A. Ercüment Çiçek, Ph.D.

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A. Ercüment Çiçek

Welcome! I am currently on sabbatical leave. I am working as a visiting professor at EPFL. I am hosted by the Laboratory for Neurodevelopmental Systems Biology.


In the background,

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

 

I was a Lane Fellow in Computational Biology at Carnegie Mellon University. My advisors were Kathryn Roeder and Ziv Bar-Joseph. I got my Ph.D. in Computer Science from Case Western Reserve University in 2013. My advisor was Gultekin Ozsoyoglu
 
 

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
Distinguished Teaching Award 2022 Bilkent University
Aziz Sancar Incentive Award 2020
Aziz Sancar Incentive Award 2020 Health Institutes of Turkey - TÜSEB
BAGEP 2020
BAGEP 2020 Young Scientist Awards Program
Research Incentive Award
Research Incentive Award 2019 - IEEE Turkey Section
Research Incentive Award
Research Incentive Award 2018 - METU Parlar Foundation
Visiting Researcher Fellowship
Visiting Researcher Fellowship Visiting University of Strasbourg in Summer 2018
Outstanding Young Scientist Award
Outstanding Young Scientist Award 2017 - Turkish Academy of Sciences
Lane Fellowship
Lane Fellowship 2013 - 2015
ACM SIGMOD Scholarship
ACM SIGMOD Scholarship ACM A.M. Turing Centenary Celebration
Choose Ohio First Scholarship
Choose Ohio First Scholarship 2011-2012
Fulbright Doctorate Fellowship
Fulbright Doctorate Fellowship 2009
CWRU Research Assistantship
CWRU Research Assistantship 2009 - 2013
TUBITAK Graduate Fellowship
TUBITAK Graduate Fellowship 2007-2009 - Technical and Scientific Research Council of Turkey
SU Undergraduate Scholarship
SU Undergraduate Scholarship 2003 - 2007

Talks

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.

Deep multitask learning of gene risk for comorbid neurodevelopmental disorders

  • Science Academy - Artificial Intelligence Summer School 2021, Sabanci University, Istanbul, Turkey. June 23, 2021.

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.

Computational Techniques and Systems For Metabolomics Analysis

  • Sabanci University, Istanbul, Turkey. Jun 6, 2012

Analyzing the Dynamics of Metabolic Networks: Computer Science Approach

  • EECS - Case Western Reserve University, @EECS Departmental Seminars, Nov. 29, 2010.

Computational Analysis of Metabolomics Data + Querying and Visualization Environment

  • School of Medicine - Case Western Reserve University, to Cystic Fibrosis Research Group, Nov. 2, 2010.

Operational Variable Job Scheduling with Eligibility Constraints

  • University of Texas at Dallas (UTD), Texas, USA, Aug. 22, 2008.

Teaching

2021-2022 Fall

2020-2021 Spring

2020-2021 Fall

2019-2020 Spring

2019-2020 Fall

2018-2019 Fall

2018-2019 Spring

2017-2018 Fall

2017-2018 Spring

2016-2017 Spring

2015-2016 Spring

2015-2016 Fall