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 401–500 of 1,039

Disrupting the phase separation of KAT8–IRF1 diminishes PD-L1 expression and promotes antitumor immunity
Yuanzhong Wu, Liwen Zhou, Yezi Zou, Yijun Zhang, Meifang Zhang, Liping Xu, Lisi Zheng, Wenting He, Kuai Yu, Ting Li et al. · 2023 · Nature Cancer
Genetic subtype-guided immunochemotherapy in diffuse large B cell lymphoma: The randomized GUIDANCE-01 trial
Mu‐Chen Zhang, Shuang Tian, Di Fu, Li Wang, Shu Cheng, Hongmei Yi, Xufeng Jiang, Qi Song, Yan Zhao, Yang He et al. · 2023 · Cancer Cell
Systems vaccinology: Enabling rational vaccine design with systems biological approaches
Thomas Hagan, Helder Imoto Nakaya, Shankar Subramaniam, Bali Pulendran · 2015 · Vaccine
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data
Coral Fustero Torre, María José Jiménez‐Santos, Santiago García‐Martín, Carlos Carretero-Puche, Luis García-Jimeno, Vadym Ivanchuk, Tomás Di Domenico, Gonzalo Goméz-López, Fátima Al‐Shahrour · 2021 · Genome Medicine
Molecular determinants of nephron vascular specialization in the kidney
David M. Barry, Elizabeth A. McMillan, Balvir Kunar, Raphaêl Lis, Tuo Zhang, Tyler M. Lu, Edward Daniel, Masataka Yokoyama, Jesús M. Gómez-Salinero, Angara Sureshbabu et al. · 2019 · Nature Communications
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer
Ruidong Li, Han Qu, Shibo Wang, John M. Chater, Xuesong Wang, Yanru Cui, Lei Yu, Rui Zhou, Qiong Jia, Ryan C. Traband et al. · 2021 · Nucleic Acids Research
eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer
Shruthy Suresh, Beibei Chen, Jingfei Zhu, Ryan J. Golden, Changzheng Lu, Bret M. Evers, Nicole Novaresi, Bethany Smith, Xiaowei Zhan, Vanessa Schmid et al. · 2020 · Nature Cancer
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma
Livnat Jerby‐Arnon, Cyril Neftel, Marni E. Shore, Hannah R. Weisman, Nathan D. Mathewson, Matthew J. McBride, Brian J. Haas, Benjamin Izar, Angela Volorio, Gaylor Boulay et al. · 2021 · Nature Medicine
Therapeutic targeting of EP300/CBP by bromodomain inhibition in hematologic malignancies
Luciano Nicosia, Gary J. Spencer, Nigel A.N. Brooks, Fabio M. R. Amaral, Naseer J. Basma, John A. Chadwick, Bradley Revell, Bettina Wingelhofer, Alba Maiqués-Díaz, Oliver J. Sinclair et al. · 2023 · Cancer Cell
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
Tu, Ang A., Gierahn, Todd M., Monian, Brinda, Morgan, Duncan M., Mehta, Naveen K., Ruiter, Bert, Shreffler, Wayne G., Shalek, Alex K., Love, J. Christopher · 2019 · Nature Immunology
Pathway and network analysis in proteomics
Xiaogang Wu, Mohammad Al Hasan, Jake Y. Chen · 2014 · Journal of Theoretical Biology
Unique Genomic Profile of Fibrolamellar Hepatocellular Carcinoma
Helena Cornellà, Clara Alsinet, Sergi Sayols, Zhongyang Zhang, Ke Hao, Laia Cabellos, Yujin Hoshida, Augusto Villanueva, Swan N. Thung, Stephen C. Ward et al. · 2015 · Gastroenterology
Prediction of synergistic anti-cancer drug combinations based on drug target network and drug induced gene expression profiles
Xiangyi Li, Yingjie Xu, Hui Song Cui, Tao Huang, Disong Wang, Baofeng Lian, Wěi Li, Guangrong Qin, Lanming Chen, Lu Xie · 2017 · Artificial Intelligence in Medicine
Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy
Teresa G. Krieger, Solange Le Blanc, Julia Jabs, Foo Wei Ten, Naveed Ishaque, Katharina Jechow, Olivia Debnath, Carl-Stephan Leonhardt, Anamika Giri, Roland Eils et al. · 2021 · Nature Communications
Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury
Christian Hinze, Christine Kocks, Janna Leiz, Nikos Karaiskos, Anastasiya Boltengagen, Shuang Cao, Christopher Mark Skopnik, Jan Klocke, Jan-Hendrik Hardenberg, Helena Stockmann et al. · 2022 · Genome Medicine
DeepOmix: a scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis
Zhao, Lianhe, Dong, Qiongye, Luo, Chunlong, Wu, Yang, Bu, Dechao, Qi, Xiaoning, Luo, Yufan, Zhao, Yi · 2021 · Computational and Structural Biotechnology Journal
Comparative Genomic Profiling of Synovium Versus Skin Lesions in Psoriatic Arthritis
Jennifer Belasco, James S. Louie, Nicholas Gulati, Nathan Wei, Kristine E. Nograles, Judilyn Fuentes‐Duculan, Hiroshi Mitsui, Mayte Suárez‐Fariñas, James G. Krueger · 2014 · Arthritis & Rheumatology
Gene function and cell surface protein association analysis based on single-cell multiomics data
Huan Hu, Zhen Feng, Hai Lin, Jinyan Cheng, Jie Lyu, Yaru Zhang, Junjie Zhao, Fei Xu, Tao Lin, Qi Zhao et al. · 2023 · Computers in Biology and Medicine
Mitochondrial isocitrate dehydrogenase impedes CAR T cell function by restraining antioxidant metabolism and histone acetylation
Xiaohui Si, Mi Shao, Xinyi Teng, Yue Huang, Meng Ye, Longyuan Wu, Jieping Wei, Lianxuan Liu, Tianning Gu, Junzhe Song et al. · 2024 · Cell Metabolism
Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease
Naoto Fujiwara, Naoto Kubota, Émilie Crouchet, Bhuvaneswari Koneru, Cesia Ammi Marquez, Arun Kumar Jajoriya, Gayatri Panda, Tongqi Qian, Shijia Zhu, Nicolas Goossens et al. · 2022 · Science Translational Medicine
p16-dependent increase of PD-L1 stability regulates immunosurveillance of senescent cells
Julia Majewska, Amit Agrawal, Avi Mayo, Lior Roitman, Rishita Chatterjee, Jarmila Sekeresova Kralova, Tomer Landsberger, Yonatan Katzenelenbogen, Tomer Meir-Salame, Efrat Hagai et al. · 2024 · Nature Cell Biology
SynaptomeDB: an ontology-based knowledgebase for synaptic genes
Pirooznia, Mehdi, Wang, Tao, Avramopoulos, Dimitrios, Valle, David, Thomas, Gareth, Huganir, Richard L., Goes, Fernando S., Potash, James B., Zandi, Peter P. · 2012 · Bioinformatics
Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism.
Schauer, Nathan J., Liu, Xiaoxi, Magin, Robert S., Doherty, Laura M., Chan, Wai Cheung, Ficarro, Scott B., Hu, Wanyi, Roberts, Rebekka M., Iacob, Roxana E., Stolte, Björn et al. · 2020 · Scientific Reports
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss
Andrew M. Gross, Ryan K. Orosco, John Paul Shen, Ann Marie Egloff, Hannah K. Carter, Matan Hofree, Michel Choueiri, Charles S. Coffey, Scott Michael Lippman, David Neil Hayes et al. · 2014 · Nature Genetics
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
LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Ling Cai, Shin-Yi Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Hao Tang et al. · 2018 · Oncogene
Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium
Renato A Polimanti, Raymond Kenney Walters, Emma C. Johnson, Jeanette N. McClintick, Amy E. Adkins, Daniel E. Adkins, Silviu‐Alin Bacanu, Laura Jean Bierut, Tim B. Bigdeli, Sandra A. Brown et al. · 2020 · Molecular Psychiatry
ERRα mediates metabolic adaptations driving lapatinib resistance in breast cancer
Geneviève Deblois, Harvey W. Smith, Ingrid S. Tam, Simon‐Pierre Gravel, Maxime Caron, Paul Savage, David P. Labbé, Louis R. Bégin, Michel L. Tremblay, Morag Park et al. · 2016 · Nature Communications
Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable Targets
Damir Varešlija, Nolan Priedigkeit, Ailís Fagan, Siobhan P. Purcell, Nicola S. Cosgrove, Philip J. O’Halloran, Elspeth Ward, Sinéad Cocchiglia, Ryan James Hartmaier, Carlos A. Castro et al. · 2018 · JNCI Journal of the National Cancer Institute
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Dylan Kotliar, Aaron E. Lin, James Logue, Travis K. Hughes, Nadine M. Khoury, Siddharth S. Raju, Marc H. Wadsworth, Han M. Chen, Jonathan R. Kurtz, Bonnie Dighero-Kemp et al. · 2020 · Cell
Noncanonical TGFβ Signaling Promotes Specialized Neuroretina Tip-Cell Sprouting and Blood-Retina Barrier Formation
Georgia Zarkada, Joel P. Howard, Xue Xiao, Hyojin Park, Mathilde Bizou, Séverine Leclerc, Steffen Emil Künzel, Blanche Boisseau, Jinyu Li, Gaël Cagnone et al. · 2021 · Developmental Cell
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
Isidro Cortés‐Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michaël Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin · 2015 · Bioinformatics
A predictive modeling approach for cell line-specific long-range regulatory interactions
Sushmita Roy, Alireza Fotuhi Siahpirani, Deborah A. Chasman, Sara Knaack, Ferhat Ay, Ron M. Stewart, Michael D. Wilson, Rupa Sridharan · 2015 · Nucleic Acids Research
A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer
Chi Zhu, Li Li, Zhao Zhang, Mingjun Bi, Hu Wang, Wenyue Su, Karen Hernandez, Pingping Liu, Junqiang Chen, Mingqiu Chen et al. · 2019 · Molecular Cell
Proteogenomic landscape of squamous cell lung cancer
Paul A. Stewart, Eric A. Welsh, Robbert J.C. Slebos, Bin Fang, Victoria Izumi, Matthew Chambers, Guolin Zhang, Ling Cen, Fredrik H. Pettersson, Yonghong Zhang et al. · 2019 · Nature Communications
Vascular smooth muscle-derived Trpv1+ progenitors are a source of cold-induced thermogenic adipocytes
Farnaz Shamsi, Mary E. Piper, Li‐Lun Ho, Tian Lian Huang, Anushka Gupta, Aaron Streets, Matthew D. Lynes, Yu‐Hua Tseng · 2021 · Nature Metabolism
Correlation AnalyzeR: functional predictions from gene co-expression correlations
Henry E. Miller, Alexander J.R. Bishop · 2021 · BMC Bioinformatics
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels
Gianni Monaco, Sipko van Dam, João Casal Novo Ribeiro, Anis Larbi, João Pedro de Magalhães · 2015 · BMC Evolutionary Biology
Sleeping Beauty screen reveals Pparg activation in metastatic prostate cancer
Imran Ahmad, Ernest J. Mui, Laura C.A. Galbraith, Rachana Patel, Ee Hong Tan, Mark J. Salji, Alistair G. Rust, Peter Repiščák, Ann Hedley, Elke Katrin Markert et al. · 2016 · Proceedings of the National Academy of Sciences
Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells
Boris J. N. Winterhoff, Makayla Maile, Amit Mitra, Attila Sebe, Martina Bazzaro, Melissa Ann Geller, Juan E. Abrahante, Molly E. Klein, Raffaele Hellweg, Sally A. Mullany et al. · 2017 · Gynecologic Oncology
Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis
Alexander Neumann, Esther Walton, Silvia Alemany, Charlotte A. M. Cecil, Juan R. González, Dereje D. Jima, Jari M. T. Lahti, Samuli Tuominen, Edward Dylan Barker, Elisabeth B. Binder et al. · 2020 · Translational Psychiatry
Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures
Martin Jinye Zhang, Angela Oliveira Pisco, Spyros Darmanis, James Zou · 2021 · eLife
Comprehensive transcriptome and mutational profiling of endemic Burkitt lymphoma reveals EBV type–specific differences
Kaymaz, Yasin, Oduor, Cliff I., Yu, Hongbo, Otieno, Juliana A., Ong'echa, John Michael, Moormann, Ann M., Bailey, Jeffrey A. · 2017 · Molecular Cancer Research
Overexpression of the vitamin D receptor (VDR) induces skeletal muscle hypertrophy
Joseph J. Bass, Asif Nakhuda, Colleen S. Deane, Matthew S. Brook, Daniel James Wilkinson, Bethan Eileen Phillips, Andrew Philp, Janelle Tarum, Fawzi Kadi, Ditte K. Andersen et al. · 2020 · Molecular Metabolism
Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i
Reinhard Dummer, Célèste Lebbé, Victoria G. Atkinson, Mario Mandalà, Paul Nathan, Ana Maria Arance, Erika Richtig, Naoya Yamazaki, Caroline Robert, Dirk Schadendorf et al. · 2020 · Nature Medicine
Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity
Hugo G. Hilton, Nimrod Daniel Rubinstein, Peter Janki, Andrea T. Ireland, Nicholas Bernstein, Nicole L. Fong, Kevin M. Wright, Megan Smith, David Finkle, Baby Martin-McNulty et al. · 2019 · PLoS Biology
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci
María Gutiérrez‐Arcelus, Yuriy Baglaenko, Jatin Arora, Susan K. Hannes, Yang Luo, Tiffany Amariuta, Nikola C. Teslovich, Deepak A. Rao, Joerg Ermann, Anna Helena Jonsson et al. · 2020 · Nature Genetics
Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential
Bjoern Meyer, Jeanne Chiaravalli, Stacy Gellenoncourt, Philip Brownridge, Dominic P. Bryne, Leonard A. Daly, Arturas Grauslys, Marius Walter, Fabrice Agou, Lisa A. Chakrabarti et al. · 2021 · Nature Communications
Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung
Carla P. Concepcion, Sai Ma, Lindsay M. LaFave, Arjun J. Bhutkar, Manyuan Liu, Lydia P. DeAngelo, Jonathan Y. Kim, Isabella S. Del Priore, Adam Jacob Schoenfeld, Manon Miller et al. · 2021 · Cancer Discovery
Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer
Ruli Gao, Charissa R. Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong‐Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric‐Bernstam, Nicholas E. Navin · 2017 · Nature Communications
Cyclin F Controls Cell-Cycle Transcriptional Outputs by Directing the Degradation of the Three Activator E2Fs
Linda Clijsters, Claire Hoencamp, Jorg J. A. Calis, Antonio Marzio, Shanna M. Handgraaf, Maria C. Cuitiño, Brad R. Rosenberg, Gustavo W. Leone, Michele Pagano · 2019 · Molecular Cell
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles
Zhenjia Wang, Mete Civelek, Clint L. Miller, Nathan C. Sheffield, Michael J. Guertin, Chongzhi Zang · 2018 · Bioinformatics
FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Kirsty Sawicka, Caryn R. Hale, Christopher Y Park, John J. Fak, Jodi E. Gresack, Sarah J. Van Driesche, Jin Joo Kang, Jennifer C. Darnell, Robert B. Darnell · 2019 · eLife
Molecular classification of hormone receptor-positive HER2-negative breast cancer
Xi Jin, Yi-Fan Zhou, Ding Ma, Shen Zhao, Cai‐Jin Lin, Yi Xiao, Tong Fu, Chenglin Liu, Yiyu Chen, Wen-Xuan Xiao et al. · 2023 · Nature Genetics
Phantasus, a web application for visual and interactive gene expression analysis
Maksim Kleverov, Daria Zenkova, Vladislav Kamenev, Margarita Sablina, Maxim N. Artyomov, Alexey Sergushichev · 2024 · eLife
MetSigDis: a manually curated resource for the metabolic signatures of diseases
Liang Cheng, Haixiu Yang, Hengqiang Zhao, Xiaoya Pei, Hongbo Shi, Jie Sun, Yunpeng Zhang, Zhenzhen Wang, Meng Zhou · 2017 · Briefings in Bioinformatics
Tamoxifen Resistance in Breast Cancer Is Regulated by the EZH2–ERα–GREB1 Transcriptional Axis
Yanming Wu, Zhao Zhang, Mauro E. Cenciarini, Cecilia Jazmín Proietti, Matías Amasino, Tao Hong, Mei Yang, Yiji Liao, Huai-Chin Chiang, Virginia Kaklamani et al. · 2017 · Cancer Research
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli Kallioniemi, Tero A. Aittokallio, Samuel Kaski A · 2016 · Bioinformatics
Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
Goutam Chakraborty, Joshua Armenia, Ying Zhang Mazzu, Subhiksha Nandakumar, Konrad Hermann Stopsack, Mohammad Omar Atiq, Kazumasa Komura, Lina E. Jehane, Rahim Hirani, Kalyani Chadalavada et al. · 2019 · Clinical Cancer Research
Clonally expanded, GPR15-expressing pathogenic effector T H 2 cells are associated with eosinophilic esophagitis
Duncan M. Morgan, Bert Ruiter, Neal Patrick Smith, Ang Andy Tu, Brinda Monian, Brandon E. Stone, Navneet Virk Hundal, Qian Yuan, Wayne G. Shreffler, John Christopher Love · 2021 · Science Immunology
Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis
Xiaobo Zheng, Jinen Song, Chune Yu, Zong‐Guang Zhou, Xiaowei Liu, Jing Yu, Guangchao Xu, Jiqiao Yang, Xiujing He, Xin Bai et al. · 2022 · Signal Transduction and Targeted Therapy
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
Aedín C. Culhane, Markus Schröder, Răzvan Sultana, S. C. Picard, Enrico Martinelli, C. Kelly, Benjamin Haibe‐Kains, Misha Kapushesky, A.-A. St Pierre, W. Flahive et al. · 2011 · Nucleic Acids Research
Long-lived T follicular helper cells retain plasticity and help sustain humoral immunity
Marco Künzli, David Schreiner, Tamara C. Pereboom, Nivedya Swarnalekha, Ludivine C. Litzler, Jonas Lötscher, Yusuf I. Ertuna, Julien Roux, Florian M. Geier, Roman Peter Jakob et al. · 2020 · Science Immunology
Efficient Generation of Transcriptomic Profiles by Random Composite Measurements
Cleary, Brian, Cong, Le, Cheung, Anthea, Lander, Eric S., Regev, Aviv · 2017 · Cell
Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism
Aregger, Michael, Lawson, Keith A., Billmann, Maximillian, Costanzo, Michael, Tong, Amy H. Y., Chan, Katherine, Rahman, Mahfuzur, Brown, Kevin R., Ross, Catherine, Usaj, Matej et al. · 2020 · Nature Metabolism
Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data
Ke Liu, Patrick A. Newbury, Benjamin Scott Glicksberg, Billy Zeng, Shreya Paithankar, Eran R. Andrechek, Bin Chen · 2019 · Nature Communications
Crosstalk with lung epithelial cells regulates Sfrp2-mediated latency in breast cancer dissemination
Marco Montagner, Rahul Bhome, Steven Hooper, Probir Chakravarty, Xiao Qin, Jahangir Sufi, Ajay Bhargava, Colin D.H. Ratcliffe, Yutaka Naito, Arianna Pocaterra et al. · 2020 · Nature Cell Biology
The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities
Elif Damla Arısan, D. Alwyn Dart, Guy H. Grant, Serdar Arısan, Songul Cuhadaroglu, Sigrun Lange, Pinar Uysal Onganer · 2020 · Viruses
Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease
Sara Bandrés‐Ciga, Sara Sáez-Atiénzar, Jeff Kim, Mary B. Makarious, Faraz Faghri, Mónica Díez-Fairén, Hirotaka Iwaki, Hampton L. Leonard, Juan Antonio Botía, Mina Ryten et al. · 2020 · Acta Neuropathologica
Telomere Length Dynamics and DNA Damage Responses Associated with Long-Duration Spaceflight
Jared J. Luxton, Miles J. McKenna, Aidan M. Lewis, Lynn E. Taylor, Kerry A. George, Sameer Mani Dixit, Matthew Moniz, Willie Benegas, Matthew J. MacKay, Christopher Mozsary et al. · 2020 · Cell Reports
Bulk and single-cell transcriptome profiling reveal the metabolic heterogeneity in human breast cancers
Tian‐Jian Yu, Ding Ma, Yingying Liu, Yi Xiao, Yue Gong, Yi‐Zhou Jiang, Zhi-Ming Shao, Xin Hu, Gen‐Hong Di · 2021 · Molecular Therapy
An NR2F1-specific agonist suppresses metastasis by inducing cancer cell dormancy
Bassem D. Khalil, Roberto Sánchez, Tasrina Rahman, Carolina Rodríguez-Tirado, Stefan Moritsch, Alba Rodríguez Martínez, Brett A. Miles, Eduardo Farias, Mihaly Mezei, Ana Rita Nobre et al. · 2021 · The Journal of Experimental Medicine
Antigen expression determines adenoviral vaccine potency independent of IFN and STING signaling
Kylie M. Quinn, Daniel E. Zak, Andréia da Silva Costa, Ayako Yamamoto, Kathrin Kastenmüller, Brenna J. Hill, Geoffrey M. Lynn, Patricia A. Darrah, Ross W. B. Lindsay, Lingshu Wang et al. · 2015 · Journal of Clinical Investigation
Transcription factor Foxo1 is essential for IL-9 induction in T helper cells
Sakshi Malik, Srikanth Sadhu, Srikanth Elesela, Ramendra Pati Pandey, Amanpreet Singh Chawla, Deepak Sharma, Lipsa Rani Panda, Deepak Kumar Rathore, Balram Ghosh, Vineet Ahuja et al. · 2017 · Nature Communications
A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions
Elena Grossi, Ivan Raimondi, Enrique Goñi, Jovanna González, Francesco P. Marchese, Vicente Chapaprieta, José Ignacio Martín-Subero, Shuling Guo, Maite Huarte · 2020 · Nature Communications
5‐Fluorouracil efficacy requires anti‐tumor immunity triggered by cancer‐cell‐intrinsic STING
Jingru Tian, Dingyao Zhang, Vadim Kurbatov, Qinrong Wang, Yadong Wang, Dorthy Fang, Lizhen Wu, Marcus Bosenberg, Mandar Deepak Muzumdar, Sajid Ali Khan et al. · 2021 · The EMBO Journal
Heterogeneity of neuroendocrine transcriptional states in metastatic small cell lung cancers and patient-derived models
Delphine Lissa, Nobuyuki Takahashi, Parth Anil Desai, Irena Manukyan, Christopher William Schultz, Vinodh N. Rajapakse, Moises J. Velez, Deborah A. Mulford, Nitin Roper, Samantha Nichols et al. · 2022 · Nature Communications
Leveraging a disulfidptosis-based signature to improve the survival and drug sensitivity of bladder cancer patients
Hualin Chen, Wenjie Yang, Yingjie Li, Lin Ma, Zhigang Ji · 2023 · Frontiers in Immunology
Alterations in PD-L1 succinylation shape anti-tumor immune responses in melanoma
Long Liang, Xinwei Kuang, Yi He, Lin Zhu, Poyee Lau, Xin Li, Dingan Luo, Lan Gong, Wenbin Zhou, Fanglin Zhang et al. · 2025 · Nature Genetics
Genetic inhibition of hepatic acetyl-CoA carboxylase activity increases liver fat and alters global protein acetylation
Jenny D.Y. Chow, Robert Lawrence, Marin E. Healy, John E. Dominy, Jason A. Liao, David S. Breen, Frances L. Byrne, Brandon M. Kenwood, Carolin Lackner, Saeko Okutsu et al. · 2014 · Molecular Metabolism
TGF-β promotes microtube formation in glioblastoma through thrombospondin 1
Justin Vareecal Joseph, Capucine Magaut, Simon Storevik, Luiz Henrique Geraldo, Thomas Mathivet, Abdul Latif, Justine Rudewicz, Joris Guyon, Matteo Gambaretti, Frida Haukås et al. · 2021 · Neuro-Oncology
Modulation of metabolic, inflammatory and fibrotic pathways by semaglutide in metabolic dysfunction-associated steatohepatitis
Maximilian Jara, Jenny Norlin, Mette Skalshøi Kjær, Kasper Almholt, Kristian Moss Bendtsen, Elisabetta Bugianesi, Kenneth J. Cusi, Elisabeth Douglas Galsgaard, Milan S. Geybels, Lise Lotte Gluud et al. · 2025 · Nature Medicine
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
Rahmatallah, Yasir, Emmert-Streib, Frank, Glazko, Galina · 2014 · Bioinformatics
A Unique Morphological Phenotype in Chemoresistant Triple-Negative Breast Cancer Reveals Metabolic Reprogramming and PLIN4 Expression as a Molecular Vulnerability
Sirois, Isabelle, Aguilar-Mahecha, Adriana, Lafleur, Josiane, Fowler, Emma, Vu, Viet, Scriver, Michelle, Buchanan, Marguerite, Chabot, Catherine, Ramanathan, Aparna, Balachandran, Banujan et al. · 2019 · Molecular Cancer Research
RNA sequencing of microglia and monocyte-derived macrophages from mice with experimental autoimmune encephalomyelitis illustrates a changing phenotype with disease course
Nuruddeen D. Lewis, Jonathan D. Hill, Kathryn W. Juchem, Dimitria E. Stefanopoulos, Louise Kelly Modis · 2014 · Journal of Neuroimmunology
Predicting and affecting response to cancer therapy based on pathway-level biomarkers
Rotem Ben‐Hamo, Adi Jacob Berger, Nancy S. Gavert, Mendy L. Miller, Guy Pines, Roni Oren, Eli Pikarsky, Cyril H. Benes, Tzahi Neuman, Yaara Zwang et al. · 2020 · Nature Communications
Long-term platinum-based drug accumulation in cancer-associated fibroblasts promotes colorectal cancer progression and resistance to therapy
Linares, Jenniffer, Sallent-Aragay, Anna, Badia-Ramentol, Jordi, Recort-Bascuas, Alba, Méndez, Ana, Manero-Rupérez, Noemí, Re, Daniele Lo, Rivas, Elisa I., Guiu, Marc, Zwick, Melissa et al. · 2023 · Nature Communications
FGFR4 regulates tumor subtype differentiation in luminal breast cancer and metastatic disease
Susana García‐Recio, Aatish Thennavan, Michael P. East, Joel S. Parker, Juan Miguel Cejalvo, Joseph P. Garay, Daniel P. Hollern, Xiaping He, Kevin Raynard Mott, Patricia Galván et al. · 2020 · Journal of Clinical Investigation
5mC regulator-mediated molecular subtypes depict the hallmarks of the tumor microenvironment and guide precision medicine in bladder cancer
Jiao Hu, Belaydi Othmane, Anze Yu, Huihuang Li, Zhiyong Cai, Xu Chen, Wenbiao Ren, Jinbo Chen, Xiongbing Zu · 2021 · BMC Medicine
Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection
Tania Wong Fok Lung, Daniel Charytonowicz, Kristin G. Beaumont, Shivang S. Shah, Shwetha Hara Sridhar, Claire L. Gorrie, Andre Mu, Casey E. Hofstaedter, David J. Varisco, Thomas Howe McConville et al. · 2022 · Cell Metabolism
A pairwise cytokine code explains the organism-wide response to sepsis
Michihiro Takahama, Ashwini Patil, Katherine Johnson, Denis Cipurko, Yoshimi Miki, Yoshitaka Taketomi, Peter S. Carbonetto, Madison Plaster, Gabriella Richey, Surya Pandey et al. · 2024 · Nature Immunology
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Emily R. Miraldi, Maria V. Pokrovskii, Aaron Watters, Dayanne M. Castro, Nicholas De Veaux, Jason A. Hall, June‐Yong Lee, Maria Ciofani, Aviv Madar, Nick Carriero et al. · 2019 · Genome Research
Machine learning approaches for drug combination therapies
Betül Güvenç Paltun, Samuel Kaski A, Hiroshi Mamitsuka · 2021 · Briefings in Bioinformatics
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer
Mary L. Stackpole, Weihua Zeng, Shuo Li, Chun-Chi Liu, Yonggang Zhou, Shanshan He, Angela Yeh, Ziye Wang, Fengzhu Sun, Qingjiao Li et al. · 2022 · Nature Communications
Pharmacologic IRE1/XBP1s activation promotes systemic adaptive remodeling in obesity
Aparajita Madhavan, Bernard P. Kok, Bibiana Rius, Julia M. D. Grandjean, Adekunle Alabi, Verena Albert, Ara Sukiasyan, Evan T. Powers, Andrea Galmozzi, Enrique Sáez et al. · 2022 · Nature Communications
MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences
Alberto L’Abbate, Doron Tolomeo, Ingrid Cifola, Marco Severgnini, Antonella Turchiano, Bartolomeo Augello, Gabriella Maria Squeo, Pietro D’Addabbo, Debora Traversa, Giulia Daniele et al. · 2018 · Leukemia
ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma
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Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor
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JUN is a key transcriptional regulator of the unfolded protein response in acute myeloid leukemia
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Sensitivity to PI3K and AKT inhibitors is mediated by divergent molecular mechanisms in subtypes of DLBCL
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