CV and Research

Associate Professor, Hunter College, City University of New York

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AI/ML Research and Teaching Highlights

  • Transcriptomics: AI for Genome Analysis, new course to start in Spring 2026 with a focus on LLMs trained with genomic data, syllabus available

  • Machine Learning for Bioinformatics course taught at CUNY since 2020, covering deep neural networks, Transformer architecture, linear algebra and math for ML, AI safety and interpretability

  • Computational Molecular Biology taught since 2015, with AI/ML for Bioinformatics included in course as of 2020

  • AutoCircuit: Automated Discovery of Interpretable Reasoning Patterns in Large Language Models

  • Python Jupyter notebooks for teaching machine learning for biological network data (graph deep neural networks)

  • Github repository for paper published on geometric and graph deep learning, reviewing ML applications for bioinformatics

  • Cloud BioLinux co-founder, first Linux for bioinformatics on the Amazon cloud (Krampis et al. 2012)

  • Extended AI Latex graph (TikZ) app to utilize models from HuggingFace Inference Endpoints

  • Modified Neovim plugin to run OpenAI Codex as panel within the editor

Education

06/2003 – 05/2009 Virginia Tech, Blacksburg, VA - Ph.D. Bioinformatics

09/1997 - 06/2003 University of Athens, Athens, Greece - B.S., M.S., Biotechnology

Employment

  • 08/2003 – 05/2009 Virginia Bioinformatics Institute - Research Assistant Bioinformatics

  • 05/2009 – 04/2014 J. Craig Venter Institute - Assistant Professor Bioinformatics

  • 09/2014 – 09/2018 Hunter College, CUNY - Director of Bioinformatics CTBR

  • 09/2014 – Present Hunter College, CUNY - Associate Professor, Biological Sciences

  • 09/2014 – Present Hunter College, CUNY - Associate Professor Biology & Computer Science Programs at the CUNY Graduate Center

  • 02/2015 – Present Weill Cornell Medical College - Adjunct Faculty Computational Biomedicine

  • 09/2018 – Present Hunter College, CUNY - Director of Bioinformatics CCHDR

Research Awards

  • 2024-2025: AI for Multimodal Analysis of the All of Us Dataset, $127,389

  • 2024-2025: PSC CUNY Research Award, $3,500

  • 2024-2025: Bioinformatics and Biostatistics Core, Hunter College, $39,468

  • 2022-2023: CTSC Grant, Weill Cornell Medicine, $44,000

  • 2020-2021: PSC CUNY Research Award, $6,000

  • 2020-2021: Temple University / Fox Chase Center Pilot Research Award, $9,500

  • 2018-2023: Bioinformatics and Biostatistics Core, Temple University – Hunter College, City University of New York U54 Partnership, National Institutes of Health, $404,635

  • 2018-2019: CUNY Advanced Science Research Center Award, $14,040

  • 2017-2020: CUNY Advanced Science Research Center Award, $43,680

  • 2017-2018: CUNY Advanced Science Research Center Seed Award, $10,000

  • 2016-2017: NIMHD Award, National Institutes of Health, $123,453

  • 2015-2017: CTSC Pilot Award, Weill Cornell Medicine, $94,885

  • 2014: Faculty startup grant, City University of New York, $150,000

  • 2014: NIMHD Award, National Institutes of Health, $485,000

  • 2012-2016: Research Award, Advances in Biological Informatics Program, National Science Foundation, $4,992,581

Teaching at the City University of New York

  • 2014 - 2015: Introduction to Python Programming

  • 2015 - 2019: Genomic Sequencing and Bioinformatics Data Science

  • 2015 - current: Computational Molecular Biology with Machine Learning

  • 2020 - current: Machine Learning for Bioinformatics

In addition to the courses above, I have mentored and trained many undergraduate students in my laboratory who performed research and presented at the Hunter College Undergraduate STEM Conference, the SPEECH Cancer Health Disparities Conference and additional scientific meetings. (Details further in the student section of the CV).

Peer-reviewed Publications (selected)

Bioinformatics, Machine Learning, Cloud Computing

  • Krampis, K., Ross, E., Ogunwobi, O., Ma, G., Mazumder, R., Wultsch, C. (2023) "Principles of Artificial Neural Networks and Machine Learning for Bioinformatics Applications". Preprints.org, 2023060042.

  • Krampis K. (2021) "Democratizing access to genomics and personalized medicine for underrepresented research and clinical institutions through easily accessible bioinformatics platforms". BioTechniques 72(2):36-38.

  • Brown SM, Chen H, Hao Y, Laungani BP, Ali TA, Dong C, Lijeron C, Kim B, Wultsch C, Pei Z and Krampis K. (2019) "MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene Catalogs". GigaScience 8:20, giz020.

  • Kim B, Ali TA, Dong C, Lijeron C, Mazumder R, Wultsch C and Krampis K. (2019) "miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines". Journal of Computational Biology 26:280-284.

  • Ali TA, Kim B, Lijeron C, Changsu D, Wultsch C and Krampis K. (2018) "Implementation of a Reproducible, Accessible and Transparent RNA-seq Bioinformatics Pipeline within the Galaxy Platform". Journal of Computer Science and Systems Biology 1(3):195-199.

  • Dong C, Lee R, Sayad J and Krampis K. (2018) "Bioinformatics Programming for Bioavailability Analysis of Sequence Patterns in Public Genomic Databases". Advances in Bioequivalence and Bioavailability 1(2):1-4.

  • Jensen TL, Frasketi M, Conway K, Villarroel L, Hill H, Krampis K and Goll JB. (2017) "RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting". F1000Research 6:2162.

  • Kim B, Ali TA, Lijeron C, Afgan E and Krampis K. (2017) "Bio-Docklets: virtualization containers for single-step execution of NGS pipelines". GigaScience 6(8):1-7.

  • Das DK, Ali TA, Krampis K and Ogunwobi OO. (2017) "Fibronectin and androgen receptor expression data in prostate cancer obtained from a RNA-sequencing bioinformatics analysis". Data in Brief 11:131-5.

  • Kim B, Ali TA and Krampis K. (2016) "The Visual Omics Explorer (VOE): a Cross-Platform Portal for Omics Data Visualization". BMC Bioinformatics 32(13):2050-2052.

  • Krampis K and Wultsch C. (2015) "A Review of Cloud Computing Bioinformatics Solutions for Next-Gen Sequencing Data Analysis and Research". Methods in Next Generation Sequencing 2(1).

  • Kumari P, Mazumder R, Simonyan V and Krampis K. (2015) "Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly". F1000 Research 4(20).

  • Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, … Krampis K et al. (2014) "Araport: the Arabidopsis Information Portal". Nucleic Acids Research 28; 43:1003–1009.

  • Krampis K, Booth T, Chapman B, Tiwari B, Field D and Nelson KE. (2012) "Cloud Biolinux: pre-configured and on-demand computing for the genomics community". BMC Bioinformatics 13:42.

  • Krampis K. (2007) "Semantic Web Bioinformatics: distilling knowledge by mining heterogeneous data". VBI e-connections 2(3):2.

Microbiomics, Cancer and other Biological Research

  • Naidoo MK, Levine F, Gillot T, Orunmuyi AT, Olapade-Olaopa EO, Ali TA, Krampis K and Ogunwobi OO. (2020) "MicroRNA-1205 regulation of FRYL in metastatic castration-resistant prostate cancer". Clinical and Experimental Metastasis 36(2).

  • King CH, Desai H, Sylvetsky A, LoTempio J, Ayanyan S, Gasparyan L, Carrie J, Keith Crandall K, Fochtman B, Naila Gulzar N, Paul Howell P, Issa N, Krampis K, Mishra L, Morizono H, Ren Y, Simonyan V, Smith K, VedBrat S and Mazumder R. (2019) "Baseline human gut microbiota profile in healthy people and standard reporting template". PLoS ONE 14(9):e0206484.

  • Di L, Wan Z, Akther S, Ying C, Larracuente A, Li L, Di C, Nunez R, Cucura DM, Goddard NL, Krampis K and Qiu W. (2018) "Genotyping and quantifying Lyme pathogen strains by deep sequencing of the outer surface protein C (ospC) locus". Journal of Clinical Microbiology 56(11):940.

  • Alterovitz G, Dean D, Goble C, Crusoe MR…Krampis K … Mazumder R. (2018) "Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results". PLoS Biology 16(12):e3000099.

  • Krampis K. (2017) "TED toolkit: A comprehensive approach for convenient transcriptomic profiling as a clinically oriented application". PeerJ E3385v1.

  • Bubnell J, Jamet S, Tomoiaga D, D’Hulst C, Krampis K and Feinstein P. (2015) "In Vitro Mutational and Bioinformatics Analysis of the M71 Odorant Receptor and Its Superfamily". PLoS ONE 10(10):0141712.

  • Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V and Mazumder R (2014) "Census-based rapid and accurate metagenome taxonomic profiling". BMC Genomics 15(1):918.

  • Cole C, Krampis K, Almeida J, Faison W, Motwani M, Simonyan V, Golikov A, Pan Y and Mazumder M (2014) "Non-synonymous single-nucleotide variations in TCGA control samples and their effect on the human proteome: workflow for NGS data biocuration and proteome-wide analysis". BMC Bioinformatics 15:28.

  • Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A … Krampis K et al. (2006) "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis". Science 313(5791):1261.

  • Krampis K, Tyler BM and Boore JL (2006) "Extensive variation in nuclear mitochondrial DNA content between the genomes of P. sojae and P. ramorum". Molecular Plant Microbe Interaction 19(12):1329.

Book Chapters

  • Dang T, Achrak E, Krampis K and Holford M. (2021) "VenomFlow: An automated venomic pipeline for identification of putative therapeutic toxins", in Marine Genomics Lab Protocols, published by Elsevier Press, Cambridge, MA, USA

  • Krampis K, Efstathiadis E, and Brown SM. (2015) "Cloud-Based Next-Generation Sequencing Informatics", in Next-Generation DNA Sequencing Informatics, Second Edition, published by Cold Spring Harbor Laboratory Press, New York, USA.

  • Rusch DB, Miller J, Krampis K, Tovchgrechko A, Sutton G, Yooseph S and Nelson KE. (2014) "Bioinformatics for Genomes and Metagenomes in Ecology Studies", in Infectious Microecology, published by Springer GmbH & Co., Berlin, Heidelberg, Germany.

  • Goll JB, Szpakowski S, Krampis K and Nelson KE. (2014) "Metagenomics and Microbiomes", in Bioinformatics and Data Analysis in Microbiology, published by Caister Academic Press, Norfolk, U.K.

  • Nelson KE, Madupu R, Szpakowski S, Goll JB, Krampis K and Methe BA. (2014) "Next-generation sequencing, metagenomes, and the human microbiome", in Next-Generation Sequencing: Current Technologies and Applications, published by Caister Academic Press, Norfolk, U.K.

  • Quirino BF, Chaves Barreto C, Pappas GJ, Zengler K, Krampis K and Krueger RH. (2013) "Genomes and Post-Genome Technology", in Prokaryotic Biology and Symbiotic Associations, published by Springer GmbH & Co., Berlin, Heidelberg, Germany.

  • Madupu R, Rogers Yu-H, Rusch D, Miller J, Krampis K and Nelson KE. (2012) "Microbiomes", in Encyclopedia of Molecular Cell Biology and Molecular Medicine, published by Wiley-VCH Verlag GmbH Germany.

  • Miller J, Rusch D, Krampis K, Tovichgrechko A, Sutton G, Yooseph S and Nelson KE. (2012) "Bioinformatics for Genomes and Metagenomes in Microbial Ecology Studies", in Infectious Micro-ecology: Theory and Applications, published by Wiley-VCH Verlag GmbH & Co., Germany.

  • Tyler BM, Jiang RHY, Zhou L, Tripathy S, Dou D, Torto-Alalibo T, Li H, Mao Y, Liu B, Vega-Sanchez M, Mideros SX, Hanlon R, Smith, BM, Krampis K et al. (2008) "Functional genomics and bioinformatics of the Phytophthora sojae soybean interaction", in Genomics of Disease, published by Springer Science, New York, USA.

Students and Mentoring

Graduate students, thesis primary advisor

  • Geoffery Yoo, Data Science Master’s Student, CUNY Graduate Center, Thesis topic "Deep Learning model training for large scale applications in epigenetics and gene expression" (2020)

  • Dennis Huang, Biology PhD Student, CUNY Graduate Center, Thesis topic "Single-cell sequencing and epigenetic networks in neuron damage in neurological disorders" (2019)

  • Enis Berg Coban, Computer Science PhD Student, Hunter College and CUNY Graduate Center, Thesis topic "Manifold Learning algorithms for Noise Control and Trajectory Inference in Single Cell Sequencing Data" (2019)

  • Priti Kumari, M.Sc. Bioinformatics, Biochemistry Department, George Washington University, Thesis project "Parallel and Cloud Computing Based Genome Assembly Using Bidirected String Graphs" (2013)

  • Vivek Sarangi, M.Sc. Bioinformatics, Biochemistry Department, George Washington University, Thesis project "Development and Evaluation of Cloud Computing Infrastructures for Next-Gen Sequencing Data analysis" (2012)

Graduate student co-mentoring

  • Melissa Ingala, Comparative Biology Ph.D. Candidate, Richard Gilder Graduate School, American Museum of Natural History, "Comparative Metagenomics of Wild Mammals for Identifying Signals of Host Ecology and Evolution" (2017)

  • Kelly Speer, Comparative Biology Ph.D. Candidate, Richard Gilder Graduate School, American Museum of Natural History, Thesis topic "Microbiomes and Feeding Ecology in Neotropical Bats" (2017)

  • Allen Pan, Biology Ph.D. Candidate, Hunter College and CUNY Graduate Center, Thesis topic "Neuroscience of addiction" (2016)

  • Hasan Zumrut, Biology Ph.D. Candidate, Lehman College and CUNY Graduate Center, Thesis topic "Development of novel NGS data analysis methods of SELEX Libraries" (2016)

  • Jason Mighty, Biology Ph.D. Candidate, Lehman College and CUNY Graduate Center, Thesis topic "Ocular degeneration genetics and small RNAs" (2016)

  • Juliette Gorson, Chemistry Ph.D. Candidate, Hunter College and CUNY Graduate Center, Thesis topic "Discovery of cancer inhibiting compounds in venomous marine snail transcriptome" (2015)

  • Samuel Hosmer, Mathematics Ph.D. Candidate, CUNY Graduate Center, Spring 2015 internship on "Implementation of cloud computing based data analysis pipeline for CHIP-seq genomic sequencing data" (2015)

Undergraduate student mentoring

  • Kerwin George, Bioinformatics and Biological Sciences Major, Hunter College (graduation spring 2021), performed research in Krampis' lab on "Ethnic and Race-Specific Variations in Carcinoma Microbiomes"

  • Jesus Lopez, Bayan Berri, Qianfan Yang, Brian Gerevits. Biological Sciences Major, "Deep Learning model development and training for microbiome analysis in minority health" Summer 2020 Cancer Research Institute (SCRI) internship as part of the Hunter College Temple University / FCCC partnership

  • Tahir Ramzan, Rajveer Singh, Olivia Senecal, Qianfan Yang, Wisam Ali. Biological Sciences Major, "Human microbiome and minority health: unraveling variations associated with health disparities" (Fall 2018 - Spring 2020), poster at Hunter College Undergraduate Student Conference and NIH U54 meeting, Temple University 2019 and 2020

  • Mohammed Rahman, Ariel Avshalom, Mathematics and Computer Sciences Majors, "MicrobiomeExplorer: An interactive and web-based R Shiny analysis platform for microbiome research" (Fall 2018 - Spring 2020), poster at Hunter College Undergraduate Student Conference and NIH U54 meeting, Temple University 2019 and 2020; poster also at Bioconductor Conference at the Rockefeller University

  • Catherine Ng, Ariel Avshalom, Anna Fernadez and Simran Kaur, Mathematics and Biological Sciences Majors, Hunter College (graduation Spring 2019), performed research in Krampis' lab on "Assessing transcriptome and transcription factor sites in RNA-seq and ChIP-seq NGS through downstream computational analysis in the Galaxy web platform" (research was presented at the Hunter College Undergraduate Student Research Conference in Spring 2018)

  • Philip Ort, Biological Sciences Major, Hunter College (graduation Fall 2018), performs research in Krampis' lab on "Computational analysis of cancer cell line differential gene expression datasets using the Galaxy web platform"

  • Joseph Sayad, Computer Science Major, Hunter College (graduation Spring 2018), performed research in Krampis' lab on "Development of Distributed Bioinformatics Algorithms using Intel Next Unit of Computing Systems"

  • Trami Dang, Physics Major, Hunter College (graduation Fall 2016), performed research in Krampis' lab on "Development of Cloud Computing Pipeline for Methylation Bi-Sulfite Sequencing Data Analysis"

  • Bobby Linguani, Biological Sciences Major, Hunter College (graduation Fall 2016), performed research in Krampis' lab on "Large-Scale Human Microbiome Bioinformatics Pipelines in Galaxy and Docker Containers", manuscript submitted with NYU collaborating group

  • Kevin Raz, Biological Sciences Major, Hunter College (graduation Fall 2016), performed research in Krampis' lab on "Implementation of Portable Metagenomic Data Analysis Pipelines with Pynast and Visualizations"

  • Roy Lee, Biological Sciences Major, Hunter College (graduation Spring 2016), performs research in Krampis' lab on "Cross-Platform Blast Toolkits using Docker Software Containers"

  • Thahmina Ali, Biological Sciences Major, Hunter College (graduation May 2015), performed research in Krampis' lab on "Implementation of a comprehensive, standardized, scalable, user-friendly, RNA-seq analysis pipeline" (accepted as Ph.D. student at Columbia University)

  • Baekdoo Kim, Computer Science Major, Hunter College (graduation December 2014), performed research in Krampis' lab on "The Visual Omics Explorer (VOE): Providing a Highly Interactive, Cross-Platform Portal for Omics Data Visualization", manuscript was published in 2016

Invited talks, workshops, and presentations

  • "Artificial Intelligence and Deep Learning for Bioinformatics: current progress and future prospects". Data Science Research Survey Seminar, PhD Program in Computer Science, CUNY Graduate Center, May 2021 (Online-remote meeting)

  • "Bioinformatics infrastructure and services development at the Bioinformatics and Biostatistics Core (BBC) of the Temple University – Fox Chase Cancer Center - Hunter College Partnership, Award year 3 progress". NIH U54 Cancer Health Disparities Progress Review Meeting, May 2021 (Online-remote meeting)

  • "Next Generation Computational Infrastructures for Accessible, Standardized, Scalable Bioinformatics". Lawrence Berkeley National Laboratory, September 2020 (Online-remote meeting)

  • "Next Generation Computational Infrastructures for Accessible, Standardized, Scalable Bioinformatics", Food and Drug Administration, July 2019, Washington, DC, USA

  • "Programmability, complexity and computability of large-scale cellular epigenetic networks", Unconventional and Natural Computation Conference, June 2019, Tokyo, Japan

  • "Bioinformatics infrastructure and services development at the Bioinformatics and Biostatistics Core (BBC) of the Temple University – Fox Chase Cancer Center - Hunter College Partnership, Award year 1 progress". NIH U54 Cancer Health Disparities Progress Review Meeting, May 2019, Philadelphia, PA, USA

  • "Exporting Biological Compute Objects (BCO) for NGS data analysis pipelines specification on the Galaxy server", Biocompute Objects Workshop, May 2019, Washington, DC, USA

  • "Next Generation Computational Infrastructures for Accessible, Standardized, Scalable Bioinformatics", Genome Institute of Singapore, October 2018, Singapore

  • "Integrating DNA computing with NGS sequencing for reading molecular output with high I/O", Unconventional and Natural Computation Conference, June 2018, Fontainebleau, France

  • "Exporting Biological Compute Objects (BCO) from Docker container running Galaxy NGS data analysis pipelines", Biocompute Objects Workshop, March 2018, Washington, DC, USA

  • "MiCloud and BioDocklets: A Plug and Play, on-Premises Bioinformatics Cloud, Providing Seamless, Single-Step Execution of NGS Pipelines", Plant and Animal Genome (PAG) Conference, January 2018, San Diego, CA, USA

  • "Building the Next Generation of Bioinformatics Infrastructures for NGS Data Analysis", Department of Human Genetics, University of Pittsburgh, October 2017, Pittsburgh, PA, USA

  • "Interoperability of NextFlow workflows on the Google Cloud and the GA4GH platform/DREAM challenge", OpenBio CodeFest, Intelligent Systems for Molecular Biology Conference (ISMB), July 2017, Prague, Czech Republic

  • "STEM Movement Science and Art Education Initiative", two art works presented, in collaboration with the DNA Learning Center - Cold Spring Harbor Laboratory, at the International Society for Computational Biology (ISCB) Art in Science Meeting, July 2017, Prague, Czech Republic

  • "Microbiome Analysis on the Cloud Workshop", was selected as participant at this workshop from a population of applicants due to the specific work performed in the bioinformatics field. The workshop was organized by the Human Microbiome Project (HMP) consortium and the Institute of Genome Sciences, University of Maryland Medical School, June 2017, Baltimore, MD, USA

  • "Bio-Docklets: virtualization containers for single-step execution of NGS pipelines". GWU-FDA Symposium on Data Standards and Interoperability, National Institutes of Health, March 2017, Rockville, MD, USA

  • "Building the Next Generation of Bioinformatics Infrastructures for NGS Data Analysis", Univ. of Michigan, Dept. of Computational Medicine and Bioinformatics seminar series, January 2017, Ann Arbor, MI, USA

  • "A Platform for Developing Bioinformatics Analytics for Cloud, Cluster and Desktop Computers", presented at: Dept. of Biological Sciences, Lehman College, City University of New York, November 2016, NY, USA

  • "Leveraging cloud computing technologies for large-scale genome sequence data analysis, and the Cloud BioLinux platform", presented at: Cloud Computing in Bioinformatics 2012, Center For Genomic Regulation, Barcelona, Spain; Translational Bioinformatics On The Cloud Conference 2012, New Brunswick, NJ, USA; NIAID Bioinformatics Festival 2012, National Institutes of Health, Bethesda, MD, USA; NIAID Genomics Standards Consortium Conference 2011, European Bioinformatics Institute, Hinxton, UK; NIAID Cloud Computing (Chair), Next-Gen Sequencing Data Management 2010, Providence, RI, USA

  • "South Africa National Research Network Workshop - Cloud BioLinux for High Performance Data Analysis", Center of High Performance Computing, December 2011, Johannesburg, South Africa

  • "Solutions for Genome Sequence Data Analysis", National Institutes of Health, University of Limpopo, June 2011, South Africa

  • "Security and Resilience, Scale-Free Metabolic Networks", Institute of Human and Machine Cognition, April 2011, Ocala, FL, USA

Academic and Professional Honors

  • 2019 Clinical and Translational Science Center Honors Award

  • 2018 Proposal Development / Faculty Research Award, City University of New York

  • 2017 President’s Travel Award, Hunter College, City University of New York

  • 2015 Entrepreneurship Lab NYC Selected Top 20 Business Plan (300+ entries)

  • 2011 Bioinformatics Open Source Conference – Best Audience Voted Presentation Award

  • 2008 Virginia Tech Graduate Association Executive Board Elected Member

  • 2008 Virginia Tech Outstanding Interdisciplinary Doctoral Student Award

  • 2008 Horace E. Alphin Doctoral Tuition Scholarship

  • 2007 Virginia Tech Graduate Student Assembly Research Grant

  • 2006 James and Ina Mae Doctoral Tuition Scholarship

Membership in Professional Societies

  • NCI Containers and Workflows Interest Group - NIH Data Science (since 2017)

  • High-performance Integrated Virtual Environment (HIVE) Consortium, FDA-GWU (since 2016)

  • IEEE Biological Compute Objects (BCO) Working Group (since 2015)

  • Open Bioinformatics Foundation (since 2006)

  • International Society for Computational Biology (since 2008)

Administration and Faculty Service

Director of Bioinformatics and Biostatistics Core, U54 Cancer Partnership Hunter College / Temple University (CCHDR, 2018-Present): Designed and implemented bioinformatics software that is foundational to the partnership research. In addition, I collaborated extensively with partnership investigators that are non-technical users, and helping them to easily access and manage large-scale genomic datasets and run bioinformatics data pipelines, enabling investigators to easily collaborate, and exchange data and analysis results.

Director of Bioinformatics Core Facility, Center for Translational and Basic Research at Hunter College (CTBR, 2014-2018): I lead the design and initial development of the facility and directed the design, budget, evaluation and acquisition of computational and genomic sequencing infrastructure, in addition to hands-on implementation by defining project budget, execution plan, and coordinating equipment acquisition and installation.

Faculty Committee Chair, Standard II, Ethics and Integrity, Middle States Commission on Higher Education (2017-2018): I was appointed for a two-year commitment to this committee by the Provost at Hunter College. I conducted extensive research and wrote a report in collaboration with the Dean for Diversity and Compliance. The work involved looking into data and processes ranging from recruitment and marketing materials, public disclosures of information, to institutional by-laws and all processes at Hunter College relevant to ethics and integrity.

Faculty Advisory Committee of Data Science at CUNY, Office of the Vice Chancellor for Research (2016-2017): I contributed to the creation of a catalogue of all the academic programs, from community-college certificate programs to Graduate Center doctoral programs that have a focus in or relevance to data science, and wrote as Principal Investigator a proposal submitted to the National Science Foundation for the creation of a PhD program in Data Science.

Education and Outreach

  • Mentored on bioinformatics research the undergraduate student Joseph Sayad who is a first-generation college student from Syrian immigrants, and he was able to win a competitive scholarship, and subsequently join Washington University’s PhD program in Computer Science, becoming the first scientist in his family.

  • Mentor, Science Research Mentoring Program (SRMP), American Museum of Natural History: supervised two minority high-school students performing bioinformatics research, students were accepted to Stanford University and University of Pittsburgh.

  • Mentor, Urban Barcoding Microbiome Program (UBMP), Cold Spring Harbor Laboratory: supervised two minority high-school students performing bioinformatics research, students were accepted to Carnegie Mellon University and Hunter College.