science

Publications

The following publications discuss work from Biswas Family Foundation funded projects.

December 15, 2024

ProCyon: A multimodal foundation model for protein phenotypes

bioRxiv
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Associated Project:
Artificial intelligence for Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript
December 10, 2024

Unified Clinical Vocabulary Embeddings for Advancing Precision

MedRxiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
November 21, 2024

Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions

National Library of Medicine
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes

Category:
Manuscript
November 15, 2024

Efficient generation of protein pockets with PocketGen

Nature
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
October 31, 2024

Empowering biomedical discovery with AI agents

Cell
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
October 7, 2024

Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine

ArXiv
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
October 7, 2024

Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine

ARXIV
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
August 29, 2024

ReXamine-Global: A Framework for Uncovering Inconsistencies in Radiology Report Generation Metrics

ARXIV
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Associated Project:
The MAIDA Initiative: Democratizing Global Medical Imaging Data Sharing for Safer and Fairer AI
Principal Investigator:

Pranav Rajpurkar, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
August 19, 2024

Quantized multi-task learning for context-specific representations of gene network dynamics

BioRxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes

Category:
Manuscript
August 7, 2024

A foundation model for clinician-centered drug repurposing

Nature Medicine
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
July 27, 2024

Deep-learning prediction of gene expression from personal genomes

Biorxiv
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Associated Project:
Biswas Center for Transformative Computational Cancer Biology
Principal Investigator:

Katherine Pollard, PhD, Director of Data Science & Biotechnology, Gladstone Institutes 

Category:
Manuscript
July 22, 2024

Contextual AI models for single-cell protein biology

Nature
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Manuscript
June 21, 2024

TDC-2: Multimodal Foundation for Therapeutic Science

Biorxiv
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Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Manuscript

PINNACLE

GitHub
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Associated Project:
CURE-Bench: Universal Benchmark for All-Disease Drug Repurposing
Principal Investigator:

Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School 

Category:
Software
Associated Project:
AI for Cancer Genomic Medicine: Circuitry, Treatment, Personalization
Principal Investigator:

Manolis Kellis, PhD, Professor of Computer Science, Massachusetts Institute of Technology

Category:
Software

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