Gut
Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription
Giacomo Cossa, Isabelle Röschert, Florian Prinz, Apoorva Baluapuri, Raphael Silveira Vidal, Christina Schülein‐Völk, Yun-Chien Chang, Carsten Patrick Ade, Guido Mastrobuoni, Cyrille Girard et al. · 2020 · Molecular Cell
STAB: a spatio-temporal cell atlas of the human brain
Liting Song, Shaojun Pan, Zi-Chao Zhang, Longhao Jia, Wei-Hua Chen, Xing‐Ming Zhao · 2020 · Nucleic Acids Research
Activation of the Nrf2 response by intrinsic hepatotoxic drugs correlates with suppression of NF-κB activation and sensitizes toward TNFα-induced cytotoxicity
Bram Herpers, Steven Wink, Lisa Fredriksson, Zi Di, Giel Hendriks, Harry Vrieling, Hans de Bont, Bob van de Water · 2015 · Archives of Toxicology
Multi-omic comparison of Alzheimer’s variants in human ESC–derived microglia reveals convergence at APOE
Liu, Tongfei, Zhu, Bing, Liu, Yan, Zhang, Xiaoming, Yin, Jun, Li, Xiaoguang, Jiang, LuLin, Hodges, Andrew P., Rosenthal, Sara Brin, Zhou, Lisa et al. · 2020 · Journal of Experimental Medicine
MEK Inhibition in a Newborn with RAF1-Associated Noonan Syndrome Ameliorates Hypertrophic Cardiomyopathy but Is Insufficient to Revert Pulmonary Vascular Disease
Alessandro Mussa, Diana Carli, Elisa Giorgio, Anna Maria Villar, Simona Cardaropoli, Caterina Carbonara, Maria Francesca Campagnoli, Paolo Galletto, Martina Palumbo, Simone Olivieri et al. · 2021 · Genes
Chemotherapy Coupled to Macrophage Inhibition Induces T-cell and B-cell Infiltration and Durable Regression in Triple-Negative Breast Cancer
Swarnima Singh, Nigel Lee, Diego A. Pedroza, Igor Bado, Clark Hamor, Licheng Zhang, Sergio Aguirre, Jingyuan Hu, Yichao Shen, Yitian Xu et al. · 2022 · Cancer Research
Associations of dietary patterns with brain health from behavioral, neuroimaging, biochemical and genetic analyses
Ruohan Zhang, Bei Zhang, Chun Shen, Barbara Jacquelyn Sahakian, Zeyu Li, Wei Zhang, Yujie Zhao, Yuzhu Li, Jianfeng Feng, Wei Cheng · 2024 · Nature Mental Health
Tumor editing suppresses innate and adaptive antitumor immunity and is reversed by inhibiting DNA methylation
Ying Zhang, Pourya Naderi Yeganeh, Haiwei Zhang, Simon Yuan Wang, Zhouyihan Li, Bowen Gu, Dian-Jang Lee, Zhibin Zhang, Athanasios Ploumakis, Ming Shi et al. · 2024 · Nature Immunology
Lipid Nanoparticles Elicit Reactogenicity and Sickness Behavior in Mice Via Toll-Like Receptor 4 and Myeloid Differentiation Protein 88 Axis
Tetiana Korzun, Abraham S. Moses, Antony Jozić, Vladislav Grigoriev, Samuel Newton, Jeonghwan Kim, Parham Diba, Ariana L. Sattler, Peter R. Levasseur, Ngoc Le et al. · 2024 · ACS Nano
An ultrasensitive method for detection of cell-free RNA
Monica C. Nesselbush, Bogdan A. Luca, Young-Jun Jeon, Isabel Jabara, Catherine Belle Meador, Andrea Garofalo, Michael Sargent Binkley, Angela Bik‐Yu Hui, Iris van ’t Erve, Nova Xu et al. · 2025 · Nature
Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial
Leigh M. Howard, Kristen L. Hoek, Johannes B. Goll, Parimal Samir, Allison C. Galassie, Tara M. Allos, Xinnan Niu, Laura E. Gordy, Clarence Buddy Creech, Nripesh Prasad et al. · 2017 · PLoS ONE
SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells
Sabine Jägle, Hauke S. Busch, Vivien Freihen, Sven Beyes, Monika Schrempp, Melanie Boerries, Andreas Hecht · 2017 · PLoS Genetics
Co-regulation of transcription by BRG1 and BRM, two mutually exclusive SWI/SNF ATPase subunits
Jesse R. Raab, John S. Runge, Camarie C. Spear, Terry Magnuson · 2017 · Epigenetics & Chromatin
Cholesterol Homeostasis Modulates Platinum Sensitivity in Human Ovarian Cancer
Daniela Criscuolo, Rosario Avolio, Giovanni Calice, Chiara Laezza, Simona Paladino, Giovanna Navarra, Francesca Maddalena, Fabiana Crispo, Cristina Pagano, Maurizio Bifulco et al. · 2020 · Cells
Neutrophil expansion defines an immunoinhibitory peripheral and intratumoral inflammatory milieu in resected non-small cell lung cancer: a descriptive analysis of a prospectively immunoprofiled cohort
Kyle Gregory Mitchell, Lixia Diao, Tatiana V. Karpinets, Marcelo Vailati Negrao, Hai Thanh Tran, Edwin Roger Parra, Erin M. Corsini, Alexandre Reuben, Lorenzo Federico, Chantale Bernatchez et al. · 2020 · Journal for ImmunoTherapy of Cancer
Aging Influences Hepatic Microvascular Biology and Liver Fibrosis in Advanced Chronic Liver Disease
Raquel Maeso‐Díaz, Martí Ortega‐Ribera, Erica Lafoz, Juan José Lozano, Anna Baiges, Rubén Francés, Agustı́n Albillos, Carmen Peralta, Juan Carlos García‐Pagán, Jaime Bosch et al. · 2019 · Aging and Disease
Comprehensive characterization of the rRNA metabolism-related genes in human cancer
Kaisa Cui, Cheng Liu, Xu Li, Qiang Zhang, Youjun Li · 2019 · Oncogene
Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer
Olena M. Vaske, Isabel Bjork, Sofie R. Salama, Holly C. Beale, Avanthi Tayi Shah, Lauren Sanders, Jacob Pfeil, Du Linh Lam, Katrina Learned, Ann Durbin et al. · 2019 · JAMA Network Open
Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire
Achia Khatun, Moujtaba Y. Kasmani, Ryan Zander, David Schauder, Jeremy P. Snook, Jian Shen, Xiaopeng Wu, Robert Burns, Yi‐Guang Chen, Chien‐Wei Lin et al. · 2020 · The Journal of Experimental Medicine
Genetic underpinnings of sociability in the general population
Janita Bralten, Nina Roth Mota, Cornelius J. H. M. Klemann, Ward De Witte, Emma Laing, David Andrew Collier, Hilde de Kluiver, Stéphanie Bauduin, Celso Arango, José Luís Ayuso‐Mateos et al. · 2021 · Neuropsychopharmacology
The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells
Xiaodong Zhuang, Senko Tsukuda, Florian Wrensch, Peter A. C. Wing, Mirjam Schilling, James M. Harris, Helene Borrmann, Sophie B. Morgan, Jennifer Cane, Laurent Mailly et al. · 2021 · iScience
Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology
Clemens Wittenbecher, Rafael R. C. Cuadrat, Luke Johnston, Fabian Eichelmann, Susanne Jäger, Olga Kuxhaus, Marcela Prada, Fabiola Del Greco M, Andrew A. Hicks, P Hoffman et al. · 2022 · Nature Communications
Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles
Randy B. Kang, Yansui Li, Carolina Rosselot, Tuo Zhang, Mustafa M. Siddiq, Prashant Rajbhandari, Andrew F. Stewart, Donald K. Scott, Adolfo Garcı́a-Ocaña, Geming Lu · 2023 · Genome Medicine
METTL3-dependent m6A methylation facilitates uterine receptivity and female fertility via balancing estrogen and progesterone signaling
Shuo Wan, Yadong Sun, Jinbao Zong, Wanqing Meng, Jiacong Yan, Kexin Chen, Sanfeng Wang, Daji Guo, Zhi‐Qiang Xiao, Qinghua Zhou et al. · 2023 · Cell Death and Disease
ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome
Erin Michelle Parry, Camilla K. Lemvigh, Stephanie Deng, Nathan J Dangle, Neil G. Ruthen, Binyamin A. Knisbacher, Julien Broséus, Sébastien Hergalant, Romain Guièze, Shuqiang Li et al. · 2023 · Cancer Cell
The human Y and inactive X chromosomes similarly modulate autosomal gene expression
Adrianna K. San Roman, Helen Skaletsky, Alexander K. Godfrey, Neha V. Bokil, Levi S. Teitz, Isani Singh, Laura V. Blanton, Daniel W. Bellott, Tatyana Pyntikova, Julian Lange et al. · 2023 · Cell Genomics
GPR84 sustains aberrant β-catenin signaling in leukemic stem cells for maintenance of MLL leukemogenesis
Philipp A. Dietrich, Chen Yang, Halina Hoi Laam Leung, Jennifer R. Lynch, Estrella Gonzales‐Aloy, Bing Liu, Michelle Haber, Murray D. Norris, Jianlong Wang, Jenny Yingzi Wang · 2014 · Blood
Role of MTA2 in human cancer
Kyle R. Covington, Suzanne A.W. Fuqua · 2014 · Cancer and Metastasis Reviews
Neuropilin-1 expression in adipose tissue macrophages protects against obesity and metabolic syndrome
Ariel Molly Wilson, Zhuo Shao, Vanessa Grenier, Gaëlle Mawambo, Jean‐François Daudelin, Agnieszka Dejda, Frédérique Pilon, Natalija Popović, Salix Boulet, Célia Parinot et al. · 2018 · Science Immunology
Survey of miRNA-miRNA cooperative regulation principles across cancer types
Tingting Shao, Guangjuan Wang, Hong Chen, Yunjin Xie, Xiyun Jin, Jing Bai, Juan Xu, Xia Li, Jian Hua Huang, Yan Jin et al. · 2018 · Briefings in Bioinformatics
Cdh1 and Pik3ca Mutations Cooperate to Induce Immune-Related Invasive Lobular Carcinoma of the Breast
Yeji An, Jessica R. Adams, Daniel P. Hollern, Anthony Zhao, Stephen G. Chang, Miki S. Gams, Philip E.D. Chung, Xiaping He, Rhea Jangra, Juhi S. Shah et al. · 2018 · Cell Reports
KLF9 suppresses gastric cancer cell invasion and metastasis through transcriptional inhibition of MMP28
Li Yang, Qiang Sun, Mingchun Jiang, Shuang Li, Jiayu Zhang, Zhangqi Xu, Dongyang Guo, Tianning Gu, Boya Wang, Lei Xiao et al. · 2019 · The FASEB Journal
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
Arezo Torang, Paraag Gupta, David J. Klinke · 2019 · BMC Bioinformatics
Immunologic alterations in the pancreatic cancer microenvironment of patients treated with neoadjuvant chemotherapy and radiotherapy
Matthew R. Farren, Layal Sayegh, Michael B. Ware, Hsiao-Rong Chen, Jingjing Gong, Yan Liang, Alyssa M. Krasinskas, Shishir Kumar Maithel, Mohammad Y. Zaidi, Juan Manuel Sarmiento et al. · 2019 · JCI Insight
Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Stott, Ryan T., Kritsky, Oleg, Tsai, Li-Huei · 2021 · PLOS ONE
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway
Di Fruscio, Giuseppina, Schulz, Angela, De Cegli, Rossella, Savarese, Marco, Mutarelli, Margherita, Parenti, Giancarlo, Banfi, Sandro, Braulke, Thomas, Nigro, Vincenzo, Ballabio, Andrea · 2015 · Autophagy
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale
Chen, Qingyu, Lee, Kyubum, Yan, Shankai, Kim, Sun, Wei, Chih-Hsuan, Lu, Zhiyong · 2020 · PLOS Computational Biology
HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus‐associated cancers
Liu, Liying, Xie, Yanan, Yang, Hong, Lin, Anqi, Dong, Minjun, Wang, Haitao, Zhang, Cangang, Liu, Zaoqu, Cheng, Quan, Zhang, Jian et al. · 2023 · iMeta
Proteomics for systems toxicology
Bjoern Titz, Ashraf Elamin, Florian Pierre Martin, Thomas L. Schneider, Sophie Dijon, Nikolai V. Ivanov, Julia Hoeng, Manuel C. Peitsch · 2014 · Computational and Structural Biotechnology Journal
Intake of Natural Compounds and Circulating microRNA Expression Levels: Their Relationship Investigated in Healthy Subjects With Different Dietary Habits
Giulio Ferrero, Sara Carpi, Beatrice Polini, Barbara Pardini, Paola Nieri, Alessia Impeduglia, Sara Grioni, Sonia Tarallo, Alessio Naccarati · 2021 · Frontiers in Pharmacology
The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life
Miriam Anne Lynn, Georgina L. Eden, Feargal J. Ryan, Julien Bensalem, Xuemin Wang, Stephen J. Blake, Jocelyn M. Choo, Yee C. Tee, Anastasia Sribnaia, Jane James et al. · 2021 · Cell Reports
Estrogen hormone is an essential sex factor inhibiting inflammation and immune response in COVID-19
Fuhai Li, Adrianus C. M. Boon, Andrew P. Michelson, Randi E. Foraker, Ming Zhan, Philip Payne · 2022 · Scientific Reports
GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis
Ricardo A. Cordova, Jagannath Misra, Parth H. Amin, Angela J. Klunk, Nur P. Damayanti, Kenneth R. Carlson, Andrew J. Elmendorf, Hyeong-Geug Kim, Emily T. Mirek, Bennet D. Elzey et al. · 2022 · eLife
Histone deacetylase-mediated tumor microenvironment characteristics and synergistic immunotherapy in gastric cancer
Yilin Lin, Xiangxiang Jing, Zhihua Chen, Xiaoxian Pan, Duo Xu, Xiang Yu, Fengyun Zhong, Long Zhao, Changjiang Yang, Bo Wang et al. · 2023 · Theranostics
Gene signatures related to B ‐cell proliferation predict influenza vaccine‐induced antibody response
Yan Qin Tan, Pablo Tamayo, Helder Imoto Nakaya, Bali Pulendran, Jill P. Mesirov, W. Nicholas Haining · 2013 · European Journal of Immunology
Systematic analysis of metastasis-associated genes identifies miR-17-5p as a metastatic suppressor of basal-like breast cancer
Meiyun Fan, Aarti Sethuraman, Martin Brown, WenLin Sun, Lawrence M. Pfeffer · 2014 · Breast Cancer Research and Treatment
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
Mirko Francesconi, Bruno Di Stefano, Clara Berenguer, Luísa de Andrés-Aguayo, Marcos Plana-Carmona, María Méndez-Lago, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Marta Gut, Ivo Glynne Gut et al. · 2019 · eLife
A wave of monocytes is recruited to replenish the long-term Langerhans cell network after immune injury
Ferrer, Ivana R., West, Heather C., Henderson, Stephen, Ushakov, Dmitry S., Santos e Sousa, Pedro, Strid, Jessica, Chakraverty, Ronjon, Yates, Andrew J., Bennett, Clare L. · 2019 · Science Immunology
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases
Daniel Domingo‐Fernándéz, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó, Martin Hofmann‐Apitius · 2018 · npj Systems Biology and Applications
Genome-Wide Analysis of Circular RNAs Mediated ceRNA Regulation in Porcine Embryonic Muscle Development
Linjun Hong, Ting Gu, Yanjuan He, Chen Zhou, Qun Hu, Xingwang Wang, Enqin Zheng, Sixiu Huang, Zheng Xu, Jie Yang et al. · 2019 · Frontiers in Cell and Developmental Biology
Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation
Abby C. Lee, Jaideep Chakladar, Wei Tse Li, Cheng‐Yu Chen, Eric Yao Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko · 2020 · International Journal of Molecular Sciences
A new thinking: deciphering the aberrance and clinical implication of copper-death signatures in clear cell renal cell carcinoma
Aimin Jiang, Peng Luo, Ming Chen, Yu Fang, Bing Liu, Zhenjie Wu, Le Qu, Anbang Wang, Linhui Wang, Chen Cai · 2022 · Cell & Bioscience
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment
Zoë Steier, Dominik A. Aylard, Laura Lynn McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Lydia Kay Lutes, Can Ergen, Tse-Shun Huang, Ellen A. Robey, Nir Yosef et al. · 2023 · Nature Immunology
Decoding anxiety–impulsivity subtypes in preadolescent internalising disorders: findings from the Adolescent Brain Cognitive Development study
Huaxin Fan, Zhaowen Liu, Xinran Wu, Gechang Yu, Xinrui Gu, Nanyu Kuang, Kai Zhang, Yu Liu, Tianye Jia, Barbara Jacquelyn Sahakian et al. · 2023 · The British Journal of Psychiatry
Ferritin Heavy Chain in Triple Negative Breast Cancer: A Favorable Prognostic Marker that Relates to a Cluster of Differentiation 8 Positive (CD8+) Effector T-cell Response
Ning Qing Liu, Tommaso De Marchi, A. Mieke Timmermans, Robin Beekhof, Anita Trapman-Jansen, Renée Foekens, Maxime P. Look, Carolien H. M. van Deurzen, Paul N. Span, Fred C.G.J. Sweep et al. · 2014 · Molecular & Cellular Proteomics
PSEA-Quant: A Protein Set Enrichment Analysis on Label-Free and Label-Based Protein Quantification Data
Mathieu Lavallée‐Adam, Navin Rauniyar, Daniel B. McClatchy, John R. Yates · 2014 · Journal of Proteome Research
The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury
Raquel Cuevas‐Díaz Durán, Han Yan, Yiyan Zheng, Xingfan Huang, Raymond J. Grill, Dong Kim, Qilin Cao, Jia Qian Wu · 2017 · Scientific Reports
The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription
Pavel Katsel, Panos Roussos, Peter S. Fam, Sonia Khan, Weilun Tan, Tetsuro Hirose, Shinichi Nakagawa, Mikhail V. Pletnikov, Vahram H. Haroutunian · 2019 · Schizophrenia
The mechanisms of skeletal muscle atrophy in response to transient knockdown of the vitamin D receptor in vivo
Joseph J. Bass, Abid A. Kazi, Colleen S. Deane, Asif Nakhuda, Stephen P. Ashcroft, Matthew S. Brook, Daniel James Wilkinson, Bethan Eileen Phillips, Andrew Philp, Janelle Tarum et al. · 2020 · The Journal of Physiology
Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma
Jonas Ecker, Venu Thatikonda, Gianluca Sigismondo, Florian Selt, Gintvile Valinciute, Ina Oehme, Carina Müller, Juliane L. Buhl, Johannes Ridinger, Diren Usta et al. · 2020 · Neuro-Oncology
Differentially expressed genes in Alzheimer’s disease highlighting the roles of microglia genes including OLR1 and astrocyte gene CDK2AP1
Qingqin S. Li, Louis De Muynck · 2021 · Brain Behavior & Immunity - Health
System-wide transcriptome damage and tissue identity loss in COVID-19 patients
Jiwoon Park, Jonathan Foox, TYLER D. HETHER, David Danko, Sarah E. Warren, Youngmi Kim, Jason Reeves, Daniel Butler, Christopher Mozsary, Joel A. Rosiene et al. · 2022 · Cell Reports Medicine
Replication Stress Defines Distinct Molecular Subtypes Across Cancers
Nobuyuki Takahashi, Se Hyun Kim, Christopher William Schultz, Vinodh N. Rajapakse, Yang Zhang, Christophe E. Redon, Haiqing Fu, Lőrinc Sándor Pongor, Suresh Kumar, Yves G. Pommier et al. · 2021 · Cancer Research Communications
Aging‐like changes in the transcriptome of irradiated microglia
Matthew Li, Terry C. Burns, Sunny Kumar, Alexander A. Morgan, Steven A. Sloan, Theo D. Palmer · 2015 · Glia
Specific covalent inhibition of MALT1 paracaspase suppresses B cell lymphoma growth
Lorena Fontán, Qi Qiao, John M. Hatcher, Gabriella Casalena, Ilkay Us, Matt R. Teater, Matt Durant, Guangyan Du, Min Xia, Natalia Bilchuk et al. · 2018 · Journal of Clinical Investigation
GENAVi: a shiny web application for gene expression normalization, analysis and visualization
Alberto Luiz P. Reyes, Tiago C. Silva, Simon G. Coetzee, Jasmine Plummer, Brian D Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther et al. · 2019 · BMC Genomics
Phosphorylation of RAB7 by TBK1/IKKϵ Regulates Innate Immune Signaling in Triple-Negative Breast Cancer
Jessica Ritter, Zehua Zhu, Tran Cam Thai, Navin R. Mahadevan, Philipp Mertins, Erik H. Knelson, Brandon P. Piel, Saemi Han, Jacob D. Jaffe, Steven A. Carr et al. · 2019 · Cancer Research
Collagen Induces a More Proliferative, Migratory and Chemoresistant Phenotype in Head and Neck Cancer via DDR1
Sook Ling Lai, May Leng Mabel Tan, Robert J. Hollows, Max Robinson, Maha Ibrahim, Sandra Margielewska, Eric Kenneth Parkinson, Anand Ramanathan, Rosnah Binti Zain, Hisham Mohamed Mehanna et al. · 2019 · Cancers
Transcriptional profiling of leukocytes in critically ill COVID19 patients: implications for interferon response and coagulation
Lawson COVID19 Study Team, Sean E. Gill, Claúdia C. dos Santos, David B. O’Gorman, David E. Carter, Eric K. Patterson, Marat Slessarev, Claudio M. Martin, Mark Daley, Michael R. Miller et al. · 2020 · Intensive Care Medicine Experimental
Selective deletion of MyD88 signaling in α-SMA positive cells ameliorates experimental intestinal fibrosis via post-transcriptional regulation
Zhao, Shuai, Dejanovic, Dina, Yao, Peng, Bhilocha, Shardul, Sadler, Tammy, Schirbel, Anja, West, Gail, Doyon, Genevieve, Lopez, Rocio, Mao, Ren et al. · 2020 · Mucosal Immunology
Expression and gene regulation network of RBM8A in hepatocellular carcinoma based on data mining
Yan Lin, Rong Liang, Yufen Qiu, Yufeng Lv, Jinyan Zhang, Gang Qin, Chunling Yuan, Zhihui Liu, Yongqiang Li, Donghua Zou et al. · 2019 · Aging
Plasma-derived extracellular vesicle analysis and deconvolution enable prediction and tracking of melanoma checkpoint blockade outcome
Alvin Shi, Gyulnara G. Kasumova, William A. Michaud, Jessica Cintolo-Gonzalez, Marta Díaz‐Martínez, Jacqueline F. Ohmura, Arnav Mehta, Isabel Chien, Dennie Tompers Frederick, Sonia Cohen et al. · 2020 · Science Advances
Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer
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