CICEKLAB - A. Ercüment Çiçek, Ph.D.

Welcome!

I am Ercument Cicek,

o an Associate Professor at the Computer Engineering Department of Bilkent University, and

o an Adj. Faculty Member at the Computational Biology Department of School of Computer Science Carnegie Mellon University.

o an associate editor of IEEE/ACM Transactions in Computational Biology and Bioinformatics.

Before,

I was a visiting professor at EPFL on my sabbatical leave during 2022-2023. I was hosted by the Laboratory for Neurodevelopmental Systems Biology.
I was a Lane Fellow in Computational Biology at Carnegie Mellon University during 2013 - 2015. My advisors were Kathryn Roeder and Ziv Bar-Joseph.

Education

Ph.D. in Computer Science

Thesis: Metabolic network-based Analyses of Omics Data Advisor: Prof. Gultekin Ozsoyoglu

August 2009 - August 2013

Case Western Reverse University

Visiting Graduate Student

Worked in Iossifov Lab.

July 2012 - October 2012

Cold Spring Harbor Labratory

M.Sc. Computer Science and Engineering

Thesis: Ensuring Location Diversity in Privacy Preserving Spatio-Temporal Data Mining

August 2007 - July 2009

Sabancı University

B.Sc. in Computer Science and Engineering

September 2003 - July 2007

Sabancı University

Awards

Distinguished Teaching Award 2022 Bilkent University

Aziz Sancar Incentive Award 2020 Health Institutes of Turkey - TÜSEB

BAGEP 2020 Young Scientist Awards Program

Research Incentive Award 2019 - IEEE Turkey Section

Research Incentive Award 2018 - METU Parlar Foundation

Visiting Researcher Fellowship Visiting University of Strasbourg in Summer 2018

Outstanding Young Scientist Award 2017 - Turkish Academy of Sciences

Lane Fellowship 2013 - 2015

ACM SIGMOD Scholarship ACM A.M. Turing Centenary Celebration

Choose Ohio First Scholarship 2011-2012

Fulbright Doctorate Fellowship 2009

CWRU Research Assistantship 2009 - 2013

TUBITAK Graduate Fellowship 2007-2009 - Technical and Scientific Research Council of Turkey

SU Undergraduate Scholarship 2003 - 2007

Talks

Privacy Challenges in Genomic Data Sharing

UCLA Computational Genomics Summer Institute 2024, Los Angeles, LA. June 15, 2024

Detecting Copy Number Variants on Exome Sequencing Data via Deep Learning

Physics of Life Seminar Series, EPFL, Lausanne, Switzerland. Feb 24, 2023.
SAFARI Seminar Series, ETH, Zurich, Switzerland, Jun 2, 2023
Lausanne CompBio Meetings, Lausanne, Switzerland, Jun 14, 2023
Special Seminar, Carnegie Mellon University, Pittsburgh PA, Jun 20, 2023
Keynote Talk, East European Bioinformatics and Computational Genomics School (EEBG) 2023, Chișinău, Moldova, June 29, 2023.

Deep multitask learning of gene risk for comorbid neurodevelopmental disorders

Science Academy - Artificial Intelligence Summer School 2021, Sabanci University, Istanbul, Turkey. June 23, 2021.
RECOMB 2023, Istanbul, Turkey. April 17, 2023.

Polishing copy number variants via deep learning

EuroCC Turkey Seminars, Sabancı University, Istanbul, Turkey. June 9, 2022.
Science Academy - Artificial Intelligence Summer School 2022, Özyeğin University, Istanbul, Turkey. June 28, 2022.

High throughput sequencing and bioinformatic analyses for characterization of genetic diseases

International Basic Oncology Congress, Istanbul, Turkey. June 4, 2022.

Machine learning models to predict drug synergy and side effects

13th International Symposium on Pharmaceutical Sciences (IPOPS) 2021, Ankara University, Ankara, Turkey.June 22, 2021.

Spatio-Temporal Gene Discovery for Autism Spectrum Disorder

Mt. Sinai, Icahn School of Medicine, New York City, NY. Apr 12, 2019.
Jackson Laboratory, Farmington, CT. Apr 10, 2019.
Bilkent University, Department of Neuroscience, Ankara, Turkey. Mar 27, 2019.
Hacettepe University, Computer Engineering Dept., Ankara, Türkiye, Nov 2, 2018.
Weill Cornell Medical College, Institute for Computational Biomedicine, New York City, NY. Apr 11, 2018.
New York University, Department of Biology, New York City, NY. Apr 12, 2018.

SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS

HIBIT 2019, Izmir, Turkey. Oct 18, 2019.
IEEE AP/MTT/EMC/ED Seminar, Electrical Engineering Dept., Middle East Technical University, Ankara, Turkey. Oct 11, 2019.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Sabanci University, Artificial Intelligence Summer School, Istanbul, Turkey, Sep 7, 2019.
Bioinformatics Workshop III, Gazi University, Ankara, Turkey, May 26, 2019.
ISCB-RSG Webinar, May 23, 2019.
Acibadem University - Medical Informatics Course, Istanbul, Turkey, May 2, 2019.
AGU, Life Sciences Congress, Kayseri, Turkey, Feb 22, 2019.
National Nanotechnology Research Center (UNAM) - Synthetic Biology Day '18, Bilkent University, Ankara, Turkey, Oct 6, 2018.
ISMB 2018, Chicago, IL. Jul 8, 2018.

Inference Attacks Against Genomic Data-Sharing Beacons

Yale University, Biomedical Informatics Dept., New Haven, CT. Apr 9, 2019.
Koc University, Istanbul, Türkiye, Mar 4, 2019
Sabanci University, Istanbul, Türkiye, Nov 14, 2018.
Middle East Technical University, Informatics Institute, Ankara, Turkey. Nov 8, 2017.
Bilkent University, Dept. of Electric and Electronics Engineering, Ankara, Turkey. Nov 1, 2017.
GenoPri 2017, Orlando, FL. Oct 15, 2017.

Makina Ogrenmesi ile Sinirsel Gelisim Hastaliklari Icin Gen Kesfi

Istanbul University, IUGEN, Istanbul, Turkey. Mar 3, 2019.
BYOYO 2018, Bogazici University, Istanbul, Jul 4, 2018.

Bioinformatics for Variant Interpretation

Cukurova University, Adana, Turkey. Sep 23, 2017.

Genomic Data Sharing and Privacy Risks

The International Symposium on Health Informatics and Bioinformatics (HIBIT) 2017, North Cyprus, Jun 28, 2017

Gene Discovery for Autism Spectrum Disorder: Relating Genotype with Phenotype

12th National Medical Genetics Congress, Izmir, Turkey, Oct 07, 2016.

Network-based Analyses of Neurodevelopmental Disorders

University of Edinburgh, Edinburgh, Scotland, UK. Aug 19, 2015.
Bilkent University, Dept. of Psychology, Ankara, Turkey. Nov 25, 2015.
Bilkent University, Dept. of Molecular Biology and Genetics, Ankara, Turkey. Dec 9, 2015.
Middle East Technical University, Informatics Institute, Ankara, Turkey. Mar 9, 2016.
Middle East Technical University, Biological Sciences Department, Ankara, Turkey. Mar 11, 2016.

Gene Expression, Regulatory Elements and Rare Sequence Variation Identify Genes and Subnetworks Underlying Autism Risk

International Meeting for Autism Research (IMFAR), Salt Lake City, UT. May 15, 2015.

Knowledge Discovery on OMICS Data Using Biochemical Networks

Ozyegin University, Istanbul, Turkey. Dec 22, 2014.
Koc University, Istanbul, Turkey. Dec 23, 2014.
Sabanci University, Istanbul, Turkey. Dec 24, 2014.
Bilkent University, Ankara, Turkey. Dec 29, 2014.

MIRA: Mutual Information-based Reporter Algorithm for Metabolic Networks

Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA. January 9, 2014.
ISMB 2014, Boston, MA. July 15, 2014.
International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey. July 25, 2014.

ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information

University of Strasbourg, France. Mar 12, 2015.
The Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY. Mar 13, 2013.
Lane Center for Computational Biology, Carrnegie Mellon University, Pittsburgh, PA. March 18, 2013.
Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH. March 21, 2013.
Gerstein Lab, Yale University, New Haven, CT. March 26, 2013.
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA. March 27, 2013.
Dept. of Genome Sciences, University of Washington, Seattle, WA. April 23, 2013.