Works by Ma'ayan, Avi

Results: 107

Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells.

Published in:

Aging Cell, 2023, v. 22, n. 6, p. 1, doi. 10.1111/acel.13809

By:

Deng, Eden Z.;
Fleishman, Reid H.;
Xie, Zhuorui;
Marino, Giacomo B.;
Clarke, Daniel J. B.;
Ma'ayan, Avi

Publication type:

Article

Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses.

Published in:

Aging Cell, 2022, v. 21, n. 10, p. 1, doi. 10.1111/acel.13665

By:

Jenkins, Edmund Charles;
Chattopadhyay, Mrittika;
Gomez, Maria;
Torre, Denis;
Ma'ayan, Avi;
Torres‐Martin, Miguel;
Sia, Daniela;
Germain, Doris

Publication type:

Article

Programming a Ferroptosis‐to‐Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy.

Published in:

Advanced Science, 2024, v. 11, n. 17, p. 1, doi. 10.1002/advs.202307263

By:

Vinik, Yaron;
Maimon, Avi;
Dubey, Vinay;
Raj, Harsha;
Abramovitch, Ifat;
Malitsky, Sergey;
Itkin, Maxim;
Ma'ayan, Avi;
Westermann, Frank;
Gottlieb, Eyal;
Ruppin, Eytan;
Lev, Sima

Publication type:

Article

Programming a Ferroptosis‐to‐Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy (Adv. Sci. 17/2024).

Published in:

Advanced Science, 2024, v. 11, n. 17, p. 1, doi. 10.1002/advs.202470098

By:

Vinik, Yaron;
Maimon, Avi;
Dubey, Vinay;
Raj, Harsha;
Abramovitch, Ifat;
Malitsky, Sergey;
Itkin, Maxim;
Ma'ayan, Avi;
Westermann, Frank;
Gottlieb, Eyal;
Ruppin, Eytan;
Lev, Sima

Publication type:

Article

Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing.

Published in:

Experimental Dermatology, 2022, v. 31, n. 3, p. 420, doi. 10.1111/exd.14481

By:

Onoufriadis, Alexandros;
Proudfoot, Laura E.;
Ainali, Chrysanthi;
Torre, Denis;
Papanikolaou, Maria;
Rayinda, Tuntas;
Rashidghamat, Ellie;
Danarti, Retno;
Mellerio, Jemima E.;
Ma'ayan, Avi;
McGrath, John A.

Publication type:

Article

Interconnected Network Motifs Control Podocyte Morphology and Kidney Function.

Published in:

Science Signaling, 2014, v. 7, n. 311, p. 1, doi. 10.1126/scisignal.2004621

By:

Azeloglu, Evren U.;
Hardy, Simon V.;
Eungdamrong, Narat John;
Yibang Chen;
Jayaraman, Gomathi;
Chuang, Peter Y.;
Wei Fang;
Huabao Xiong;
Neves, Susana R.;
Jain, Mohit R.;
Hong Li;
Ma'ayan, Avi;
Gordon, Ronald E.;
Cijiang He, John;
Iyengar, Ravi

Publication type:

Article

Introduction to Network Analysis in Systems Biology.

Published in:

Science Signaling, 2011, v. 4, n. 190, p. 1, doi. 10.1126/scisignal.2001965

By:

Ma'ayan, Avi

Publication type:

Article

Introduction to Statistical Methods for Analyzing Large Data Sets: Gene-Set Enrichment Analysis.

Published in:

Science Signaling, 2011, v. 4, n. 190, p. 1, doi. 10.1126/scisignal.2001966

By:

Clark, Neil R.;
Ma'ayan, Avi

Publication type:

Article

Introduction to Statistical Methods to Analyze Large Data Sets: Principal Components Analysis.

Published in:

Science Signaling, 2011, v. 4, n. 190, p. 1, doi. 10.1126/scisignal.2001967

By:

Clark, Neil R.;
Ma'ayan, Avi

Publication type:

Article

Systems Pharmacology of Arrhythmias.

Published in:

Science Signaling, 2010, v. 3, n. 121, p. 1, doi. 10.1126/scisignal.2000723

By:

Berger, Seth I.;
Ma'ayan, Avi;
Iyengar, Ravi

Publication type:

Article

Systems Pharmacology of Arrhythmias.

Published in:

Science Signaling, 2010, v. 3, n. 118, p. 1, doi. 10.1126/scisignal.2000723

By:

Berger, Seth I.;
Ma'ayan, Avi;
Iyengar, Ravi

Publication type:

Article

Neuro2A Differentiation by Gα<sub>i/o</sub> Pathway.

Published in:

Science Signaling, 2009, v. 2, n. 54, p. 1, doi. 10.1126/scisignal.254cm1

By:

Ma'ayan, Avi;
Jenkins, Sherry L.;
Barash, Alexander;
Iyengar, Ravi

Publication type:

Article

Oct4 links multiple epigenetic pathways to the pluripotency network.

Published in:

Cell Research, 2012, v. 22, n. 1, p. 155, doi. 10.1038/cr.2011.179

By:

Ding, Junjun;
Xu, Huilei;
Faiola, Francesco;
Ma'ayan, Avi;
Wang, Jianlong

Publication type:

Article

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 1, p. 1, doi. 10.1371/journal.pcbi.1005911

By:

Koplev, Simon;
Lin, Katie;
Dohlman, Anders B.;
Ma’ayan, Avi

Publication type:

Article

Genetic driver mutations introduced in identical cell‐of‐origin in murine glioblastoma reveal distinct immune landscapes but similar response to checkpoint blockade.

Published in:

Glia (0894-1491), 2020, v. 68, n. 10, p. 2148, doi. 10.1002/glia.23883

By:

Chen, Zhihong;
Herting, Cameron J.;
Ross, James L.;
Gabanic, Ben;
Puigdelloses Vallcorba, Montse;
Szulzewsky, Frank;
Wojciechowicz, Megan L.;
Cimino, Patrick J.;
Ezhilarasan, Ravesanker;
Sulman, Erik P.;
Ying, Mingyao;
Ma'ayan, Avi;
Read, Renee D.;
Hambardzumyan, Dolores

Publication type:

Article

Transcriptome analysis of human dermal fibroblasts following red light phototherapy.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-86623-2

By:

Austin, Evan;
Koo, Eugene;
Merleev, Alexander;
Torre, Denis;
Marusina, Alina;
Luxardi, Guillaume;
Mamalis, Andrew;
Isseroff, Roslyn Rivkah;
Ma'ayan, Avi;
Maverakis, Emanual;
Jagdeo, Jared

Publication type:

Article

Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity.

Published in:

Nature Cell Biology, 2012, v. 14, n. 11, p. 1139, doi. 10.1038/ncb2603

By:

MacArthur, Ben D.;
Sevilla, Ana;
Lenz, Michel;
Müller, Franz-Josef;
Schuldt, Berhard M.;
Schuppert, Andreas A.;
Ridden, Sonya J.;
Stumpf, Patrick S.;
Fidalgo, Miguel;
Ma'ayan, Avi;
Wang, Jianlong;
Lemischka, Ihor R.

Publication type:

Article

Functional atlas of the integrin adhesome.

Published in:

Nature Cell Biology, 2007, v. 9, n. 8, p. 858, doi. 10.1038/ncb0807-858

By:

Zaidel-Bar, Ronen;
Itzkovitz, Shalev;
Ma'ayan, Avi;
Iyengar, Ravi;
Geiger, Benjamin

Publication type:

Article

SIRT6 haploinsufficiency induces BRAF<sup>V600E</sup> melanoma cell resistance to MAPK inhibitors via IGF signalling.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05966-z

By:

Strub, Thomas;
Ghiraldini, Flavia G.;
Carcamo, Saul;
Li, Man;
Wroblewska, Aleksandra;
Singh, Rajendra;
Goldberg, Matthew S.;
Hasson, Dan;
Wang, Zichen;
Gallagher, Stuart J.;
Hersey, Peter;
Ma’ayan, Avi;
Long, Georgina V.;
Scolyer, Richard A.;
Brown, Brian;
Zheng, Bin;
Bernstein, Emily

Publication type:

Article

Massive mining of publicly available RNA-seq data from human and mouse.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03751-6

By:

Lachmann, Alexander;
Torre, Denis;
Keenan, Alexandra B.;
Jagodnik, Kathleen M.;
Lee, Hoyjin J.;
Lily Wang;
Silverstein, Moshe C.;
Ma’ayan, Avi

Publication type:

Article

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01383-w

By:

Niepel, Mario;
Hafner, Marc;
Qiaonan Duan;
Zichen Wang;
Paull, Evan O.;
Mirra Chung;
Xiaodong Lu;
Stuart, Joshua M.;
Golub, Todd R.;
Subramanian, Aravind;
Ma’ayan, Avi;
Sorger, Peter K.

Publication type:

Article

Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens.

Published in:

Frontiers in Molecular Neuroscience, 2016, v. 9, p. 1, doi. 10.3389/fnmol.2016.00144

By:

Pfau, Madeline L.;
Purushothaman, Immanuel;
Jian Feng;
Golden, Sam A.;
Aleyasin, Hossein;
Lorsch, Zachary S.;
Cates, Hannah M.;
Flanigan, Meghan E.;
Menard, Caroline;
Heshmati, Mitra;
Zichen Wang;
Ma'ayan, Avi;
Li Shen;
Hodes, Georgia E.;
Russo, Scott J.

Publication type:

Article

Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis.

Published in:

Intensive Care Medicine, 2024, v. 50, n. 12, p. 2031, doi. 10.1007/s00134-024-07665-4

By:

Baillie, J. Kenneth;
Angus, Derek;
Burnham, Katie;
Calandra, Thierry;
Calfee, Carolyn;
Gutteridge, Alex;
Hacohen, Nir;
Khatri, Purvesh;
Langley, Raymond;
Ma'ayan, Avi;
Marshall, John;
Maslove, David;
Prescott, Hallie C.;
Rowan, Kathy;
Scicluna, Brendon P.;
Seymour, Christopher;
Shankar-Hari, Manu;
Shapiro, Nathan;
Joost Wiersinga, W.;
Singer, Mervyn

Publication type:

Article

Dynamics of the discovery process of protein-protein interactions from low content studies.

Published in:

BMC Systems Biology, 2015, v. 9, n. 1, p. 1, doi. 10.1186/s12918-015-0173-z

By:

Zichen Wang;
Clark, Neil R.;
Ma'ayan, Avi

Publication type:

Article

Dynamics of the discovery process of proteinprotein interactions from low content studies

Published in:

BMC Systems Biology, 2015, v. 9, n. 1, p. 26, doi. 10.1186/s12918-015-0173-z

By:

Zichen Wang;
Clark, Neil R.;
Ma’ayan, Avi

Publication type:

Article

Sets2Networks: network inference from repeated observations of sets.

Published in:

BMC Systems Biology, 2012, v. 6, n. 1, p. 89, doi. 10.1186/1752-0509-6-89

By:

Clark, Neil R.;
Dannenfelser, Ruth;
Tan, Christopher M.;
Komosinski, Michael E.;
Ma'ayan, Avi

Publication type:

Article

SVM classifier to predict genes important for selfrenewal and pluripotency of mouse embryonic stem cells.

Published in:

BMC Systems Biology, 2010, v. 4, p. 173, doi. 10.1186/1752-0509-4-173

By:

Huilei Xu;
Lemischka, Ihor R.;
Ma'ayan, Avi

Publication type:

Article

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.

Published in:

BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-10

By:

Ma'ayan, Avi;
Jenkins, Sherry L.;
Webb, Ryan L.;
Berger, Seth I.;
Purushothaman, Sudarshan P.;
Abul-Husn, Noura S.;
Posner, Jeremy M.;
Flores, Tony;
Iyengar, Ravi

Publication type:

Article

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pcbi.1003777

By:

Xu, Huilei;
Ang, Yen-Sin;
Sevilla, Ana;
Lemischka, Ihor R.;
Ma'ayan, Avi

Publication type:

Article

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002319

By:

Mazloom, Amin R.;
Dannenfelser, Ruth;
Clark, Neil R.;
Grigoryan, Arsen V.;
Linder, Kathryn M.;
Cardozo, Timothy J.;
Bond, Julia C.;
Boran, Aislyn D. W.;
Iyengar, Ravi;
Malovannaya, Anna;
Lanz, Rainer B.;
Ma'ayan, Avi

Publication type:

Article

Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Published in:

Nature, 2012, v. 485, n. 7397, p. 242, doi. 10.1038/nature11011

By:

Neale, Benjamin M.;
Kou, Yan;
Liu, Li;
Ma'ayan, Avi;
Samocha, Kaitlin E.;
Sabo, Aniko;
Lin, Chiao-Feng;
Stevens, Christine;
Wang, Li-San;
Makarov, Vladimir;
Polak, Paz;
Yoon, Seungtai;
Maguire, Jared;
Crawford, Emily L.;
Campbell, Nicholas G.;
Geller, Evan T.;
Valladares, Otto;
Schafer, Chad;
Liu, Han;
Zhao, Tuo

Publication type:

Article

Mesenchymal and haematopoietic stem cells form a unique bone marrow niche.

Published in:

Nature, 2010, v. 466, n. 7308, p. 829, doi. 10.1038/nature09262

By:

Méndez-Ferrer, Simón;
Michurina, Tatyana V.;
Ferraro, Francesca;
Mazloom, Amin R.;
MacArthur, Ben D.;
Lira, Sergio A.;
Scadden, David T.;
Ma'ayan, Avi;
Enikolopov, Grigori N.;
Frenette, Paul S.

Publication type:

Article

Systems-level dynamic analyses of fate change in murine embryonic stem cells.

Published in:

Nature, 2009, v. 462, n. 7271, p. 358, doi. 10.1038/nature08575

By:

Lu, Rong;
Markowetz, Florian;
Unwin, Richard D.;
Leek, Jeffrey T.;
Airoldi, Edoardo M.;
MacArthur, Ben D.;
Lachmann, Alexander;
Rozov, Roye;
Ma'ayan, Avi;
Boyer, Laurie A.;
Troyanskaya, Olga G.;
Whetton, Anthony D.;
Lemischka, Ihor R.

Publication type:

Article

Getting Started with LINCS Datasets and Tools.

Published in:

Current Protocols, 2022, v. 2, n. 7, p. 1, doi. 10.1002/cpz1.487

By:

Xie, Zhuorui;
Kropiwnicki, Eryk;
Wojciechowicz, Megan L.;
Jagodnik, Kathleen M.;
Shu, Ingrid;
Bailey, Allison;
Clarke, Daniel J. B.;
Jeon, Minji;
Evangelista, John Erol;
V. Kuleshov, Maxim;
Lachmann, Alexander;
Parigi, Abhijna A.;
Sanchez, Jose M.;
Jenkins, Sherry L.;
Ma'ayan, Avi

Publication type:

Article

Getting Started with the IDG KMC Datasets and Tools.

Published in:

Current Protocols, 2022, v. 2, n. 1, p. 1, doi. 10.1002/cpz1.355

By:

Kropiwnicki, Eryk;
Binder, Jessica L.;
Yang, Jeremy J.;
Holmes, Jayme;
Lachmann, Alexander;
Clarke, Daniel J. B.;
Sheils, Timothy;
Kelleher, Keith J.;
Metzger, Vincent T.;
Bologa, Cristian G.;
Oprea, Tudor I.;
Ma'ayan, Avi

Publication type:

Article

Systems biology of stem cell fate and cellular reprogramming.

Published in:

Nature Reviews Molecular Cell Biology, 2009, v. 10, n. 10, p. 672, doi. 10.1038/nrm2766

By:

MacArthur, Ben D.;
Ma'ayan, Avi;
Lemischka, Ihor R.

Publication type:

Article

Predicting opioid dependence from electronic health records with machine learning.

Published in:

BioData Mining, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13040-019-0193-0

By:

Ellis, Randall J.;
Wang, Zichen;
Genes, Nicholas;
Ma'ayan, Avi

Publication type:

Article

From components to regulatory motifs in signalling networks.

Published in:

Briefings in Functional Genomics & Proteomics, 2006, v. 5, n. 1, p. 57, doi. 10.1093/bfgp/ell004

By:

Ma'ayan, Avi;
Iyengar, Ravi

Publication type:

Article

Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06177-7

By:

Clarke, Daniel J. B.;
Marino, Giacomo B.;
Deng, Eden Z.;
Xie, Zhuorui;
Evangelista, John Erol;
Ma'ayan, Avi

Publication type:

Article

A systems approach identifies HIPK2 as a key regulator of kidney fibrosis.

Published in:

Nature Medicine, 2012, v. 18, n. 4, p. 580, doi. 10.1038/nm.2685

By:

Jin, Yuanmeng;
Ratnam, Krishna;
Chuang, Peter Y;
Fan, Ying;
Zhong, Yifei;
Dai, Yan;
Mazloom, Amin R;
Chen, Edward Y;
D'Agati, Vivette;
Xiong, Huabao;
Ross, Michael J;
Chen, Nan;
Ma'ayan, Avi;
He, John Cijiang

Publication type:

Article

Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease.

Published in:

2021

By:

Zhang, Lu;
Wang, Zichen;
Liu, Ruijie;
Li, Zhengzhe;
Lin, Jennifer;
Wojciechowicz, Megan L.;
Huang, Jiyi;
Lee, Kyung;
Ma'ayan, Avi;
He, John Cijiang

Publication type:

journal article

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.

Published in:

BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04590-5

By:

Kropiwnicki, Eryk;
Lachmann, Alexander;
Clarke, Daniel J. B.;
Xie, Zhuorui;
Jagodnik, Kathleen M.;
Ma'ayan, Avi

Publication type:

Article

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics.

Published in:

Molecular Autism, 2014, v. 5, n. 1, p. 1, doi. 10.1186/2040-2392-5-22

By:

Li Liu;
Jing Lei;
Sanders, Stephan J.;
Willsey, Arthur Jeremy;
Yan Kou;
Cicek, Abdullah Ercument;
Klei, Lambertus;
Cong Lu;
Xin He;
Mingfeng Li;
Muhle, Rebecca A.;
Ma'ayan, Avi;
Noonan, James P.;
Sestan, Nenad;
McFadden, Kathryn A.;
State, Matthew W.;
Buxbaum, Joseph D.;
Devlin, Bernie;
Roeder, Kathryn

Publication type:

Article

Transforming L1000 profiles to RNA-seq-like profiles with deep learning.

Published in:

BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04895-5

By:

Jeon, Minji;
Xie, Zhuorui;
Evangelista, John E.;
Wojciechowicz, Megan L.;
Clarke, Daniel J. B.;
Ma'ayan, Avi

Publication type:

Article

Far away from the lamppost.

Published in:

PLoS Biology, 2018, v. 16, n. 12, p. 1, doi. 10.1371/journal.pbio.3000067

By:

Oprea, Tudor I.;
Jan, Lily;
Johnson, Gary L.;
Roth, Bryan L.;
Ma’ayan, Avi;
Schürer, Stephan;
Shoichet, Brian K.;
Sklar, Larry A.;
McManus, Michael T.

Publication type:

Article

Network2Canvas: network visualization on a canvas with enrichment analysis.

Published in:

Bioinformatics, 2013, v. 29, n. 15, p. 1872, doi. 10.1093/bioinformatics/btt319

By:

Tan, Christopher M.;
Chen, Edward Y.;
Dannenfelser, Ruth;
Clark, Neil R.;
Ma’ayan, Avi

Publication type:

Article

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.

Published in:

Bioinformatics, 2012, v. 28, n. 1, p. 105, doi. 10.1093/bioinformatics/btr625

By:

Chen, Edward Y.;
Xu, Huilei;
Gordonov, Simon;
Lim, Maribel P.;
Perkins, Matthew H.;
Ma'ayan, Avi

Publication type:

Article

FNV: light-weight flash-based network and pathway viewer.

Published in:

Bioinformatics, 2011, v. 27, n. 8, p. 1181, doi. 10.1093/bioinformatics/btr098

By:

Dannenfelser, Ruth;
Lachmann, Alexander;
Szenk, Mariola;
Ma'ayan, Avi

Publication type:

Article

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Published in:

Bioinformatics, 2010, v. 26, n. 19, p. 2438, doi. 10.1093/bioinformatics/btq466

By:

Lachmann, Alexander;
Huilei Xu;
Krishnan, Jayanth;
Berger, Seth I.;
Mazloom, Amin R.;
Ma'ayan, Avi

Publication type:

Article

GATE: software for the analysis and visualization of high-dimensional time series expression data.

Published in:

Bioinformatics, 2010, v. 26, n. 1, p. 143, doi. 10.1093/bioinformatics/btp628

By:

MacArthur, Ben D.;
Lachmann, Alexander;
Lemischka, Ihor R.;
Ma'ayan, Avi

Publication type:

Article