Pamela Milani

Pamela Milani

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Pamela Milani

Pamela Milani

Publications by authors named "Pamela Milani"

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18Publications

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A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.

Sci Rep 2020 Jan 22;10(1):954. Epub 2020 Jan 22.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1038/s41598-020-57691-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976599PMC
January 2020

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Authors:
Alexandra B Keenan Sherry L Jenkins Kathleen M Jagodnik Simon Koplev Edward He Denis Torre Zichen Wang Anders B Dohlman Moshe C Silverstein Alexander Lachmann Maxim V Kuleshov Avi Ma'ayan Vasileios Stathias Raymond Terryn Daniel Cooper Michele Forlin Amar Koleti Dusica Vidovic Caty Chung Stephan C Schürer Jouzas Vasiliauskas Marcin Pilarczyk Behrouz Shamsaei Mehdi Fazel Yan Ren Wen Niu Nicholas A Clark Shana White Naim Mahi Lixia Zhang Michal Kouril John F Reichard Siva Sivaganesan Mario Medvedovic Jaroslaw Meller Rick J Koch Marc R Birtwistle Ravi Iyengar Eric A Sobie Evren U Azeloglu Julia Kaye Jeannette Osterloh Kelly Haston Jaslin Kalra Steve Finkbiener Jonathan Li Pamela Milani Miriam Adam Renan Escalante-Chong Karen Sachs Alex Lenail Divya Ramamoorthy Ernest Fraenkel Gavin Daigle Uzma Hussain Alyssa Coye Jeffrey Rothstein Dhruv Sareen Loren Ornelas Maria Banuelos Berhan Mandefro Ritchie Ho Clive N Svendsen Ryan G Lim Jennifer Stocksdale Malcolm S Casale Terri G Thompson Jie Wu Leslie M Thompson Victoria Dardov Vidya Venkatraman Andrea Matlock Jennifer E Van Eyk Jacob D Jaffe Malvina Papanastasiou Aravind Subramanian Todd R Golub Sean D Erickson Mohammad Fallahi-Sichani Marc Hafner Nathanael S Gray Jia-Ren Lin Caitlin E Mills Jeremy L Muhlich Mario Niepel Caroline E Shamu Elizabeth H Williams David Wrobel Peter K Sorger Laura M Heiser Joe W Gray James E Korkola Gordon B Mills Mark LaBarge Heidi S Feiler Mark A Dane Elmar Bucher Michel Nederlof Damir Sudar Sean Gross David F Kilburn Rebecca Smith Kaylyn Devlin Ron Margolis Leslie Derr Albert Lee Ajay Pillai

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements.

Nat Commun 2017 09 20;8(1):623. Epub 2017 Sep 20.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.

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http://dx.doi.org/10.1038/s41467-017-00353-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606996PMC
September 2017

Revealing disease-associated pathways by network integration of untargeted metabolomics.

Nat Methods 2016 09 1;13(9):770-6. Epub 2016 Aug 1.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209295PMC
September 2016

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

Sci Rep 2016 06 29;6:28668. Epub 2016 Jun 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.

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http://dx.doi.org/10.1038/srep28668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926112PMC
June 2016

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells.

Sci Rep 2016 05 5;6:25474. Epub 2016 May 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States of America.

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http://dx.doi.org/10.1038/srep25474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857123PMC
May 2016

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

Proc Natl Acad Sci U S A 2016 Mar 10;113(9):2544-9. Epub 2016 Feb 10.

Synthetic Biology Group, Massachusetts Institute of Technology (MIT) Synthetic Biology Center, MIT, Cambridge, MA 02139; Research Laboratory of Electronics, MIT, Cambridge, MA 02139; Department of Biological Engineering, MIT, Cambridge, MA 02139; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139;

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http://dx.doi.org/10.1073/pnas.1517883113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780610PMC
March 2016

Hydrogen peroxide-mediated induction of SOD1 gene transcription is independent from Nrf2 in a cellular model of neurodegeneration.

Biochim Biophys Acta 2016 Feb 24;1859(2):315-23. Epub 2015 Nov 24.

Laboratory of Experimental Neurobiology, "C. Mondino" National Institute of Neurology Foundation, IRCCS, Via Mondino 2, 27100 Pavia, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2015.11.009DOI Listing
February 2016

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements.

Cell Rep 2016 Jan 31;14(2):310-9. Epub 2015 Dec 31.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831719PMC
January 2016

SOD1 and DJ-1 converge at Nrf2 pathway: a clue for antioxidant therapeutic potential in neurodegeneration.

Oxid Med Cell Longev 2013 28;2013:836760. Epub 2013 Jul 28.

Laboratory of Experimental Neurobiology, National Neurological Institute C. Mondino, IRCCS, Pavia, Italy.

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http://dx.doi.org/10.1155/2013/836760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745953PMC
February 2014

Posttranscriptional regulation of SOD1 gene expression under oxidative stress: Potential role of ELAV proteins in sporadic ALS.

Neurobiol Dis 2013 Dec 20;60:51-60. Epub 2013 Aug 20.

Laboratory of Experimental Neurobiology, "C. Mondino" National Institute of Neurology Foundation, IRCCS, Via Mondino 2, 27100 Pavia, Italy; Department of Public Health, Neuroscience, Experimental and Forensic Medicine, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.nbd.2013.08.005DOI Listing
December 2013

Regulation of FMO and PON detoxication systems in ALS human tissues.

Neurotox Res 2013 May 17;23(4):370-7. Epub 2012 Oct 17.

Laboratory of Experimental Neurobiology, IRCCS National Neurological Institute C. Mondino, Via Mondino, 2, 27100, Pavia, Italy.

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http://dx.doi.org/10.1007/s12640-012-9356-1DOI Listing
May 2013

From Transcriptome to Noncoding RNAs: Implications in ALS Mechanism.

Neurol Res Int 2012 17;2012:278725. Epub 2012 Jun 17.

Laboratory of Experimental Neurobiology, IRCCS National Neurological Institute "C. Mondino," 27100 Pavia, Italy.

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http://dx.doi.org/10.1155/2012/278725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385659PMC
August 2012

SOD1 Transcriptional and Posttranscriptional Regulation and Its Potential Implications in ALS.

Neurol Res Int 2011 17;2011:458427. Epub 2011 Apr 17.

Laboratory of Experimental Neurobiology, IRCCS, National Neurological Institute "C. Mondino," Via Mondino 2, 27100 Pavia, Italy.

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http://dx.doi.org/10.1155/2011/458427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096450PMC
July 2011