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 501–600 of 1,039

Refinement of breast cancer molecular classification by miRNA expression profiles
Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén et al. · 2019 · BMC Genomics
Genetics of common cerebral small vessel disease
Constance Bordes, Muralidharan Sargurupremraj, Aniket Mishra, Stéphanie Debette · 2022 · Nature Reviews Neurology
Electrically Conductive Collagen‐PEDOT:PSS Hydrogel Prevents Post‐Infarct Cardiac Arrhythmia and Supports hiPSC‐Cardiomyocyte Function
Kaveh Roshanbinfar, Miriam Schiffer, E. Carls, Miriam Angeloni, Maria M. Koleśnik-Gray, Stefan Schrüfer, Dirk Wolfram Schubert, Fulvia Ferrazzi, Vojislav Krstić, Bernd K. Fleischmann et al. · 2024 · Advanced Materials
Hepatitis C Virus-Induced Upregulation of MicroRNA miR-146a-5p in Hepatocytes Promotes Viral Infection and Deregulates Metabolic Pathways Associated with Liver Disease Pathogenesis
Simonetta Bandiera, Sophie Pernot, Hussein El Saghire, Sarah Durand, Christine Thumann, Émilie Crouchet, Tao Ye, Isabel Fofana, Marine A. Oudot, Jochen Barths et al. · 2016 · Journal of Virology
PAX7 target genes are globally repressed in facioscapulohumeral muscular dystrophy skeletal muscle
Christopher R. S. Banerji, Maryna Panamarova, Husam Hebaishi, Robert B. White, Frédéric Relaix, Simone Severini B, Peter S. Zammit · 2017 · Nature Communications
Low-Dose Vertical Inhibition of the RAF-MEK-ERK Cascade Causes Apoptotic Death of KRAS Mutant Cancers
Irem Ozkan‐Dagliyan, J. Nathaniel Diehl, Samuel D. George, Antje Schaefer, Bjoern Papke, Kathleen Klotz‐Noack, Andrew M. Waters, Craig M. Goodwin, Prson Gautam, Mariaelena Pierobon et al. · 2020 · Cell Reports
Computational drug repurposing: approaches, evaluation of in silico resources and case studies
Ziaurrehman Tanoli, Adrià Fernández‐Torras, Umut Onur Özcan, Aleksandr Kushnir, Kristen Michelle Nader, Yojana Gadiya, Laura Fiorenza, Aleksandr Ianevski, Markus J. V. Vähä-Koskela, Mitro Miihkinen et al. · 2025 · Nature Reviews Drug Discovery
Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
Tsai, Yihsuan S., Woodcock, Mark G., Azam, Salma H., Thorne, Leigh B., Kanchi, Krishna L., Parker, Joel S., Vincent, Benjamin G., Pecot, Chad V. · 2022 · Journal of Clinical Investigation
MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer
Juan Xu, Tingting Shao, Mingxu Song, Yunjin Xie, Jialiang Zhou, Jiaqi Yin, Na Ding, Haozhe Zou, Yongsheng Li, Jiwei Zhang · 2020 · Molecular Cancer
Combined inhibition of Aurora-A and ATR kinases results in regression of MYCN-amplified neuroblastoma
Isabelle Röschert, Evon Poon, Anton George Henssen, Heathcliff Dorado García, Marco Gatti, Celeste Giansanti, Yann Jamin, Carsten Patrick Ade, Peter Gallant, Christina Schülein‐Völk et al. · 2021 · Nature Cancer
Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins
Milagros Pereira Luppi, Maite Azcorra, Giuliana Caronia, Jean-Francois Poulin, Zachary A. Gaertner, Serafin Gatica, Oscar Andrés Moreno-Ramos, Navid Nouri, Marilyn Dubois, Yongchao C. Ma et al. · 2021 · Cell Reports
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
Stephanie Y. Yang, Christina A. Castellani, Ryan J. Longchamps, Vamsee Pillalamarri, Brian P O'Rourke, Eliseo Güallar, Dan E. Arking · 2021 · Genome Research
Protein signatures of centenarians and their offspring suggest centenarians age slower than other humans
Sebastiani, Paola, Federico, Anthony, Morris, Melody, Gurinovich, Anastasia, Tanaka, Toshiko, Chandler, Kevin B., Andersen, Stacy L., Denis, Gerald, Costello, Catherine E., Ferrucci, Luigi et al. · 2021 · Aging Cell
DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts
Goyal, Ashish, Bauer, Jens, Hey, Joschka, Papageorgiou, Dimitris N., Stepanova, Ekaterina, Daskalakis, Michael, Scheid, Jonas, Dubbelaar, Marissa, Klimovich, Boris, Schwarz, Dominic et al. · 2023 · Nature Communications
NFATc1 Links EGFR Signaling to Induction of Sox9 Transcription and Acinar–Ductal Transdifferentiation in the Pancreas
NM Chen, Garima Singh, Alexander Otto König, Geou‐Yarh Liou, Peter Störz, Jin‐San Zhang, Lisanne Regul, Sankari Nagarajan, Benjamin Kühnemuth, Steven A. Johnsen et al. · 2015 · Gastroenterology
Gene set selection via LASSO penalized regression (SLPR)
Hildreth Robert Frost, Christopher Ian Amos · 2017 · Nucleic Acids Research
Plant Regulomics: a data‐driven interface for retrieving upstream regulators from plant multi‐omics data
Xiaojuan Ran, Fei Zhao, Yuejun Jessie Wang, Jian Liu, Yili Zhuang, Luhuan Ye, Meifang Qi, Jingfei Cheng, Yijing Zhang · 2019 · The Plant Journal
A Transcriptional and Metabolic Signature of Primary Aneuploidy Is Present in Chromosomally Unstable Cancer Cells and Informs Clinical Prognosis
Jason M. Sheltzer · 2013 · Cancer Research
Scalable genetic screening for regulatory circuits using compressed Perturb-seq
Yao, Douglas, Binan, Loic, Bezney, Jon, Simonton, Brooke, Freedman, Jahanara, Frangieh, Chris J., Dey, Kushal, Geiger-Schuller, Kathryn, Eraslan, Basak, Gusev, Alexander et al. · 2024 · Nature Biotechnology
Evidence for widespread dysregulation of circadian clock progression in human cancer
Jarrod Shilts, Guanhua Chen, Jacob Hughey · 2018 · PeerJ
Addressing confounding artifacts in reconstruction of gene co-expression networks
Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis J. Battle, Jeffrey T. Leek · 2019 · Genome biology
Transcriptome meta-analysis reveals differences of immune profile between eutopic endometrium from stage I-II and III-IV endometriosis independently of hormonal milieu
Omero Benedicto Poli‐Neto, Juliana Meola, Júlio César Rosa e Silva, Daniel Guimarães Tiezzi · 2020 · Scientific Reports
B cell receptor signaling in germinal centers prolongs survival and primes B cells for selection
Spencer T. Chen, Thiago Y. Oliveira, Anna Gazumyan, Melissa Cipolla, Michel C. Nussenzweig · 2023 · Immunity
Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities
Yi‐Zhou Jiang, Ding Ma, Xi Jin, Yi Xiao, Ying Yu, Jinxiu Shi, Yi-Fan Zhou, Tong Fu, Cai‐Jin Lin, Lei-Jie Dai et al. · 2024 · Nature Cancer
Biologically informed deep learning to query gene programs in single-cell atlases
Lotfollahi, Mohammad, Rybakov, Sergei, Hrovatin, Karin, Hediyeh-zadeh, Soroor, Talavera-López, Carlos, Misharin, Alexander V., Theis, Fabian J. · 2023 · Nature Cell Biology
Domestic dog lineages reveal genetic drivers of behavioral diversification
Emily V. Dutrow, James A. Serpell, Elaine A. Ostrander · 2022 · Cell
Pan-cancer proteogenomics characterization of tumor immunity
Francesca Petralia, Weiping Ma, Tomer M. Yaron, Francesca Pia Caruso, Nicole L. Tignor, Joshua M. Wang, Daniel Charytonowicz, Jared Lee Johnson, Emily M. Huntsman, Giacomo B. Marino et al. · 2024 · Cell
Nicotinamide metabolism face-off between macrophages and fibroblasts manipulates the microenvironment in gastric cancer
Yu Jiang, Yawen Wang, Guofeng Chen, Fei Sun, Qijing Wu, Qiong Huang, Dongqiang Zeng, Wenjun Qiu, Jiao Wang, Zhiqi Yao et al. · 2024 · Cell Metabolism
Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response
Xabier Agirre, Cem Meydan, Yanwen Jiang, Leire Gárate, Ashley S. Doane, Zhuoning Li, Akanksha Verma, Bruno Paiva, José Ignacio Martín-Subero, Olivier Elemento et al. · 2019 · Nature Communications
HDAC Inhibition Enhances the In Vivo Efficacy of MEK Inhibitor Therapy in Uveal Melanoma
Fernanda Faião‐Flores, Michael F. Emmons, Michael A. Durante, Fumi Kinose, Biswarup Saha, Bin Fang, John M. Koomen, Srikumar Chellappan, Silvya Stuchi Maria–Engler, Uwe Rix et al. · 2019 · Clinical Cancer Research
LncRNA-MTA2TR functions as a promoter in pancreatic cancer via driving deacetylation-dependent accumulation of HIF-1α
Zhu Zeng, Fengyu Xu, Hai Zheng, Ping Chen, Qingyong Chen, Ye Zeng, Jianxin Zhong, Shi-Jiang Deng, Mingliang Liu, Kang Huang et al. · 2019 · Theranostics
Genetic analysis of right heart structure and function in 40,000 people
James P. Pirruccello, Paolo Di Achille, Victor Nauffal, Mahan Nekoui, Sam Freesun Friedman, Marcus D. R. Klarqvist, Mark D. Chaffin, Lu-Chen C Weng, Jonathan W. Cunningham, Shaan S. Khurshid et al. · 2022 · Nature Genetics
Supervised discovery of interpretable gene programs from single-cell data
Russell Kunes, Thomas Walle, Max Land, Tal Nawy, Dana Pe’er · 2023 · Nature Biotechnology
Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer
Inga-Maria P. Launonen, Iga Niemiec, María Mercedes Hincapié-Otero, Erdoğan Pekcan Erkan, Ada Junquera, Daria Afenteva, Matías Marín Falco, Zhihan Liang, Matilda Salko, Foteini Chamchougia et al. · 2024 · Cancer Cell
Enterococcus faecalis Infection Causes Inflammation, Intracellular Oxphos-Independent ROS Production, and DNA Damage in Human Gastric Cancer Cells
Jesper A.B. Strickertsson, Claus Desler, Tomas Martin-Bertelsen, Ana Manuel Dantas Machado, Torkel Wadström, Ole Winther, Lene Juel Rasmussen, Lennart Jan Friis-Hansen · 2013 · PLoS ONE
Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease
Vasanthakumar, Aparna, Davis, Justin W., Idler, Kenneth, Waring, Jeffrey F., Asque, Elizabeth, Riley-Gillis, Bridget, Grosskurth, Shaun, Srivastava, Gyan, Kim, Sungeun, Nho, Kwangsik et al. · 2020 · Clinical Epigenetics
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration
Noori, Ayush, Mezlini, Aziz M., Hyman, Bradley T., Serrano-Pozo, Alberto, Das, Sudeshna · 2021 · Neurobiology of Disease
Building towards precision medicine: empowering medical professionals for the next revolution
Scott McGrath, Dario Ghersi · 2016 · BMC Medical Genomics
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization
Hisashi Miura, Saori Takahashi, Rawin Poonperm, Akie Tanigawa, Shin‐ichiro Takebayashi, Ichiro Hiratani · 2019 · Nature Genetics
Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-γ in NK cells
Edy Yong Kim, Hadas Ner‐Gaon, Jack Varon, Aidan M. Cullen, Jingyu Guo, Jiyoung Elizabeth Choi, Diana Barragan-Bradford, Angelica Higuera, Mayra Pinilla-Vera, Samuel Short et al. · 2020 · Journal of Clinical Investigation
Circulating immune cell phenotype dynamics reflect the strength of tumor–immune cell interactions in patients during immunotherapy
Jason I. Griffiths, Pierre Wallet, Lance T. Pflieger, David Dean Stenehjem, Xuan Liu, Patrick A. Cosgrove, Neena A. Leggett, Jasmine A. McQuerry, Gajendra Shrestha, Maura Maria Rossetti et al. · 2020 · Proceedings of the National Academy of Sciences
GeneAgent: self-verification language agent for gene-set analysis using domain databases
Zhizheng Wang, Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po‐Ting Lai, Qingqing Zhu, Chi‐Ping Day, Christina Ross, Robert Leaman, Zhiyong Lu · 2025 · Nature Methods
Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing
Wang, Li, Sfakianos, John P., Beaumont, Kristin G., Akturk, Guray, Horowitz, Amir, Sebra, Robert P., Farkas, Adam M., Gnjatic, Sacha, Hake, Austin, Izadmehr, Sudeh et al. · 2021 · Clinical Cancer Research
IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation
Park, Sun-Mi, Cho, Hyunwoo, Thornton, Angela M., Barlowe, Trevor S., Chou, Timothy, Chhangawala, Sagar, Fairchild, Lauren, Taggart, James, Chow, Arthur, Schurer, Alexandria et al. · 2019 · Cell Stem Cell
LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
Jordan M. Singer, Jacob Hughey · 2018 · Journal of Biological Rhythms
PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein–protein interaction network
Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Chen Tang, Xiaohan Chen, Yunjie Li, Qi Liu, Qin Liu · 2021 · Briefings in Bioinformatics
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer
Antti Kiviaho, Sini K. Eerola, Heini M. L. Kallio, Maria K. Andersen, Miina Hoikka, Aliisa M. Tiihonen, Iida Salonen, Xander Spotbeen, Alexander Giesen, Charles T. A. Parker et al. · 2024 · Nature Communications
BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses
Lionel Spinelli, Sabrina Carpentier, Frédéric Montañana-Sanchis, Marc Dalod, Thien‐Phong Vu Manh · 2015 · BMC Genomics
Exploring the genetic overlap between twelve psychiatric disorders
Cato Romero, Josefin Werme, Philip R. Jansen, Joel E. Gelernter, Murray B. Stein, Daniel F. Levey, Renato A Polimanti, VA Million Veteran Program, Christiaan de Leeuw, Danielle Posthuma et al. · 2022 · Nature Genetics
Distinct tumor architectures and microenvironments for the initiation of breast cancer metastasis in the brain
Siting Gan, Danilo G. Macalinao, Sayyed Hamed Shahoei, Lin Hai Tian, Xin Jin, Harihar Basnet, Catherine Bibby, James Muller, Pranita Atri, Evan Seffar et al. · 2024 · Cancer Cell
MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway
Bilal N. Sheikh, Belinda Phipson, Farrah El-Saafin, Hannah Kate Vanyai, Natalie L. Downer, Matthew Bird, Andrew J. Kueh, Rose E. May, Gordon K. Smyth, Anne Kathrin Voss et al. · 2015 · Oncogene
Obesity-Associated Extracellular Matrix Remodeling Promotes a Macrophage Phenotype Similar to Tumor-Associated Macrophages
Nora L. Springer, Neil M. Iyengar, Rohan Bareja, Akanksha Verma, Maxine S. Jochelson, Dilip D. Giri, Xi Kathy Zhou, Olivier Elemento, Andrew J. Dannenberg, Claudia Fischbach · 2019 · American Journal Of Pathology
BAP1 regulates epigenetic switch from pluripotency to differentiation in developmental lineages giving rise to BAP1-mutant cancers
Jeffim N. Kuznetsov, Tristan H. Aguero, Dawn A. Owens, Stefan Kurtenbach, Matthew G. Field, Michael A. Durante, Daniel A. Rodriguez, Mary Lou King, J. William Harbour · 2019 · Science Advances
Intestinal microbes influence development of thymic lymphocytes in early life
Maria Ennamorati, Chithirachelvi Vasudevan, Kara Clerkin, Stefan C. Halvorsen, Smriti Verma, Samira Ibrahim, Shaniah Prosper, Caryn L. Porter, Vladimir Yeliseyev, Margot Kim et al. · 2020 · Proceedings of the National Academy of Sciences
Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types
Sara Sáez-Atiénzar, Sara Bandrés‐Ciga, Rebekah G. Langston, Jonggeol Jeffrey Kim, Shing Wan Choi, Regina Hertfelder Reynolds, ITALSGEN, Yevgeniya A. Abramzon, Ramita Dewan, Sarah Ahmed et al. · 2021 · Science Advances
Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review
Xue Yang, Kexin Huang, Dewei Yang, Weiling Zhao, Xiaobo Zhou · 2023 · Global Challenges
The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer
Jiacheng He, Xiaolei Chai, Qiansen Zhang, Yang Wang, Yijie Wang, Xinyu Yang, Jingbo Wu, Bo Feng, Jing Ping Sun, Weiwei Rui et al. · 2025 · Nature Immunology
Profilin-1 phosphorylation directs angiocrine expression and glioblastoma progression through HIF-1α accumulation
Yi Fan, Alka A. Potdar, Yanqing Gong, Sandeepa M. Eswarappa, Shannon B. Donnola, Justin Durla Lathia, Dolores Hambardzumyan, Jeremy N. Rich, Paul L. Fox · 2014 · Nature Cell Biology
Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction
Dokyoon Kim, Je‐Gun Joung, Kyung-Ah Sohn, Hyunjung Shin, Yu Rang Park, Marylyn DeRiggi Ritchie, Ju Han Kim · 2014 · Journal of the American Medical Informatics Association
Haemopedia: An Expression Atlas of Murine Hematopoietic Cells
Carolyn A. de Graaf, Jarny Choi, Tracey M. Baldwin, Jessica E. Bolden, Kirsten A. Fairfax, Aaron J. Robinson, Christine Biben, Clare Morgan, Kerry A Ramsay, Ashley P. Ng et al. · 2016 · Stem Cell Reports
Identification of genomic alterations in nasopharyngeal carcinoma and nasopharyngeal carcinoma-derived Epstein–Barr virus by whole-genome sequencing
Chaofeng Tu, Zhaoyang Zeng, Peng Qi, Xiayu Li, Can Jie Guo, Fang Xiong, Bo Xiang, Ming Zhou, Qianjin Liao, Jianjun Yu et al. · 2018 · Carcinogenesis
Immunogenomic Landscape Contributes to Hyperprogressive Disease after Anti-PD-1 Immunotherapy for Cancer
Donghai Xiong, Yian Wang, Arun K. Singavi, Alexander Craig Mackinnon, Ben George, Ming You · 2018 · iScience
Serial single-cell genomics reveals convergent subclonal evolution of resistance as patients with early-stage breast cancer progress on endocrine plus CDK4/6 therapy
Jason I. Griffiths, Jinfeng Chen, Patrick A. Cosgrove, Anne P. O’Dea, Priyanka Sharma, Cynthia X. Ma, Meghna S. Trivedi, Kevin M. Kalinsky, Kari Braun Wisinski, Ruth M O'Regan et al. · 2021 · Nature Cancer
A growth factor–expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15
Andreas Patsalos, László Halász, Miguel A. Medina-Serpas, Wilhelm K. Berger, Bence Dániel, Petros Tzerpos, Máté Kiss, Gergely Nagy, Cornelius Fischer, Zoltán Simándi et al. · 2021 · The Journal of Experimental Medicine
Decoding the multicellular ecosystem of vena caval tumor thrombus in clear cell renal cell carcinoma by single-cell RNA sequencing
Yue Xi Shi, Qi Zhang, Hai Bi, Min Lu, Yezhen Tan, Daojia Zou, Liyuan Ge, Zhigang Chen, Cheng Liu, Weimin Ci et al. · 2022 · Genome biology
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma
Andrew C. Nelson, Nischalan Pillay, Stephen R Henderson, Nadège Presneau, Roberto Tirabosco, Dina Halai, Fitim Berisha, Paul Flicek, Derek L. Stemple, Claudio D. Stern et al. · 2012 · The Journal of Pathology
Correction to: Identification of key biomarkers and immune infiltration in systemic lupus erythematosus by integrated bioinformatics analysis
Xingwang Zhao, Longlong Zhang, Juan Wang, Min Zhang, Zhiqiang Song, Bing Ni, Yi You · 2021 · Journal of Translational Medicine
Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling
Marja Driessen, Anne S. Kienhuis, Jeroen L. A. Pennings, Tessa E. Pronk, Evert‐Jan van den Brandhof, Marianne Roodbergen, Herman P. Spaink, Bob van de Water, Leo T.M. van der Ven · 2013 · Archives of Toxicology
DNA damage repair alterations modulate M2 polarization of microglia to remodel the tumor microenvironment via the p53-mediated MDK expression in glioma
Xiangqi Meng, Chunbin Duan, Hengyuan Pang, Qun Chen, Bo Ram Han, Caijun Zha, Magafurov Dinislam, Pengfei Wu, Ziwei Li, Shihong Zhao et al. · 2019 · EBioMedicine
Cancer-associated fibroblasts undergoing neoadjuvant chemotherapy suppress rectal cancer revealed by single-cell and spatial transcriptomics
Pengfei Qin, Huaxian Chen, Yuhang Wang, Liang Huang, Ke Huang, Guozhong Xiao, Changpeng Han, Jiancong Hu, Dezheng Lin, Xingyang Wan et al. · 2023 · Cell Reports Medicine
METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation
Meilin Xue, Lei Dong, Honghai Zhang, Yangchan Li, Kangqiang Qiu, Zhicong Zhao, Min Gao, Li Han, Anthony Chan, Wei Li et al. · 2024 · Journal of Hematology & Oncology
Essential role of IRF4 and MYC signaling for survival of anaplastic large cell lymphoma
André Weilemann, Michael Grau, Tabea Erdmann, Olaf Merkel, Ulduz Sobhiafshar, Ioannis Anagnostopoulos, Michael Hummel, Antje Siegert, Claudia Hayford, Hannelore Madle et al. · 2014 · Blood
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals
Wynn K. Meyer, Jerrica M. Jamison, Rebecca J. Richter, Stacy E. Woods, Raghavendran Partha, Amanda M. Kowalczyk, Charles Kronk, Maria D. Chikina, Robert K. Bonde, Daniel E. Crocker et al. · 2018 · Science
Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Verónica Jiménez Jacinto, Alejandro Sánchez‐Flores, Leticia Vega‐Alvarado · 2019 · Frontiers in Genetics
Pan-mammalian analysis of molecular constraints underlying extended lifespan
Kowalczyk, Amanda, Partha, Raghavendran, Clark, Nathan L, Chikina, Maria · 2020 · eLife
Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color
Mark J. Simcoe, Ana Maria Valdes, Fan Liu, Nicholas A. Furlotte, David M. Evans, Gibran Hemani, Susan M. Ring, George Davey Smith, David L. Duffy, Gu Zhu et al. · 2021 · Science Advances
Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer
Shrabanti Chowdhury, Jacob J. Kennedy, Richard G. Ivey, Oscar D. Murillo, Noshad Hosseini, Xiaoyu Song, Francesca Petralia, Anna Pamela Calinawan, Sara R. Savage, Anna Belinda Berry et al. · 2023 · Cell
Functional Reprogramming of Neutrophils within the Brain Tumor Microenvironment by Hypoxia-Driven Histone Lactylation
Alessio Ugolini, Alessandra De Leo, Xiaoqing Yu, Fabio Scirocchi, Xiaoxian Liu, Bárbara Peixoto, Delia Scocozza, Angelica Pace, Michela Perego, Alessandro Gardini et al. · 2025 · Cancer Discovery
Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma
Jain, Michael D., Ziccheddu, Bachisio, Coughlin, Caroline A., Faramand, Rawan, Griswold, Anthony J., Reid, Kayla M., Menges, Meghan, Zhang, Yonghong, Cen, Ling, Wang, Xuefeng et al. · 2022 · Blood
Methylation and transcription patterns are distinct in IDH mutant gliomas compared to other IDH mutant cancers
Dusten J. Unruh, Makda Getachew Zewde, Adam Buss, Michael R. Drumm, Anh Nhat Tran, Denise M. Scholtens, Craig Horbinski · 2019 · Scientific Reports
Stable gene expression for normalisation and single-sample scoring
Dharmesh Dinesh Bhuva, Joseph Cursons, Melissa J. Davis · 2020 · Nucleic Acids Research
Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank
Keira J.A. Johnston, Joey Ward, Pradipta R. Ray, Mark J. Adams, Andrew Mark McIntosh, Blair H. Smith, Rona J. Strawbridge, Theodore John Price, Daniel J. Smıth, Barbara I. Nicholl et al. · 2021 · PLoS Genetics
Genetic Association Between Schizophrenia and Cortical Brain Surface Area and Thickness
Weiqiu Cheng, Oleksandr Frei, Dennis van der Meer, Yunpeng Wang, Kevin Sean O’Connell, Yunhan Chu, Shahram Bahrami, Alexey A. Shadrin, Dag Alnæs, Guy Hindley et al. · 2021 · JAMA Psychiatry
A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans
Anoma Nellore, Esther Zumaquero, Christopher D. Scharer, Christopher Fucile, Christopher M. Tipton, Rodney Glenn King, Mi Tian, Betty J. Mousseau, John Bradley, Fen Zhou et al. · 2023 · Immunity
scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration
Xiuhui Yang, Koren Kathleen Mann, Hao Wu, Jun Ding · 2024 · Genome biology
The tumor virus landscape of AIDS-related lymphomas
Aaron J. Arvey, Akinyemi I. Ojesina, Chandra Sekhar Pedamallu, Gianna Ballon, Joonil Jung, Fujiko F. Duke, Lorenzo Leoncini, Giulia De Falco, Eric Bressman, Wayne Tam et al. · 2015 · Blood
A Practical Guide To Filtering and Prioritizing Genetic Variants
Mahjoubeh Jalali Sefid Dashti, Junaid Gamieldien · 2017 · BioTechniques
Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma
Petri Pölönen, Ashik Jawahar Deen, Hanna M. Leinonen, Henna-Kaisa Jyrkkänen, Suvi Linna-Kuosmanen, Mimmi Mononen, Ashish Jain, Tomi Tuomainen, Sanna Pasonen‐Seppänen, Jaana M. Hartikainen et al. · 2019 · Oncogene
Six-gene signature for predicting survival in patients with head and neck squamous cell carcinoma
Juncheng Wang, Xun Chen, Yuxi Tian, Gangcai Zhu, Yuexiang Qin, Xuan Chen, Leiming Pi, Ming Wei, Guancheng Liu, Zhexuan Li et al. · 2020 · Aging
IGLV3-21R110 identifies an aggressive biological subtype of chronic lymphocytic leukemia with intermediate epigenetics
Ferran Nadeu, Romina Royo, Guillem Clot, Martí Duran‐Ferrer, Alba Navarro, Silvia Martín, Junyan Lu, Thorsten Zenz, Tycho Baumann, Pedro Jares et al. · 2020 · Blood
Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation
Àlvaro Quintanal-Villalonga, Hirokazu Taniguchi, Yingqian Ada Zhan, Maysun Hasan, Shweta S. Chavan, Fanli Meng, Fathema Z. Uddin, Viola Allaj, Parvathy Manoj, Nisargbhai Shah et al. · 2021 · Journal of Hematology & Oncology
Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma
Linsong Tang, Rongli Wei, Ronggao Chen, Guanghan Fan, Junbin Zhou, Zhetuo Qi, Kai Wang, Qiang Wei, Xuyong Wei, Xiao Xu · 2022 · Computational and Structural Biotechnology Journal
Respiratory viral infections awaken metastatic breast cancer cells in lungs
Shi B. Chia, Bryan J. Johnson, Junxiao Hu, Felipe Valença-Pereira, Marc Chadeau‐Hyam, Fernando Guntoro, Hugh Montgomery, Meher P. Boorgula, Varsha Sreekanth, Andrew E. Goodspeed et al. · 2025 · Nature
A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations
Tao Xie, Giovanni d’ Ario, John R. Lamb, Eric S. Martin, Kai Wang, Sabine Tejpar, Mauro Delorenzi, Fred T. Bosman, Arnaud D. Roth, Pu Yan et al. · 2012 · PLoS ONE
Alzheimer’s disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model
Carling, Gillian K., Fan, Li, Foxe, Nessa R., Norman, Kendra, Wong, Man Ying, Zhu, Daphne, Corona, Carlo, Razzoli, Agnese, Yu, Fangmin, Yarahmady, Allan et al. · 2024 · Neuron
Transcriptome sequencing in Sézary syndrome identifies Sézary cell and mycosis fungoides-associated lncRNAs and novel transcripts
Carolyn S. Lee, Alexander Ungewickell, Aparna Bhaduri, Kun Qu, Dan E. Webster, Randall J. Armstrong, Wen‐Kai Weng, Cody J. Aros, Angela Mah, Richard Chen et al. · 2012 · Blood
PRMT5 is essential for B cell development and germinal center dynamics
Ludivine C. Litzler, Astrid Zahn, Alexandre P. Meli, Steven Hébert, Anne‐Marie Patenaude, Stephen P. Methot, Adrien Sprumont, Thérence Bois, Daisuke Kitamura, Santiago Costantino et al. · 2018 · Nature Communications
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination
Quan Xu, Γεώργιος Γεωργίου, Siebren Frölich, Maarten van der Sande, Gert Jan C. Veenstra, Huiqing Zhou, Simon J. van Heeringen · 2021 · Nucleic Acids Research
Extracellular vesicles released by human retinal pigment epithelium mediate increased polarised secretion of drusen proteins in response to AMD stressors
Miguel Flores‐Bellver, Jason Mighty, Silvia Aparicio‐Domingo, Kang V. Li, Cui Shi, Jing Zhou, Hannah Cobb, Patrick S. McGrath, Germán Michelis, Patricia Lenhart et al. · 2021 · Journal of Extracellular Vesicles
Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma
Katie Marie Campbell, Meelad Amouzgar, Shannon M. Pfeiffer, Timothy R. Howes, Egmidio Medina, Michael Travers, Gabriela Steiner, Jeffrey S. Weber, Jedd D. Wolchok, James Larkin et al. · 2023 · Cancer Cell