Publications
2025
2024
In-Context Principle Learning from Mistakes
WEBARENA: A REALISTIC WEB ENVIRONMENT FOR BUILDING AUTONOMOUS AGENTS
LEARNING PERFORMANCE-IMPROVING CODE EDITS
2023
Physiology
Systems Medicine
Tissue Dynamics
Systems Medicine: Physiological Circuits and the Dynamics of Disease
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Systems Medicine
Tissue Dynamics
The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts
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Immunology
Systems Medicine
Autoimmune thyroid diseases as a cost of physiological autoimmune surveillance
Systems Medicine
Tissue Dynamics
An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis
Unlimiformer: Long-Range Transformers with Unlimited Length Input
On the Expressivity Role of LayerNorm in Transformers' Attention
DocPrompting: GENERATING CODE BY RETRIEVING THE DOCS
SELF-REFINE: Iterative Refinement with Self-Feedback
Why do Nearest Neighbor Language Models Work?
PAL: Program-aided Language Models
2022
HOW ATTENTIVE ARE GRAPH ATTENTION NETWORKS?
Language Models of Code are Few-Shot Commonsense Learners
Neuro-Symbolic Language Modeling with Automaton-augmented Retrieval
2021
Physiology
Systems Medicine
Hormone seasonality in medical records suggests circannual endocrine circuits
Systems Medicine
Tissue Dynamics
Distinct extracellularmatrix remodeling events precede symptoms of inflammation
ON THE BOTTLENECK OF GRAPH NEURAL NETWORKS AND ITS PRACTICAL IMPLICATIONS
2020
Structural language models of code
2019
Evolution
Microbiology
Pareto
Central dogma rates and the trade-off between precision and economy in gene expression
Systems Biology
An introduction to systems biology: design principles of biological circuits
Code2Seq: Generating sequences from structured representations of code
2018
2017
Systems Biology
Systems Medicine
Prediction of drug cocktail effects when the number of measurements is limited
2016
Systems Biology
Systems Medicine
Prediction of multidimensional drug dose responses based on measurements of drug pairs
Evolution
Systems Biology
Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness
Systems Medicine
Theater Lab
Manipulating the placebo response in experimental pain by altering doctor's performance style
2015
2014
2013
Evolution
Systems Biology
Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems
2012
Microbiology
Network Motifs
Systems Biology
A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli
2011
Microbiology
Systems Biology
Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C 4 Plants by a Bi-functional Enzyme
Microbiology
Network Motifs
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
Systems Biology
Input symmetry invariance, and applications to biological systems
Microbiology
Network Motifs
Architecture and Dynamics of Transcriptional Networks
2010
Microbiology
Systems Biology
Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy
Dynamic Proteomics
Systems Biology
Systems Medicine
Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses
2009
Network Motifs
Systems Biology
The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
Immunology
Systems Medicine
Predicting and controlling the reactivity of immune cell populations against cancer
2008
Microbiology
Network Motifs
Systems Biology
The incoherent feed-forward loop can generate non-monotonic input functions for genes
2007
Microbiology
Systems Biology
Accurate prediction of gene feedback circuit behavior from component properties
Evolution
Systems Biology
The genetic code is nearly optimal for allowing additional information within protein-coding sequences
Network Motifs
Systems Biology
A module of negative feedback regulators defines growth factor signaling
2006
Immunology
Network Motifs
The immune-body cytokine network defines a social architecture of cell interactions
Microbiology
Systems Biology
Optimal gene partition into operons correlates with gene functional order
Microbiology
Network Motifs
Systems Biology
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
2005
Evolution
Microbiology
Systems Biology
Optimality and evolutionary tuning of the expression level of a protein
Microbiology
Systems Biology
Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria
Evolution
Microbiology
Network Motifs
Systems Biology
Environmental selection of the feed-forward loop circuit in gene-regulation networks
Correlation profiles and motifs in complex networks
Microbiology
Network Motifs
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli.
2004
Microbiology
Network Motifs
Systems Biology
Just-in-time transcription program in metabolic pathways
2003
Network Motifs
Systems Biology
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
2002
Network Motifs
Systems Biology
Negative autoregulation speeds the response times of transcription networks
Microbiology
Network Motifs
Systems Biology