List of works by Emek Demir

A flexible search system for high-accuracy identification of biological entities and molecules

scientific article published on 12 November 2021

Algorithms for effective querying of compound graph-based pathway databases

scientific article

An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer

scientific article published on 15 February 2022

Analyzing causal relationships in proteomic profiles using CausalPath

scientific article published on 24 November 2021

Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach

scientific article published in February 2017

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

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

scientific article published on 03 December 2021

Automated network analysis identifies core pathways in glioblastoma

scientific article

BioPAX support in CellDesigner

scientific article published on 21 October 2011

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

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

scientific article published on 05 May 2020

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

journal article from 'Molecular Systems Biology' published in 2021

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

scientific article published on 15 August 2019

Capturing scientific knowledge in computable form

scientific article published on 11 March 2021

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge

scientific article published on 12 May 2021

ChiBE: interactive visualization and manipulation of BioPAX pathway models

scientific article

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

scientific article

Discovering modulators of gene expression

scientific article

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

scientific article

Integrating biological pathways and genomic profiles with ChiBE 2.

scientific article

Large-scale automated machine reading discovers new cancer-driving mechanisms

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

scientific article published on November 2011

Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps

scientific article published on 03 October 2020

PATIKAmad: putting microarray data into pathway context

scientific article

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

scientific article published on 01 January 2020

Pathway Commons, a web resource for biological pathway data

scientific article

Pattern search in BioPAX models

scientific article

PaxtoolsR: pathway analysis in R using Pathway Commons

scientific article published on 18 December 2015

Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells

scientific article

Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs

scientific article published on 08 July 2020

Platelet procoagulant phenotype is modulated by a p38 - MK2 axis regulating RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis

scientific article published on 7 February 2018

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

scientific article

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

scientific article (publication date: 2015)

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps

scientific article published on June 2015

Software support for SBGN maps: SBGN-ML and LibSBGN.

scientific article

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

scientific article

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes

scientific article published on 06 May 2021

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

scientific article

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

scientific article

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

scientific article

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

scientific article published on 13 June 2019

The BioPAX Validator

scientific article

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

scientific article published on 01 April 2020

The reactome pathway knowledgebase 2022

scientific article published on 14 October 2021

Using biological pathway data with paxtools

scientific article

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