Raga Krishnakumar

Principal Member of Technical Staff

Author profile picture

Principal Member of Technical Staff

rkrishn@sandia.gov

(925) 294-3292

Sandia National Laboratories, California
 P.O. Box 969
 Livermore, CA 94551-0969

Biography

Raga Krishnakumar’s background is in the regulation of gene expression in biological systems. Her PhD research at Cornell University was focused on chromatin-binding proteins and transcriptional regulation. At UCSF, she performed postdoctoral research on the role of microRNAs and epigenetics in early development, with a focus on multi-omic (genomic, transcriptomic, epigenomci) analysis. She started at Sandia National Laboratories as a postdoctoral appointee, focused on long-read sequencing for pathogen detection and identification of mobile genomic elements in prokaryotic genomes. During her time at Sandia, her projects have included engineering of mammalian cells for optimizing antimicrobial activity, deep learning for cross-species prediction of gene regulation through epigenomics in fungi, identification of molecular signatures associated with biomanufacturing scale-up, data fusion techniques for multi-modal sensors, and large language model-based evaluation of antibody-based therapeutics.

Education

BA (honours), Natural Sciences (Biochemistry), University of Cambridge, Cambridge, UK, 2004

PHD, Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, 2010

Research Interests

Raga Krishnakumar’s research area is multi-modal data integration and analysis for predictive power in biological systems. Specifically, her projects are focused on using data science and machine learning to integrate sequence language, phenotypic observations and multi-omic molecular data in organisms ranging from fungi to mammals, with a goal of predicting biological outcomes.

Awards

  • 2011 – 2014 A.P. Giannini Medical Research Fellow , A.P. Giannini
  • 2011 – 2011 NIH Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Research Training Grant (Parent T32), NIH
  • 2008 – 2010 Predoctoral Fellowship, American Heart Association
  • 2001 – 2004 Trinity College Overseas Trust Fellowship, University of Cambridge, UK

Publications

  • Smith, M., Carbajal, A., Domschot, E., Johnson, N., Goyal, A., Lamb, C., Lubars, J., Kegelmeyer, W., Krishnakumar, R., Quynn, S., Ramyaa, R., Verzi, S., Zhou, X., & Zhou, X. (2022). MalGen: Malware Generation with Specific Behaviors to Improve Machine Learning-based Detectors. https://doi.org/10.2172/1893244 Publication ID: 80379
  • Robinson, D., Foster, M., Bennett, C., Bhandarkar, A., Fuller, E., Stavila, V., Spataru, D., Krishnakumar, R., Cole-Filipiak, N., Schrader, P., Ramasesha, K., Allendorf, M., Talin, A., & Talin, A. (2022). Proton Tunable Analog Transistor for Low Power Computing. https://doi.org/10.2172/1889340 Publication ID: 80273
  • Krishnakumar, R., Sjoberg, K., Fisher, A., Doudoukjian, G., Webster, E., & Webster, E. (2022). Combined Imaging and RNA-Seq on a Microfluidic Platform for Viral Infection Studies. https://doi.org/10.2172/1888155 Publication ID: 80227
  • Verzi, S., Krishnakumar, R., Levin, D., Krofcheck, D., Williams, K., & Williams, K. (2022). Data Science and Machine Learning for Genome Security. https://doi.org/10.2172/1855003 Publication ID: 75932
  • Krishnakumar, R., Ruffing, A.M., & Ruffing, A.M. (2022). OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PLoS Computational Biology, 18(1). https://doi.org/10.1371/journal.pcbi.1009731 Publication ID: 79977
  • Verzi, S., Johnson, N., Khanna, K., Zhou, X., Quynn, S., Krishnakumar, R., Smith, M., & Smith, M. (2021). Malware Generation with Specific Behaviors to Improve Machine Learning-based Detectors [Conference Presenation]. https://doi.org/10.2172/1899508 Publication ID: 76852
  • Ruffing, A.M., Podlevsky, J., Krishnakumar, R., Smallwood, C., Dallo, T., Torres, X., Kolker, S., Morgan, J., King, N., Marsing, M., & Marsing, M. (2021). CERES: CRISPR Engineering for the Rapid Enhancement of Strains. https://doi.org/10.2172/1820694 Publication ID: 75713
  • Verzi, S., Krishnakumar, R., Levin, D., Krofcheck, D., Boskin, C., Williams, K., & Williams, K. (2021). Data Science for Detection of Genome Editing [Presentation]. https://www.osti.gov/biblio/1889012 Publication ID: 79387
  • Verzi, S., Krishnakumar, R., Levin, D., Krofcheck, D., Boskin, C., Williams, K., & Williams, K. (2021). Data Science for Characterization of Genome Noise/Mutation [Presentation]. https://www.osti.gov/biblio/1884061 Publication ID: 79291
  • Hirakawa, M., Tjahjono, N., Light, Y., Chintalapudi, P., Branda, S., Butler, K.S., Krishnakumar, R., & Krishnakumar, R. (2021). Augmentation of Antibacterial Activity in Mesenchymal Stromal Cells Through Systems-Level Analysis and CRISPR-mediated Activation of CD14 [Conference Poster]. https://doi.org/10.2172/1868446 Publication ID: 78467
  • Hirakawa, M., Krishnakumar, R., Timlin, J., Carney, J., Butler, K.S., & Butler, K.S. (2020). Gene editing and CRISPR in the clinic: Current and future perspectives. Bioscience Reports, 40(4). https://doi.org/10.1042/bsr20200127 Publication ID: 73844
  • Hirakawa, M., Tjahjono, N., Light, Y., Chintalapudi, P., Butler, K.S., Branda, S., Krishnakumar, R., & Krishnakumar, R. (2020). Engineering mesenchymal stromal cells for anti-microbial therapy [Conference Poster]. https://www.osti.gov/biblio/1768163 Publication ID: 72795
  • Jayamohan, H., Sinha, A., Krishnakumar, R., Edwards, H.S., Younis, T.A., Trevithick, J.D., Patel, K., Bartsch, M.S., & Bartsch, M.S. (2020). Library preparation for the Oxford Minion sequencer with ‘ASPIRE’: Automated sample PrEP by indexed rotary exchange [Conference Poster]. 21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85079638132&origin=inward Publication ID: 57742
  • Krishnakumar, R., Branda, C., Branda, S., Butler, K.S., Tjahjono, N., Light, Y., & Light, Y. (2019). Characterizing and Engineering Mesenchymal Stromal Cells for Anti-Microbial Therapy [Conference Poster]. https://www.osti.gov/biblio/1643235 Publication ID: 66184
  • Mageeney, C., Lau, B., Branda, S., Sinha, A., Krishnakumar, R., Williams, K., & Williams, K. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1643273 Publication ID: 66274
  • Smallwood, C., Ruffing, A.M., Podlevsky, J., Krishnakumar, R., Kolker, S., Hines, V., & Hines, V. (2019). Accelerating Photosynthetic Adaptations to Environmental Responses in Synechococcus sp. PCC 7002 [Conference Poster]. https://www.osti.gov/biblio/1642053 Publication ID: 64987
  • Krishnakumar, R., Boskin, C., Levin, D., Carmody, D., Finley, P., Verzi, S., Williams, K., Carney, J., & Carney, J. (2019). Data Science for Detection of Genome Editi [Presentation]. https://www.osti.gov/biblio/1645734 Publication ID: 70337
  • Krishnakumar, R., Hirakawa, M., Tjahjono, N., Talin, A., Casadevall, C., & Casadevall, C. (2019). Capturing and modifying cell fates ? bioengineering interfaces and informatics [Conference Poster]. https://www.osti.gov/biblio/1641658 Publication ID: 70490
  • Mageeney, C., Rokes, A., Lau, B., Branda, S., Sinha, A., Krishnakumar, R., Williams, K., & Williams, K. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1641506 Publication ID: 70235
  • Chintalapudi, P., Hirakawa, M., Tjahjono, N., Branda, S., Butler, K.S., Krishnakumar, R., & Krishnakumar, R. (2019). CRISPR-based Genetic Engineering of Mesenchymal Stem Cells [Conference Poster]. https://www.osti.gov/biblio/1641290 Publication ID: 69980
  • Casadevall, C., Calvo, J., Li, Y., Fuller, E., Hirakawa, M., Krishnakumar, R., Talin, A., & Talin, A. (2019). INKJET-PRINTED ORGANIC REDOX TRANSISTORS FOR NEUROMORPHICS AND NEURAL INTERFACING [Presentation]. https://www.osti.gov/biblio/1807129 Publication ID: 69964
  • Mageeney, C., Rokes, A., Lau, B., Branda, S., Krishnakumar, R., Williams, K., & Williams, K. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1640900 Publication ID: 69317
  • Mageeney, C., Williams, K., Branda, S., Krishnakumar, R., & Krishnakumar, R. (2019). Diverse therapeutic phage cocktails through a computational front end [Conference Poster]. https://www.osti.gov/biblio/1640653 Publication ID: 68942
  • Ruffing, A.M., Krishnakumar, R., Smallwood, C., Podlevsky, J., Kolker, S., Hines, V., & Hines, V. (2019). Development of Genetic and Computational Tools for CRISPRi/a Screening in Synechococcus sp. PCC 7002 [Conference Poster]. https://www.osti.gov/biblio/1640704 Publication ID: 68882
  • Mageeney, C., Rokes, A., Lau, B., Branda, S., Krishnakumar, R., Williams, K., & Williams, K. (2019). Diverse therapeutic phage cocktails through a computational front end [Conference Poster]. https://www.osti.gov/biblio/1639435 Publication ID: 67521
  • Krishnakumar, R., Sinha, A., Bird, S.W., Jayamohan, H., Edwards, H.S., Schoeniger, J., Patel, K., Branda, S., Bartsch, M.S., & Bartsch, M.S. (2018). Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-21484-w Publication ID: 58764
  • Bartsch, M.S., Bird, S., Branda, S., Edwards, H., Jayamohan, H., Krishnakumar, R., Patel, K., Schoeniger, J., Sinha, A., & Sinha, A. (2018). Real-Time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) LDRD Final Report. https://doi.org/10.2172/1481615 Publication ID: 59412
  • Light, Y., Hirakawa, M., Tjahjono, N., Branda, S., Butler, K.S., Krishnakumar, R., & Krishnakumar, R. (2018). Mesenchymal stem cell-based therapy for infectious disease [Presentation]. https://www.osti.gov/biblio/1594331 Publication ID: 59391
  • Bartsch, M.S., Branda, S., Krishnakumar, R., Sinha, A., Edwards, H., Bird, S., Jayamohan, H., Patel, K., & Patel, K. (2018). LDRD Ending Project ReviewReal-time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) [Presentation]. https://www.osti.gov/biblio/1806834 Publication ID: 58981
  • Peddireddy, N., Tjahjono, N., Krishnakumar, R., Light, Y., & Light, Y. (2018). Developing Genetically and Chemically Converted Stem Cells for Cell Therapy [Conference Poster]. https://www.osti.gov/biblio/1806706 Publication ID: 63278
  • Bartsch, M.S., Krishnakumar, R., Sinha, A., Patel, K., Edwards, H., & Edwards, H. (2018). Real-Time Selective Sequencing with RUBRIC (Read Until with Basecall- and Reference-Informed Criteria) [Conference Poster]. https://www.osti.gov/biblio/1515754 Publication ID: 62185
  • Bartsch, M.S., Edwards, H., Krishnakumar, R., Sinha, A., Patel, K., & Patel, K. (2018). Read Until with Basecall- and Reference-Informed Criteria [Conference Poster]. https://www.osti.gov/biblio/1501982 Publication ID: 61116
  • Bartsch, M.S., Krishnakumar, R., Sinha, A., Schoeniger, J., Branda, S., Patel, K., Edwards, H., Bird, S., Jayamohan, H., & Jayamohan, H. (2018). Characterizing the Performance of the MinION for Real-Time Detection [Conference Poster]. https://www.osti.gov/biblio/1503084 Publication ID: 61161
  • Bartsch, M.S., Krishnakumar, R., Sinha, A., Patel, K., Edwards, H., & Edwards, H. (2018). Read Until with Basecall- and Reference Informed Criteria (RUBRIC) [Conference Poster]. https://www.osti.gov/biblio/1501981 Publication ID: 61117
  • Bartsch, M.S., Edwards, H., Krishnakumar, R., Sinha, A., Patel, K., & Patel, K. (2018). The Evolution of MinION Selective Sequencing: Read Until with Basecall- and Reference-Informed Criteria (RUBRIC) [Conference Poster]. https://www.osti.gov/biblio/1501983 Publication ID: 61115
  • Krishnakumar, R., Bartsch, M.S., Patel, K., Branda, S., Schoeniger, J., Edwards, H., Bird, S., Jayamohan, H., & Jayamohan, H. (2017). Selective Long-Read Nanopore Sequencing for Real-Time Point-of-need Pathogen Identification [Conference Poster]. https://www.osti.gov/biblio/1511977 Publication ID: 54662
  • Lau, B., Krishnakumar, R., Wagner, J., Sinha, A., Hudson, C.M., Schoeniger, J., Branda, S., Williams, K., & Williams, K. (2017). Discovering and converting temperate phages for therapy [Conference Poster]. https://www.osti.gov/biblio/1483224 Publication ID: 54346
  • Jayamohan, H., Sinha, A., Krishnakumar, R., Edwards, H., Younis, T., Trevithick, J., Patel, K., Bartsch, M.S., & Bartsch, M.S. (2017). Library Preparation and Analysis Methods for the Oxford MinION Nanopre Sequencer for Pathogen Identification [Conference Poster]. https://www.osti.gov/biblio/1481358 Publication ID: 53994
  • Krishnakumar, R. (2017). Harnessing the power of genomics for detection diagnosis and mechanistic analysis of cellular responses [Presentation]. https://www.osti.gov/biblio/1480221 Publication ID: 53797
  • Krishnakumar, R., Edwards, H., Sinha, A., Bird, S., Patel, K., Bartsch, M.S., & Bartsch, M.S. (2017). Selective Long-Read Nanopore Sequencing for Rapid Real-Time Pathogen Identification [Presentation]. https://www.osti.gov/biblio/1510603 Publication ID: 53467
  • Sinha, S., Krishnakumar, R., Williams, K., Schoeniger, J., & Schoeniger, J. (2017). Comparative Analysis between Genomic Islands and Host Species [Presentation]. https://www.osti.gov/biblio/1508231 Publication ID: 57547
  • Williams, K., Lau, B., Krishnakumar, R., Wagner, J., Hudson, C.M., Schoeniger, J., & Schoeniger, J. (2017). Reconsidering temperate phages for therapy [Conference Poster]. https://www.osti.gov/biblio/1458119 Publication ID: 56671
  • Williams, K., Krishnakumar, R., Wagner, J., Hudson, C.M., Schoeniger, J., Williams, K., & Williams, K. (2017). The Bacterial and Archaeal Pan-Mobilome [Conference Poster]. https://www.osti.gov/biblio/1456320 Publication ID: 55476
  • Jayamohan, H., Bartsch, M.S., Krishnakumar, R., Patel, K., Branda, S., Sinha, A., Edwards, H.S., Throckmorton, D., Bird, S.W., Schoeniger, J., & Schoeniger, J. (2017). Nanopore Sequencing for Real-Time Pathogen Identification [Conference Poster]. https://www.osti.gov/biblio/1507629 Publication ID: 55103
  • Bartsch, M.S., Krishnakumar, R., Sinha, A., Bird, S.W., Schoeniger, J., Patel, K., & Patel, K. (2016). Real-Time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) [Conference Poster]. https://www.osti.gov/biblio/1422120 Publication ID: 48006
Showing 10 of 45 publications.