Author details

Full Name

Tommi S Jaakkola

Affiliation

Massachusetts Institute of Technology

ORCID

Career Start Year

1992

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37064532	EigenFold: Generative Protein Structure Prediction with Diffusion Models.	ArXiv	2023
38076509	Removing Biases from Molecular Representations via Information Maximization.	ArXiv	2023
37433327	De novo design of protein structure and function with RFdiffusion.	Nature	2023
37231267	Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii.	Nat Chem Biol	2023
36065847	Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.	Mol Syst Biol	2022
34526388	Deep learning identifies synergistic drug combinations for treating COVID-19.	Proc Natl Acad Sci U S A	2021
32302574	A Deep Learning Approach to Antibiotic Discovery.	Cell	2020
32084340	A Deep Learning Approach to Antibiotic Discovery.	Cell	2020
32243158	Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis.	J Med Chem	2020
31361484	Analyzing Learned Molecular Representations for Property Prediction.	J Chem Inf Model	2019
31814400	Correction to Analyzing Learned Molecular Representations for Property Prediction.	J Chem Inf Model	2019
30746086	A graph-convolutional neural network model for the prediction of chemical reactivity.	Chem Sci	2018
30906084	Modeling Persistent Trends in Distributions.	J Am Stat Assoc	2018
28696688	Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction.	J Chem Inf Model	2017
28573205	Prediction of Organic Reaction Outcomes Using Machine Learning.	ACS Cent Sci	2017
27456004	A synergistic DNA logic predicts genome-wide chromatin accessibility.	Genome Res	2016
24441470	Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.	Nat Biotechnol	2014
22689769	Lineage-based identification of cellular states and expression programs.	Bioinformatics	2012
20966006	Discovering homotypic binding events at high spatial resolution.	Bioinformatics	2010
17696603	Automated discovery of functional generality of human gene expression programs.	PLoS Comput Biol	2007
16597252	Modeling the combinatorial functions of multiple transcription factors.	J Comput Biol	2006
16873502	Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo.	Bioinformatics	2006
16900145	High-resolution computational models of genome binding events.	Nat Biotechnol	2006
15998451	Validation and refinement of gene-regulatory pathways on a network of physical interactions.	Genome Biol	2005
15285891	Physical network models.	J Comput Biol	2004
12801867	K-ary clustering with optimal leaf ordering for gene expression data.	Bioinformatics	2003
12935332	Continuous representations of time-series gene expression data.	J Comput Biol	2003
12934016	Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.	Proc Natl Acad Sci U S A	2003
14555958	Computational discovery of gene modules and regulatory networks.	Nat Biotechnol	2003
11928497	Combining location and expression data for principled discovery of genetic regulatory network models.	Pac Symp Biocomput	2002
12209052	Bayesian network approach to cell signaling pathway modeling.	Sci STKE	2002
11472989	Fast optimal leaf ordering for hierarchical clustering.	Bioinformatics	2001
11262961	Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.	Pac Symp Biocomput	2001
11572776	Serial regulation of transcriptional regulators in the yeast cell cycle.	Cell	2001
10890390	A discriminative framework for detecting remote protein homologies.	J Comput Biol	2000
10786297	Using the Fisher kernel method to detect remote protein homologies.	Proc Int Conf Intell Syst Mol Biol	1999
20725286	Binary surface-relief gratings for array illumination in digital optics.	Appl Opt	1992

1 - 37 of 37

Jian Peng

University of Illinois

Career Start Year 2009

Number of shared co-authors 2

Anthony Gitter

University of Wisconsin

Career Start Year 2007

Number of shared co-authors 1

Stefan R Maetschke

Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics

Career Start Year 2007

Number of shared co-authors 0

Yanjun Qi

University of Virginiagrid.27755.32

Career Start Year 2005

Number of shared co-authors 1

Alberto Paccanaro

University of London

Career Start Year 2005

Number of shared co-authors 0

Dongxiao Zhu

Wayne State University

Career Start Year 2005

Number of shared co-authors 0

Stephen A Ramsey

Oregon State University

Career Start Year 2004

Number of shared co-authors 0

Quaid Morris

Sloan Kettering Institute

Career Start Year 2003

Number of shared co-authors 2

Tanusya M Murali

Yong Loo Lin School of Medicine, National University of Singapore

Career Start Year 2003

Number of shared co-authors 0

Su-In Lee

University of Washington

Career Start Year 2003

Number of shared co-authors 2

Daphne Koller

Stanford University

Career Start Year 2001

Number of shared co-authors 1

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 2

Ilya Shmulevich

Institute for Systems Biology

Career Start Year 2001

Number of shared co-authors 1

Roded Sharan

Tel Aviv University

Career Start Year 2000

Number of shared co-authors 3

Wei Wang

IBM Thomas J Watson Research Center, University of California Los Angeles, University of North Carolina at Chapel Hill

Career Start Year 1999

Number of shared co-authors 1

Blaz Zupan

University of Ljubljana

Career Start Year 1998

Number of shared co-authors 0

Benno Schwikowski

Center for Bioinformatics, Institut Pasteur CNRS

Career Start Year 1997

Number of shared co-authors 2

Panayiotis V Benos

University of Florida

Career Start Year 1996

Number of shared co-authors 3

Asa Ben-Hur

Colorado State University

Career Start Year 1996

Number of shared co-authors 0

Samuel Kaski

Aalto University

Career Start Year 1995

Number of shared co-authors 0

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 3

Hiroshi Mamitsuka

Institute for Chemical Research, Kyoto University

Career Start Year 1994

Number of shared co-authors 0

Pietro Li??

University of Cambridge

Career Start Year 1994

Number of shared co-authors 0

Dennis Shasha

Courant Institute of Mathematical Sciences, New York University

Career Start Year 1994

Number of shared co-authors 0

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 1

Joel S Bader

Johns Hopkins University

Career Start Year 1993

Number of shared co-authors 1

Wing Hung Wong

Stanford University

Career Start Year 1991

Number of shared co-authors 2

Michael F Ochs

The College of New Jersey

Career Start Year 1988

Number of shared co-authors 0

Donald Geman

Johns Hopkins University

Career Start Year 1984

Number of shared co-authors 0

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Career Start Year 1983

Number of shared co-authors 3

row(s) 1 - 30 of 30

Ziv Bar-Joseph

Carnegie Mellon University

Co-authored papers 5

Chen-Hsiang Yeang

Institute of Statistical Science

Co-authored papers 3

Julia Zeitlinger

Stowers Institute for Medical Research, University of Kansas School of Medicine

Co-authored papers 2

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 2

Mark Diekhans

Genomics Institute, University of California Santa Cruz

Co-authored papers 2

Ernest Fraenkel

Co-authored papers 2

David Haussler

Genomics Institute, University of California Santa Cruz

Co-authored papers 2

Douglas A Lauffenburger

Massachusetts Institute of Technology

Co-authored papers 1

Scott McCuine

Whitehead Institute for Biomedical Research

Co-authored papers 1

George M Church

Harvard Medical School

Co-authored papers 1

H Craig Mak

University of California San Diego

Co-authored papers 1

Bonnie Berger

Massachusetts Institute of Technology

Co-authored papers 1

Karen Sachs

Co-authored papers 1

David Baker

University of Washington

Co-authored papers 1

David Benjamin Gordon

Co-authored papers 1

Minkyung Baek

Seoul National University

Co-authored papers 1

Frank DiMaio

University of Washington

Co-authored papers 1

Fran??ois Robert

Institut de recherches cliniques de Montreal

Co-authored papers 1

Brian L Trippe

Co-authored papers 1

Nisha Rajagopal

Co-authored papers 1

Peter K Sorger

Co-authored papers 1

P Alexander Rolfe

Co-authored papers 1

Christopher T Workman

Technical University of Denmark

Co-authored papers 1

1 - 23

Author Details

Column Actions

Recommended Authors

Collaborators