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List of works by John Bachman

Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature

scientific article published on 16 January 2020

Author-sourced capture of pathway knowledge in computable form using Biofactoid

scientific article published on 03 December 2021

Automated assembly of molecular mechanisms at scale from text mining and curated databases

preprint published on 31 August 2022

BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response

scientific article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Capturing scientific knowledge in computable form

scientific article published on 11 March 2021

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

scientific article published on 28 June 2018

From word models to executable models of signaling networks using automated assembly.

scientific article

Fundamental trade-offs between information flow in single cells and cellular populations.

scientific article published on 12 May 2017

GeneWalk identifies relevant gene functions for a biological context using network representation learning

scientific article published on 02 February 2021

INDRA-IPM: interactive pathway modeling using natural language with automated assembly

scientific article published on 01 November 2019

Integrated Network and Dynamical Reasoning Assembler

Text mining and systems biology modeling software

Maintenance and Enrichment of Disease Maps in Biological Expression Language ⬇️

conference poster

New approaches to modeling complex biochemistry ⬇️

scientific article published on February 1, 2011

Optimizing ring assembly reveals the strength of weak interactions

scientific article published on 30 January 2012

Programming biological models in Python using PySB

scientific article

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs ⬇️

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

BioRxiv article

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.

scientific article

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

preprint published on 18 August 2021

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

scientific article published on 5 January 2022

Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers

scientific article published on 01 October 2019

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data

scientific article published on 08 February 2021

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