Krampis Lab

Konstantinos Krampis, Associate Professor of Biological Sciences PI, Bioinformatics Core Informatics Infrastructures Laboratory (BCIL) Director of Bioinformatics, Center for Translational and Basic Research (CTBR) Faculty at the Institute for Computational Biomedicine (ICB), Weill Cornell Medical College Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it Office:Rm. 467F Belfer Research Building 413 East 69th Street New York, NY 10021 Phone: (212) 396-6930

Lab Web Site:

• https://krampis.bioweb.hunter.cuny.edu

Research Web Site:

• https://agbiotec.github.io/website/

Education:

• Ph. D., 2009, Virginia Polytechnic Institute and State University
• M. Sc., 2003, University of Athens, Greece

List of Current Manuscripts:

• http://tinyurl.com/krampis-publications

Academic Appointments:

• 4/2014 - Present   City University of New York                        Associate Professor
• 4/2014 - Present   Center for Translational & Basic Research  Director of Bioinformatics
• 4/2014 - Present   Weill Cornell Medical College                     Faculty, Computational Biomedicine
• 5/2009 - 4/2014    J. Craig Venter Institute                               Assistant Professor
• 8/2003 - 5/2009    Virginia Bioinformatics Institute                 RA & Bioinformatics Engineer
• 8/2000 - 8/2003    University of Athens, Greece                      Research Assistant (RA)

Research Areas:

1. High-throughput bioinformatics infrastructures for cluster and cloud computing platforms.
   1. Scalability of data analysis pipelines using distributed computing: Kubernetes, NextFlow, Docker Swarm.
   2. Cross-platform bioinformatics through Docker virtualization in clinical and basic research.
   3. Visualization of genomic data on cloud databases using HTML5 / D3.js and in-browser computing.
2. Bioinformatics for Next Generation Sequencing (NGS) clinical and personal genomics.
   1. NGS data pipelines for QC, RNA-seq, Hi-C, metagenomics, variant discovery, genome assembly.
   2. Integrative analysis of variation, expression, chromatin and epigenetic data from TCGA, Encode, 4DN.
   3. Scalable, accessible pipelines for metagenomics, clinical samples and personal genomics on Galaxy.
3. Interdisciplinary research and novel applications of genomic sequencing and bioinformatics.
   1. Portable NGS and bioinformatics with Nanopore Minion and Intel Next Units of Computing (NUC).
   2. Touch-enabled, mobile computing interfaces for personal genomics and clinical NGS data visualization.
   3. Metabarcoding for conservation and biodiversity monitoring using environmental DNA (eDNA).
4. Algorithmic Information Theory, Computability, and Biologically-Inspired Computing.
   1. Emergence, complexity, information content and compressibility of epigenetic networks.
   2. Integrating DNA computing with NGS sequencing for reading molecolar output with high I/O.
   3. Computability and decidability of biologically-inspired and DNA computing models.

Grants:

1. Principal Investigator.

   2017 - 2018	CUNY Advanced Science Research Center (ASRC) Seed Award Program. Project Title: "Next Generation Sequencing for environmental DNA monitoring: understanding global biodiversity through bioinformatics”. Amount: $10,000
   2016 - 2017	CUNY Center for Translational and Basic Research Pilot Award. Project Title: "Democratizing access to bioinformatics computing for health disparities research”. Amount: $78,000
   2015 - 2016	National Institutes of Health. Project Title: “Expanding Infrastructure and Services of CUNY-CTBR Bioinformatics and Genomics Core”. Amount: $123,832
   2015 - 2017	Weill Cornell Medical College, Clinical and Translational Science Center Pilot Award. Project Title: "Cross-platform, scalable Science as a Service (SciaaS) infrastructures for NGS data analysis”. Amount: $110,660
   2014 - 2016	City University of New York. “Faculty startup award”. Amount $100,000
   2014 - 2015	National Institutes of Health. “Development of a Bioinformatics Core and Sequencing Facility at Hunter College for Minority Health Disparities Research”. Amount: $485,000
   2011 - 2014	National Institutes of Health. "Large-Scale Prokaryotic and Viral Next-Gen Sequencing Data Pipelines Using Cloud Computing”. Amount: $661,217

2. Co-Principal Investigator.

   2017 - 2018	National Institutes of Health. Project Title: “Mechanisms of regulation of progenitor proliferation and transformation” (ASRC Neuroscience sub-contract). Amount: $10,920
   2014 - 2015	National Science Foundation. Project Title: “Development of the next-generation Arabidopsis Informatics Portal”. Amount: $2,434,910

Honors and Awards:

Teaching and Mentoring:

1. Courses Developed and Taught.

   2014 - 2016	“Programming for Computational Biology”. Computer coding for biologists, covering basic data types, program flow control, functions, regular expressions, working with NGS files, and object-oriented programming.
   2015 - Present	“Computational Molecular Biology”. Sequence pattern matching, alignment, read mapping, variant calling, genome assembly, and gene prediction algorithms, in addition to data structures for efficient NGS data storage, taught based on the latest literature.
   2015 - Present	“Next-Generation Sequencing Data Analysis”. Concepts of sequencing technology, data formats and bioinformatics tools, implementation of data pipelines on the command line or online Galaxy interface for RNA-seq, ChIP-seq, and metagenomics.

2. Workshops Developed and Taught.

   2018	“A Plug and Play, on-Premises Bioinformatics Cloud, Providing Seamless, Single-Step Execution of NGS Pipelines”, Plant and Animal Genome International Conference, San Diego, CA.
   2017	“Deploying Large-Scale Bioinformatics Workflows with Kubernetes on a Google Cloud Computer Cluster”, Bioinformatics Open Source Conference & Hackathon, Prague, Czech Republic.
   2016	“NGS Sample Processing and Data Analysis through the CTBR Facility and Bioinformatics Computer Cluster”, workshop for CUNY and Weill Cornell Medical College faculty and students, New York, NY.
   2015	“Scalable, Intuitive Genomic Sequencing Data Analysis with Galaxy and Cloud BioLinux”, New York City College of Technology, New York, NY.
   2014	“Cloud BioLinux: Pre-Configured and On-Demand Virtual Machines for NGS Data Analysis”, 27th CTBR Symposium: Bioinformatics Applications in Health Disparities, New York, NY.
   2013	“Genomic Sequencing Data Analysis using Cloud Computing and the Amazon EC2 platform”, NYU Center for Health Informatics and Bioinformatics, New York, NY.
   2012	“South Africa National Research Network Workshop - Cloud BioLinux for High Performance Data Analysis”, Center of High Performance Computing, Johannesburg, South Africa.
   2012	“Empowering Genomics in South Africa Workshop - Cloud Computing Solutions for Genome Sequence Data Analysis”, University of Limpopo, Polokwane, South Africa.
   2011	“Cloud BioLinux for Bioinformatics Open Source Applications”, International Society for Computational Biology Conference, Vienna, Austria.
   2011	“Biologically Inspired Approaches to Resilience”, Institute of Human and Machine Cognition, Ocala, FL.
   2010	“From monolithic to distributed bioinformatics on the cloud”, Amazon Web Services, Seattle, WA.

3. Graduate Students Mentored.

   2015 - Present	Jason Mighty, Ph.D. Candidate, Biological Sciences Dept. at Lehman College & CUNY Graduate Center, Thesis topic: "Characterization of small RNAs Toward Development of Novel Biomarkers for Retinal Disease".
   2015 - Present	Allen Pan, Ph.D. Candidate, Biological Sciences Dept. at Hunter College & CUNY Graduate Center, Thesis topic: "Transcriptomics of Neuroprotective Mechanism of Epigallocatechin-3-gallate on Methamphetamine-induced neurotoxicity".
   2014 - Present	Juliette Gorson, Ph.D. Candidate, Chemistry Dept. at Hunter College & CUNY Graduate Center, Thesis topic: "Connecting venom gene expression, function and species diversity in predatory marine snails of the Terebridae".
   2014 - 2017	Samuel Hosmer, Ph.D. Candidate, Mathematics Dept. at Hunter College & CUNY Graduate Center, Spring 2015 internship on "Implementation of cloud computing based data analysis pipeline for CHIP-seq genomic sequencing data".
   2010 - 2012	Priti Kumari, M.Sc. Bionformatics, Biochemistry Dept. at George Washington University, Thesis topic: "Parallel and Cloud Computing Based Genome Assembly Using Bidirected String Graphs".
   2010 - 2012	Vivek Sarangi, M.Sc. Bionformatics, Biochemistry Dept. at George Washington University, Thesis topic: "Development and Evaluation of Cloud Computing Infrastructures for Next-Gen Sequencing Data analysis".

4. Undergraduate Students and Interns Mentored.

   2014 - Present	Bioinformatics Internship in Bioinformatics Core Infrastructures Lab. Undergraduate interns join my research group for 3 to 6 months and participate in various research projects.
   2016	Science Research Mentor at Urban Barcoding Project (UBRP) by Cold Spring Harbor Laboratory, NY. Mentored high-school students 1-2 hours weekly during the course of 9 months; the students worked on a metagenomics study to assess marine biodiversity.
   2015	Mentor, Science Research Mentoring Program (SRMP), American Museum of Natural History, NY. Mentored high-school students 4 hours weekly during the course of 9 months, who worked NGS bioinformatics pipelines and data visualization using the Galaxy server.
   2014	Summer Bioinformatics Workshop organized by Hunter Science High-School in New York City. Taught high-school students 3 hours weekly during the course of 9 months on bioinformatics programming and analysis of genomic sequencing datasets.

Institutional Committee and Scientific Service:

1. Graduate and undergraduate education committees.

   2016 - Present	Co-Chair, Ethics and Integrity Committee at the City University of New York. Organized a faculty working group to perform research and write a report as part the application for accreditation of CUNY by the Middle States Committee in Fall 2019.
   2015 - Present	Bioinformatics M.Sc. Program at CUNY. Designed and wrote the program proposal, assembling a group of faculty and curriculum using existing and newly designed courses.
   2015 - 2016	CUNY Data Science Committee. Contributed towards designing Data Science courses and developed two training grant proposals (NSF, NIH) to fund a Bioinformatics Data Science Ph.D. program.
   2014 - 2015	CUNY Quantitative Biology Program Faculty. Worked towards planning new bioinformatics syllabi and course modules, contributing to undergraduate (e.g., biology, computer science) and graduate (e.g., bioinformatics) curricula.

2. Editorial Positions, Boards and Peer-Review Service. .

   Oxford Bioinformatics; BMC Bioinformatics; BMC Research Notes; Nature Methods; Nature Scientific Reports; PLoS ONE; In Silico Biology; Future Generation Computer Systems; BioMed Research International; British Journal of Mathematics and Computer Science; Journal of Bioinformatics & Computational Biology; Genome Technology; GigaScience; F1000 Research.

3. Memberships in Professional Societies. .

   Since 2013	Illumina Basespace Developers Community
   Since 2009	Open Bioinformatics Foundation
   Since 2009	Bioinformatics Open Source Conference
   Since 2009	Galaxy Developers Community
   Since 2006	Bioinformatics IT World
   Since 2003	International Society for Computational Biology

Extramural Invited Presentations:

1. Graduate and undergraduate education committees.

   2018	High-Throughput Sequencing Computational Standards for Regulatory Sciences, Washington, DC .
   2017	Dept. of Public Health Sciences, Penn State College of Medicine, Hershey, PA
   2017	Dept. of Human Genetics, University of Pittsburgh, Pittsburgh, PA.
   2017	Intelligent Systems for Molecular Biology (ISMB), Prague, Czech Republic.
   2017	High-Throughput Sequencing Computational Standards for Regulatory Sciences, Washington, DC .
   2017	Dept. of Computational Medicine, University of Michigan, Ann Arbor, MI
   2016	Bioinformatics Ph.D. Program Guest Lecture, NYU Langonne Medical Center, New York, NY
   2015	Global Health Informatics Conference, University of South Florida, Tampa, FL
   2015	Biological Sciences Research Seminar, Lehman College, New York, NY
   2015	Illumina Basespace Conference, Broad Institute, Cambridge, MA
   2014	Galaxy Developer’s Conference, John Hopkins University, Baltimore, MD
   2014	CTBR 27th Symposium: Bioinformatics & Medical Applications, New York, NY
   2012	Cloud Computing Bioinformatics Symposium, Center Genomic Regulation, Spain
   2012	Translational Bioinformatics On The Cloud, J&J Inc., New Brunswick, NJ
   2012	NIH-NIAID Bioinformatics Symposium, Bethesda, MD
   2011	Genomics Standards Consortium, European Bioinformatics Institute, Hinxton, UK

Bibliography - Published Manuscripts

• High-throughput bioinformatics infrastructures for cluster and cloud computing platforms.
  1. Jensen T.L., Frasketi M., Conway K., Villarroel L., Hill H., Krampis K. and Goll J.B. (2017). F1000Research, 6, 2162. “RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting”.
  2. Ali T., Kim B., Lijeron C., Ogunwobi O.O., Mazumder R. and Krampis K. (2017). PeerJ Preprints, 5, p.e3385v1. “TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically oriented application”.
  3. Kim B., Ali T., Lijeron C. and Krampis K. (2017). Gigascience. 6(8), 1–7. “Bio-Docklets: Virtualization Containers for Portable, Scalable NGS Data Analysis”.
  4. Alterovitz G., Dean D.A., …. Krampis K., et al. (2017). bioRxiv, p.191783. “Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results”.
  5. Kim B., Ali T., Dong C., Laungani B., Wultsch C., Lijeron C. and Krampis K. (2017). bioRxiv, p.209734. “miCloud: a plug and play, on-premises bioinformatics cloud, providing seamless integration with Illumina genome sequencers”.
  6. Kim B., Ali T., Hosmer S. and Krampis K. (2016). Bioinformatics, 10, 1093. “Visual Omics Explorer (VOE): a Cross-Platform Portal for Interactive Data Visualization”.
  7. Afgan E., Krampis K., Goonasekera N., Skala K. and Taylor J. (2015). IEEE-MIPRO, 38, 223-228. “Building and provisioning bioinformatics environments on public and private clouds”.
  8. Krampis K. and Wultsch C. (2015). Methods in Next Generation Sequencing, 2(1). “A Review of Cloud Computing Bioinformatics Solutions for Next-Gen Sequencing Data Analysis and Research”.
  9. Kumari P., Mazumder R., Simonyan V. and Krampis K. (2015). F1000 Research, 4, 20. “Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly”.
  10. Krishnakumar V., Hanlon M.R., Contrino S., Ferlanti E.S., Krampis K…and Town C.D. (2014). Nucleic Acids Research, 28(43), 1003-1009. “Araport: the Arabidopsis Information Portal”.
  11. Krampis K., Booth T., Chapman B., Tiwari B., Field D. and Nelson K.E. (2012). BMC Bioinformatics, 13, 42. “Cloud Biolinux: pre-configured and on-demand computing for the genomics community”.
• Bioinformatics for Next Generation Sequencing (NGS) clinical and personal genomics.
  1. Brown S.M., Hao Y., Chen H., Laungani B.P., Ali T.A., Dong C., Lijeron C., Kim B., Krampis K. and Pei Z. (2017). bioRxiv, p.120402. "Fast functional annotation of metagenomic shotgun data by DNA alignment to a microbial gene catalog".
  2. Das D.K., Ali T., Krampis K. and Ogunwobi O. (2017). Data in Brief, 11, 131-35. “Fibronectin and androgen receptor expression data in prostate cancer obtained from a RNA-sequencing bioinformatics analysis”
  3. Das D.K., Naidoo M., Ilboudo A., Park J.Y., Ali T., Krampis K., Robinson B.D., Osborne J.R. and Ogunwobi O. (2016). Experimental Cell Research, 348(2), 190-200. “miR-1207-3p regulates the androgen receptor in prostate cancer via FNDC1/fibronectin”.
  4. Bubnell J., Jamet S., Tomoiaga D., D’Hulst C., Krampis K. and Feinstein P. (2015). PloS ONE, 10(10), p.e0141712. “In Vitro Mutational and Bioinformatics Analysis of the M71 Odorant Receptor and Its Superfamily”.
  5. Cole C., Krampis K., Karagiannis K., Almeida J.S., Faison W.J., Motwani M., Wan Q., Golikov A., Pan Y., Simonyan V. and Mazumder R. (2014). BMC Bioinformatics, 15, 28. “ Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.”
  6. Shamsaddini A., Yang P., Johnson E., Krampis K., Simonyan V. and Mazumder M. (2014). BMC Genomics, 15, 918. “Census-based rapid and accurate metagenome taxonomic profiling”.
• Interdisciplinary research and novel applications of genomic sequencing and bioinformatics.
  1. Wultsch C., Perkins S.L., Kelly M.J., Waits L.P., Quigley H., Amato G., and Krampis K. (In Prep). Molecular Ecology. “A new perspective in carnivore ecology and conservation: comparative gut microbiome composition, diversity, and functionality in sympatric Neotropical jaguars and pumas”.
  2. Wultsch C., DeBarba M, Schmieder A., Graham T., Wait L.P., Kelly M.J. and Krampis K. (In Prep). Scientific Reports. “Carnivore Feeding Ecology: Advances using a DNA Metabarcording Approach”.
  3. Ingala M.R., Simmons N.B., Wultsch C., Krampis K., Speer K.A., and S.L. Perkins. (In Prep). Applied and Environmental Microbiology. “Comparing Fecal and Intestinal Sampling Methods in Mammal Microbiome Research”.
  4. Prince S.J., Song L., Qiu D., dos Santos J.V.M., Chai C., Joshi T., Patil G., Valliyodan B., Vuong T.D., Murphy M. and Krampis, K. (2015). BMC Genomics, 16(1), 132. “Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean”.
  5. Wang H., Waller L., Tripathy S., St. Martin S.K., Zhou L., Krampis K. et al. (2010). The Plant Genome 3(1), 23-40. “Analysis of genes underlying soybean QTLs conferring partial resistance to P. sojae”.
  6. Zhou L., Mideros S.X., Bao L., Hanlon R., Arredondo F., Tripathy S., Krampis K. et al. (2009). BMC Genomics, 26(10), 49. "Infection and genotype remodel the entire Soybean transcriptome".
  7. Tyler B.M., Tripathy S., Kale S.D., Zhou L., Ferreira A., Dou D., Arredondo F.D., Mideros S.X., Bao L., Krampis K. and Jerauld, A. (2010). Phytopathology 99 (6), S164. “Comparative and functional genomics of oomycete infection”.
  8. Prasinos C., Haralampidis K., Milioni D., Samakovli D., Krampis K. and Hatzopoulos P. (2008). Plant Molecular Biology, 67(4), 323. “Complexity of Hsp90 in organelle targeting”.
  9. Wang H., Berry S., St. Martin S.K., Zhou L., Krampis K. et al. (2008). Phytopathology 98 (6), S165. “Allele mining for genes associated with partial resistance to Phytophthora sojae in soybean”.
  10. Krampis K., Tyler B.M. and Boore J.L. (2006) Molecular Plant Microbe Interactions, 19(12), 1329-1336. "Extensive variation in nuclear mitochondrial DNA content between the genomes of P. sojae and P. ramorum".
  11. Tyler B.M., Tripathy S…, Krampis K., et al. (2006) Science 313(5791), 1261-1266. "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis".
  12. Prasinos C., Krampis K., Samakovli D. and Hatzopoulos P. (2005). Journal of Experimental Botany, 56(412), 633-644. “Tight regulation of expression of two Arabidopsis cytosolic Hsp90 genes during embryo development”.

Bibliography - Monographs

1. .Krampis K. “Cloud Computing for Bioinformatics: Next-Gen Sequencing and Large-Scale Data Analytics” Monograph to be published in 2019, contract signed with Cambridge University Press, Cambridge, UK.

Bibliography - Book Chapters

1. Krampis K., Efstratios E. and Brown S.T. (2015, 2017). “Cloud-Based Next-Generation Sequencing Informatics”. Book Chapter in Next-Generation DNA Sequencing Informatics (pp. 361-370), First & Second Edition. Cold Spring Harbor Press, NY.
2. Rusch D.B., Miller J., Krampis K., Tovchigrechko A., Sutton G., Yooseph S. and Nelson K.E. (2014). “Bioinformatics for Genomes and Metagenomes in Ecology Studies”. Book Chapter in Infectious Microecology (pp. 203-226). Springer GmbH & Co, Berlin, Germany.
3. Goll J.B, Szpakowski S., Krampis K. and Nelson K.E. (2014). “Next-generation sequencing, metagenomes, and the human microbiome”. Book chapter in Bioinformatics and Data Analysis in Microbiology (Chpt. 7). Caister Academic Press, Norfolk, U.K.
4. Nelson K.E., Madupu R., Szpakowski S., Goll J.B., Krampis K. and Methe B.A. (2014). “Next-generation sequencing, metagenomes, and the human microbiome”. Book chapter in Next-generation Sequencing: Current Technologies and Applications (pp. 141-155). Caister Academic Press, Norfolk, U.K.
5. Quirino B.F., Barreto C.C., Pappas G.J., Zengler K., Krampis K. and Krüger R.H. (2013). “Genomes and Post-Genome Technology” Book Chapter in Prokaryotes (pp. 329-344). Springer GmbH & Co., Berlin, Germany.
6. Madupu R., Rogers Yu-H., Rusch D., Miller J., Krampis K. and Nelson K.E. (2012). “Microbiomes”. Book Chapter in Encyclopedia of Molecular Cell Biology and Molecular Medicine. Wiley-VCH Verlag GmbH & Co., Weinheim, Germany.
7. Miller J., Rusch D., Krampis K., Tovichgrechko A., Sutton G., Yooseph S. and Nelson K.E. (2012). “Bioinformatics for Genomes and Metagenomes in Microbial Ecology Studies”. Book Chapter in Encyclopedia of Molecular Cell Biology and Molecular Medicine. Wiley-VCH Verlag GmbH & Co., Weinheim, Germany.
8. Tyler B.M., Jiang R.H., Zhou L., Tripathy S., Dou D., Torto-Alalibo T., Li H., Mao Y., Liu B., Vega-Sanchez M., Mideros S.X., Hanlon R., Smith B.M., Krampis K., Ye K., Martin S.S., Dorrance A.E., Hoeschele I. and Sagahi Maroof M.A. (2008). “Functional genomics and bioinformatics of the Phytophthora sojae soybean interaction”. Book Chapter in Genomics of Disease (pp. 67-78). Springer GmbH & Co, NY.

Bibliography - Other Media: