Abdulkadir Elmas's Home Page

Abdulkadir Elmas

Icahn School of Medicine at Mount Sinai
Dept. of Genetics and Genomic Sciences
1399 Park Ave #428
New York 10029
abdulkadir [dot] elmas [at] mssm [dot] edu


Covering certain topics in signal processing and statistics: Bayesian inference, state-space models, convex optimization and machine learning. Developing bioinformatics algorithms addressing the challenges in genetics and genomic sciences: multi-omics of cancer, survival and prognostic biomarkers, DNA sequence/motifs, gene regulatory networks, tag SNPs and haplotype phasing.

Ongoing projects

Elmas A, Tharakan S, Jaladanki S, Liu T, Huang K. Pan-cancer Proteogenomic Investigations Identify Post-transcriptional Kinase Targets. (In review Nat Comm Biol)

Protein targets in liver cancer. (In prep)

Protein-driven dependency identify new cancer vulnerabilities. (In prep)

The immune proteome and signaling landscape across 12 cancer types. (In prep)

Cellular Dependency Analysis Identifies Genes Implicated in Alzheimer's Disease (AD) as Potential Treatment Targets. (In prep)

Pan-cancer protein networks portray landscapes of aberrant cancer proteomes and pro-tumorigenic drivers. (In prep)

Ongoing collaborations

Huang K et al. Spatially Interacting Phosphorylation Sites and Mutations in Cancer. (In revision Nat Comm)

List of publications

Molina-Sanchez P et al. Cooperation Between Distinct Cancer Driver Genes Underlies Intertumor Heterogeneity in Hepatocellular Carcinoma. Gastroenterology, 2020.

Ogundijo OE, Elmas A, Wang X. Reverse engineering gene regulatory networks from measurement with missing values. EURASIP J Bioinform Syst Biol, 2017.

Elmas A, Wang X, Dresch JM. The folded k-spectrum kernel: a machine learning approach to detecting transcription factor binding sites with nucleotide dependencies. PLOS ONE, 2017. [Script]

Elmas A, Ou Yang T, Wang X, Anastassiou D. Discovering genome-wide tagSNPs based on the mutual-information of the variants. PLOS ONE, 2017.

Elmas A. Topics in Signal Processing: applications in genomics and genetics. PhD Thesis, 2016.

Elmas A, Wang X, Samoilov MS. Reconstruction of novel transcription factor regulons through inference of their binding sites. BMC Bioinformatics, 2015. [Script]

Elmas A, Jajamovich GH, Wang X. Maximum parsimony xor haplotyping by sparse dictionary selection. BMC Genomics, 2013. [Script]

Elmas A, Jajamovich GH, Wang X. Designing DNA barcodes orthogonal in melting temperature by simulated annealing optimization. Nucleic Acid Therapeutics, 2013. [Script].

Elmas A, Wang X, Samoilov MS. Reconstruction of novel transcription factor regulons through inference of their binding sites.
IEEE Signals, Systems and Computers, Asilomar Conference, 2013.