Karathia, Hiren

Senior Bioinformatics Scientist

Karathia, Hiren

During his Pre-Doctoral scientific career, Dr. Karathia worked as Research Scientist at Institute of Bioinformatics in Banglore, India and successfully designed the entire relational architecture of the currently running HPRD. Also he worked for two years as Lecturer and taught Biotechnology and Bioinformatics at B. Tech and M. Tech levels in AMITY University in India.

After receiving his Ph.D. degree in Integrated Molecular Systems Biology from University of Lleida in Spain, Dr. Karathia joined University of Maryland at College Park as Postdoctoral Research Associate at the Center for Bioinformatics and Computational Biology (CBCB) where he completed his research on understanding impacts of changes in 3D organization of genomes to dysregulation of transcriptional activities in cancers. He also performed collaborative research towards deciphering the impact of metabolic dysregulation towards biased mutagenesis of human genome across pan-cancers integrating Exome-Seq, RNA-Seq and mass-spec data of cancer patients.

After finishing his Postdoctoral research, Dr. Karathia joined as Scientist at CosmosID Inc. in 2018 and developed his skills in the area of metagenomics and metatranscriptomics and applied it to understand abundance of microbiome and metabolome impacts on infectious diseases and food safety in collaboration with academicians and industrial partners. Lastly, before joining the GGC, Dr. Karathia was a Staff Scientist at the National Cancer Institute (NCI) at the NIH in Bethesda MD where he developed his skills in the area of epi-transcriptomics and applied the skills to understand impact of chemical modifications on mRNA molecule at single nucleotide resolution and linked its impact on fidelity of its protein’s translation process by processing nano-pore sequencing data. Also at the NCI Dr. Karathia worked in the area of single-cell transcriptomics to understand hierarchical lineage of tumor cells during development of glioblastoma tumor within the brain’s cancer microenvironment of an individual patient. Currently, at the GGC, Dr. Karathia’s area of research interest is to develop machine learning and artificial intelligence approaches leveraging the OMICS data in an integrated fashion and apply these developed setup to address questions in the area of neurological disorders focusing towards diagnostics and treatments.

Contact Information

Office: (864)-941-8177


  • B.Sc., Biochemistry, Saurashtra University, Rajkot, Gujarat, India, 1999
  • M.Sc., Biomedical Technology, Gujarat University, Ahmedabad, Gujarat, India, 2001
  • M.Sc., Bioinformatics, Sikkim Manipal University, Ahmedabad, Gujarat, India, 2004
  • Ph.D., Integrated Molecular Systems Biology, Lleida, Catalonia, Spain, 2012

Selected Publications

  • Leonard M.M, Valitutti F., Karathia H., et al. Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study, PNAS July 20, 2021 118 (29) e2020322118.
  • Auslander N., Ramos D.M., Zelaya I., Karathia H., Crawford T.O., Schäffer A.A., Sumner C.J., Ruppin E. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases, Mol Syst Biol (2020) 16:e9701.
  • Leonard M.M, Karathia H., Pujolassos M., Troisi J., Valitutti F., Subramanian P., Camhi S., Kenyon V., Colucci A., Serena G., Cucchiara S., Montuori M., Malamisura B., Francavilla R., Elli L., Fanelli B., Colwell R., Hasan N., Zomorrodi A.R., Fasano A., CD-GEMM Team. Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. Microbiome. 2020 Sep 11;8(1):130.
  • Wolf Y., Bartok O., Patkar S., Eli G.B., Cohen S., Litchfield K., Levy R., Jiménez-Sánchez A., Trabish S., Lee J.S., Karathia H., Barnea E., Day C.P., Cinnamon E., Stein I., Solomon A., Bitton L., Pérez-Guijarro E., Dubovik T., Shen-Orr S.S., Miller M.L., Merlino G., Levin Y., Pikarsky E., Eisenbach L., Admon A., Swanton C., Ruppin E., Samuels Y. UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma. Cell. 2019 Sep 19;179(1):219-235.e21.
  • Lee J.S., Adler L., Karathia H., Carmel N., Rabinovich S., Auslander N., Keshet R., Stettner N., Silberman A., Agemy L., Helbling D., Eilam R., Sun Q., Brandis A., Malitsky S., Itkin M., Weiss H., Pinto S., Kalaora S., Levy R., Barnea E., Admon A., Dimmock D., Stern-Ginossar N., Scherz A., Nagamani S.C.S., Unda M., Wilson D.M. 3rd, Elhasid R., Carracedo A., Samuels Y., Hannenhalli S., Ruppin E., Erez A. Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures. Cell. 2018 Sep 6;174(6):1559-1570.e22.
  • Karathia H., Kingsford C., Girvan M., Hannenhalli S. A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Sci Rep. 2016 Dec 15;6:39279.
  • Karathia H., Vilaprinyo E., Sorribas A., Alves R. Saccharomyces cerevisiae as a model organism: a comparative study. PLoS One. 2011 Feb 2;6(2):e16015.

Lucy's Story

When our daughter Lucy had a metabolic crisis at 7 days old, we were shocked and devastated to find out that she was born with a rare genetic disorder (MSUD). Her newborn screening results did not make it back in time to prevent the crisis, and no one at our local hospital was familiar with the disease. They did not know how to treat her. Calls were made to Greenwood Genetic Center to confirm her diagnosis and guide her care. Dr. Champaigne and Ami...

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