Konstantinos Krampis

Konstantinos Krampis is currently an Associate Professor in the Department of Biological Sciences at Hunter College and Faculty of the Computer Science and Biology Ph.D. programs at CUNY. In addition, he is the Director of Bioinformatics and Biostatistics Core within the Cancer Health Disparity Partnership of Hunter College with Temple University / FCCC, and Adjunct Faculty at the Institute of Computational Biomedicine at Weill Cornell Medical College. Previously, he was an Assistant Professor at the J. Craig Venter Institute, and did graduate studies at the Virginia Bioinformatics Institute at Virginia Tech.

Up to now, he has funded his research with multiple awards by the National Science Foundation (NSF) and the National Institutes of Health (NIH) both as co-PI and PI. With these awards he has performed research and development of scalable bioinformatics solutions, running on compute clusters and the cloud by abstracting the underlying software complexity, enabling portability, scalability and seamless access across computing platforms. In addition, Prof. Krampis has implemented a Next-Generation Sequencing (NGS) facility and high-performance bioinformatics computing cluster at CUNY, and novel bioinformatics tools that enable broad application of genomics, in areas ranging from basic biological research to clinical genomics.

His current research focuses on Large Language Models and Artificial Intelligence interpretability, deep learning and machine learning, with applications for personal genomics and broadly in the field of genomic data science.

• PI, Professional Staff Congress CUNY, $3,500 (2024-25)  
• Co-PI, " Artificial Intelligence for Multi-Modal Analysis of Cancer Health Disparities in the All of Us Dataset", National Institutes of Health - NCI: $200,000 (2024-25)
• PI, Bioinformatics and Biostatistics Core, "Temple University / FCCC - Hunter College Regional Comprehensive Cancer Health Disparity Partnership U54", National Institutes of Health - NCI: $324,050 (2023-28) 
• PI, Bioinformatics and Biostatistics Core, "Temple University / FCCC - Hunter College Regional Comprehensive Cancer Health Disparity Partnership U54", National Institutes of Health - NCI: $392,180 (2018-23)
• PI (sub-contract), "Histone Deacetylation in Oligodendrocyte Differentiation", CUNY Advanced Science Research Center (ASRC) Neuroscience Initiative - Dr. Casaccia: $14,040 (2018-19)
• PI (sub-contract), "Mechanism of regulation of progenitor proliferation and transformation", CUNY Advanced Science Research Center (ASRC) Neuroscience Initiative: $43,680 ($10,920 per year, 2017-21)
• PI, "Next-generation environmental DNA monitoring: bioinformatics tools to understand global biodiversity", CUNY Advanced Science Research Center (ASRC) Seed Award: $10,000 (2017)
• co-PI, "Expanding Infrastructure and Services of CUNY-CTBR Bioinformatics and Genomics Core", National Institutes of Health - NIMHD award to Center for Translational and Basic Research: $123,453 (2016)
• PI, "Cross-platform, scalable Science as a Service (SciaaS) infrastructures for genomic sequencing data analysis", Pilot Award, Weill Cornell Medical College, Clinical Translational Science Center (CTSC): $94,885 (2015-17)
• PI, "Development of a Bioinformatics Computing Core and Sequencing Facility at Hunter College for Minority Health Disparities Research", National Institutes of Health - NIMHD: $485,000 (2014)
• PI, Faculty startup grant, City University of New York, New York, NY: $150,000 (2014)
• Co-PI, "Development of a next-generation Arabidopsis Informatics Portal", National Science Foundation - Division of Biological Infrastructure, Advances in Biological Informatics Program: $2,434,910 (2012-2014), total $4,992,581 (2012-2016)
• PI, "Large-Scale Prokaryotic and Viral Next-Gen Sequencing Data Pipelines Using Cloud Computing", National Institutes of Health - NIAID Infectious Disease Center at Craig Venter Institute: $661,217 (2011-2012)

• Since 2017 NCI Containers and Workflows Interest Group - NIH Data Science
• Since 2016 High-performance Integrated Virtual Environment (HIVE) Consortium, FDA-GWU
• Since 2015 IEEE Biological Compute Objects (BCO) Working Group
• Since 2013 Illumina Basespace Developers Community
• Since 2009  Open Bioinformatics Foundation
• Since 2009  Galaxy Developers Community
• Since 2006 Bioinformatics IT World

• BIO 42500, Computational Molecular Biology, every spring semester since 2015, Hunter College.
• BIO 47106 / BIO 79006 Machine Learning for Bioinformatics, every fall semester since 2021, Hunter College.
• BIO 48001 / 2, Introduction to Experimental Biology, every spring and fall semesters since 2015, Hunter College.
• BIO 47105 / BIO 79005 Python for Bioinformatics, fall semesters 2014 - 2015, Hunter College.
• BIO 23100, Microbiology with Bioinformatics Applications, every spring semester since 2021-2022, Hunter College. 
• BIO 79303 / CS 87100 Next-Gen Sequencing and Bioinformatics, fall semesters 2015-2020, CUNY Graduate Center.
• BIO 79303 Machine Learning & AI for Bioinformatics, every fall semester since 2021, CUNY Graduate Center.
• BIOL 89800 / CS 86190, Capstone - PhD mentoring, fall and spring semesters since 2014, CUNY Graduate Center.

Selected Publications on Machine Learning, AI and Bioinformatics:

• Krampis K, Ross E, Ogunwobi O, Ma G, Mazumder R, Wultsch C. 2024 Principles of Artificial Neural Networks and Machine Learning for Bioinformatics Applications. Preprints: 202306.0042 
• Krampis K. Democratizing bioinformatics through easily accessible software platforms for non-experts in the field. 2022 BioTechniques. Feb 1;72(2):36-8.
• Kim, B., T.A. Ali, C. Dong, C. Lijeron, R. Mazumder, C. Wultsch, and K. Krampis. 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.
• Kim, B., T. Ali, C. Lijeron, E. Afgan, and K. Krampis. 2017. Bio-Docklets: virtualization containers for single-step execution of NGS pipelines. GigaScience 6(8):gix048.
• Kim, B., T. Ali, S. Hosmer, and K. Krampis. 2016. Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization. Bioinformatics 32:2050-2052.
• Krampis, K., and C. Wultsch. 2015. A review of cloud computing bioinformatics solutions for next-gen sequencing data analysis and research. Methods in Next Generation Sequencing 2(1):23-34.
• Krampis, K., T. Booth, B. Chapman, B. Tiwari, M. Bicak, D. Field, and K.E. Nelson. 2012. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 13:42.

Selected Publications on Metagenomics, Cancer and Personal Genomics:

• Ghosh J., Schultz B.M., Chan J., … Krampis et al. 2022 Epigenome-Wide Study Identifies Epigenetic Outliers in Normal Mucosa of Patients with Colorectal Cancer. Cancer prevention research (Philadelphia, Pa.) Nov 1;15(11):755-66.
• Speer, K.A., Teixeira, T.S.M., Brown, A.M., Perkins, S.L., Dittmar, K., Ingala, M.R., Wultsch, C., Krampis, K., Dick, C.W., Galen, S.C. and Simmons, N.B., 2022. Cascading effects of habitat loss on ectoparasite-associated bacterial microbiomes. ISME communications, 2(1), p.67.
• Naidoo, M., Levine, F., Gillot, T., Orunmuyi, A.T., Olapade-Olaopa, E.O., Ali, T., Krampis, K., Pan, C., Dorsaint, P., Sboner, A. and Ogunwobi, O.O., 2021. MicroRNA-1205 Regulation of FRYL in Prostate Cancer. Frontiers in Cell and Developmental Biology, 9.
• Brown, S.M., H. Chen, Y. Hao, B.P. Laungani, T.A. Ali, C. Dong, C. Lijeron, B. Kim, C. Wultsch, Z. Pei, and K. Krampis. 2019. MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. GigaScience 8:giz020.
• Alterovitz, G., D. Dean, C. Goble, M.R. Crusoe, S. Soiland-Reyes, ..., K. Krampis, et al. 2018. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biology 16(12):e3000099.
• Cole, C., K. Krampis, K. Karagiannis, J.S. Almeida, W.J. Faison, M. Motwani, Q. Wan, A. Golikov, Y. Pan, and V. Simonyan. 2014. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics 15:28.
• Tyler, B. M., S. Tripathy, X. Zhang, P. Dehal, R.H. Jiang, A. Aerts,.., K. Krampis et al. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261-1266.