cv

Staff Scientist

• Integrating multi-omics (TF/Histone ChIP-seq, DHS, ATAC-seq, HiC, RNA-binding proteins’ binding sites, methylome) data to model disease transcriptional codes using multi-modal fusion deep neural networks to detect disease-causal genetic variation
• Using Deep Learning to assess the phenotypic impacts of human-specific (vs. Macaques and Chimpanzees) INDELs in enhancers.

Research Fellow

• Developed TREDNet - A novel Deep Learning method for enhancer detection.
• Lead a large multidisciplinary collaboration project to apply TREDNet to detect GWAS candidate causal mutations linked to Type 2 Diabetes and experimentally verified.
• Developed a model for explaining the high-occupancy target (HOT) regions in humans using transcriptional condensates.

Postdoctoral Fellow

• Spearheaded the transition to Deep Learning methods to study the enhancers.
• Automated the distributed training of large models (Keras+Tensorflow) on Google Cloud and Biowulf (NIH’s HPC cluster).
• Applied ConvNets and LSTMs to model gene regulation and decompose LD blocks.
• Managed and implemented the deployment of decades-worth codebase developed in-house to containers (Docker, singularity) and workflows management systems (Nextflow, Snakemake).

Postdoctoral Fellow

• Studied the general evolution of CRISPR/Cas systems, as well as deep focus on protein CRISPR-associated 4 (Cas4). Paper is cited >55 times, including by Prof. Jennifer Doudna, and has given me an Erdös number of 3.
• Analyzed evolutionary links between microbial adaptive immune systems and other selfish elements.
• Gained an expert understanding of microbial genetics, comparative genomics, molecular evolutionary analysis.

Graduate research program

• Thesis project - Functional annotation of Quorum Sensing systems in bacteria using subsystem based approach.
• Implemented a wide range of algorithms and tools of computational genomics and sequence analysis

Software developer

• Developed a concept for data analysis module for an existing commercial software for micro-financing.
• Implemented financial data analysis module in .NET environment using C# and MS SQL Server.
• Developed an ETL module to consolidate the data from government and third-party vendors using Pentaho and Python.

Oracle Database Developer

• Designed and implemented backup strategies of Oracle database and decreased the backup time by a factor of 10.
• Lead the project of transitioning the existing infrastructure to Oracle Blade Modules.
• Conducted SQL tuning and optimization which lead to reduction in ATM transaction latencies during the peak times from 10 seconds to < 1 second.

Research assistant

• Designed and implemented Machine Learning experiments on protein function prediction using profile-HMMs.
• Obtained a formal graduate training on classical Machine Learning (PRML by Christopher Bishop)

PhD in Bioinformatics

• Thesis - “Computational analysis of quorum sensing systems in bacterial genomes - Developing automated annotation tools.”
• Supervisor - Prof. Sándor PONGOR

MSc in Machine Learning

BSc in Computer Engineering

• Sequence characteristics and an accurate model of abundant hyperactive loci in the human genome NLM IRP Seminar

• Transcriptional regulation and disease genetics using Deep Learning NLM IRP Seminar

• Deep causality in non-coding GWAS SNPs. NLM Summer Lectures Series. NLM

• Using Deep Learning to to infer causality of GWAS SNPs. METU, Ankara, Turkey

• Recurrent Language model for enhancers. NLM Summer Lectures Series. NLM
• Understanding the grammar of enhancers using Deep Learning. NHGRI
• Causal mutations in ZRS enhancer region using Deep Learning. LBNL, Berkeley

• Phylogenomics of Cas4 family nucleases. AiChE. Raleigh, NC

• Current topics in biological sequence analysis. ICGEB. Trieste, Italy

• Hyperactive loci within non-coding regulatory regions of human genome. Mechanisms of Eukaryotic Transcription, CSHL, NY.

• Two-stage Deep Learning cross-tissue predictor of enhancers shows unprecedented accuracy in detection of causal regulatory variants. Mechanisms of Eukaryotic Transcription, CSHL, NY.
• Using Deep Learning to understand the grammar of enhancers. RECOMB, Washington DC

• Phylogenomics of Cas4 family nucleases. International conference on CRISPR. Technologies, Raleigh, NC

• Computational approaches to microbial communication/quorum sensing signaling. BAGECO, Ljubljana, Slovenia

• Fellows Award for Research Excellence NIH, Bethesda, MD

• ICGEB PhD fellowship ICGEB, Trieste, Italy

• Scholarship for research in Machine Learning/Bioinformatics. TUBITAK, Istanbul, Turkey

• Scholarship for BS final year project. TUBITAK, Kayseri, Turkey

• Scholarship of Turkish ministry of education for undergraduate studies. 2002/2007, Turkey

• Bronze medals in national physics olympiads for highschool students. 2001/2002, Kyrgyzstan

• Co-mentor, Post-bac student, NIH

• Co-mentor, Summer research student, NIH

• Lead instructor, Summer intern journal club, NIH
• Co-mentor, Summer research student, NIH