Computational Biology Ph.D.

Rajendra KC

*** * ******* ******

Urbana *****, Illinois, USA

B *.*******@*****.*** ; ****@********.*** H +1-217-***-**** Research Interests

Computational Biology

Computational Genomics

Bioinformatics

Network Biology

Molecular Dynamics Simulation and Analysis

Education

University of Illinois at Urbana Champaign, Illinois, USA PhD in Biophysics and Quantitative Biology Aug. 2021 – present. Cumulative GPA: 3.88/4

Indian Institute of Technology, Kharagpur, West Bengal, India Bachelor and Master of Tech.(Dual-Degree) in Biotechnology and Biochemical Engineering Jul. 2015 – Apr. 2020 Cumulative GPA: 8.63/10

Pace Junior College, Andheri, Mumbai, Maharashtra, India Higher Secondary Education, MSBSHSE May. 2013 – Apr. 2015 Aggregate- 86.62 %

Top 1% in Board

Summit English Boarding High School, Butwal, Province-5, Nepal Secondary Education, SLC May. 2000 – Apr. 2013

Aggregate- 89.25 %

Rank-1 in school

Research Projects

Ph.D. dissertation : “Data-driven maps of RNA polymerase III transcription and macromolecular inter- actions identifies new gene targets and regulatory mechanisms”, Van Bortle lab, University of Illinois Urbana Champaign, USA Jan. 2022 – Present. Advisor: Prof. Kevin Van Bortle

The goal of this project is to expand the current understanding of RNA polymerase III.

In the first part, I am using a purely data-driven method to find new gene targets of RNA polymerase III. We have found strong evidences of RNA Pol III occupancy and transcription at thousands of protein coding genes and unannotated regions in the genome.

In the second part, I am building a huge Protein Protein Interaction (PPI) network. I am using ”effective conductance” as a measure of closeness between two proteins. Currently, I am developing a novel way to remove the popularity bias from the network.

Further, I am developing new effective ways of visualizing dominance like Rope plot(between 2 factors), Triangle Plot (between 3 factors), Tetrahedron plot (between 4 factors). Master’s dissertation: ”A Molecular Dynamics Study of NLS-Domain of FUS Protein in Complex with Transportin 1 on the Context of P525L Mutation”,

Computational Structural Biology lab, IIT Kharagpur, India May. 2019 – April. 2020 Advisor: Prof. Ranjit Prasad Bahadur

The goal of this project is to find the exact mechanism of inhibition of the translocation of FUS protein into the nucleus, which causes ALS( a neurological disease).

I did a series of MD simulation of FUS and Transportin1 ( both in their bound and unbound form) in a water solvent and in an amphiphilic solvent (50 % v/v TFE:Water)

Using various tools of GROMACS on the simulation trajectory, I did a careful analysis of the hydrogen bond pattern, root mean square deviation, root mean square fluctuation, etc.

I also performed Principal Component Analysis(PCA) and filtered the motion of protein along the prominent eigenvectors to study prominent global motions of the protein.

I used MD-TASK to perform various operations like Betweenness Centrality(BC) and Dynamic Cross- Correlation(DCC) to find out the hotspot residues(responsible for inter-domain communication in protein) and to get insight on the relative motion between the domains of the protein. Bachelor’sdissertation : “Elucidating SOCS1 and CISHMediatedDampeningofIFN-gamma Signaling During Tuberculosis using in-silico study ”,

MICM lab, IIT Kharagpur, India May. 2018 – April. 2019 Advisor: Prof. Somdeb Bose Dasgupta

The goal of this project is to find the mechanism by which SOCS1 and CISH dampen the IFN-gamma signaling during Tuberculosis.

First, I surveyed literatures to shortlist few important proteins involved in IFN-gamma signaling and few other proteins (SOCS1 and CISH) that act as an inhibitor for this signalling pathway.

Then, I performed extensive Homology Modeling of these shortlisted proteins and performed computa- tional docking on some of these proteins using online servers which finally led us to come up with a probable hypothesis of competitive binding by SOCS1 to a protein in the IFN-gamma signalling pathway.

To confirm the above hypothesis, we started wet-lab experiments to perform co-immunoprecipitation in order to check the interaction of those two suspected proteins. During the time period of this project, I could sub-clone the genes of these two protein in an expression vector and finally express them. Technical Skills

Bioinformatics tools

Bedtools, SAMtools, MEMEsuite, deeptools, SeqKit, RSeQC, Salmon, Bowtie Programming Languages

R, Shell, Python, Visual Basic

R packages

tidyverse, ggplot, plotgardener, edgeR, DESeq2

Operating System

Linux (Ubuntu), OS X, Windows

Molecular Dynamics Softwares

GROMACS, PyMOL, MD-TASK, VMD, NAMD

Wet-lab skills

Plasmid isolation, Cell culturing, ELISA, Western blotting Conferences

Rustbelt RNA meeting 2024

- Abstract shortlisted for a talk in the conference. Teaching Experience

Teaching Assistance (TA)

- Computing in Molecular Biology(MCB432)

Github

- multiClassPromoterCuration

- NascentT4Score

- RNApolymerase metamap

- dominatR (an R package)

Publications

2024

-Rajendra K C, Ruiying Cheng, Sihang Zhou, Simon Lizarazo, Duncan J. Smith, Kevin Van Bortle, Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters, Molecular Cell, 2024 ISSN 1097 2765

https://doi.org/10.1016/j.molcel.2024.09.019

-DeepakK.Singh,ZhengminCong,You Jin Song,Minxue Liu,RituChaudhary,Dazhen Liu,YuWang,Rishabh Prasanth,Rajendra K C,Simon Lizarazo,Miriam Akhnoukh,Omid Gholamalamdari,Anurupa Moitra,Lisa M. Jenkins,Rohit Bhargava,Erik R. Nelson,Kevin Van Bortle,Supriya G. Prasanth, Kannanganattu V. Prasanth

(2024). MANCR lncRNA Modulates Cell-Cycle Progression and Metastasis by Cis-Regulation of Nuclear Rho-GEF. Molecular and Cellular Biology, 44(9), 372–390. https://doi.org/10.1080/10985549.2024.2383773

2023

- Cheng, Ruiying, Sihang Zhou, Rajendra K C, Simon Lizarazo, Leela Mouli, Anshita Jayanth, Qing Liu, and Kevin Van Bortle. 2023. ”A Combinatorial Regulatory Platform Determines Expression of RNA Polymerase III Subunit RPC7 (POLR3G) in Cancer” Cancers 15, no. 20: 4995. https://doi.org/10.3390/cancers15204995

2022

- Sushmita Basu, K.C. Rajendra, Suresh Alagar, Ranjit Prasad Bahadur, Impaired nuclear transport induced by juvenile ALS causing P525L mutation in NLS domain of FUS: A molecular mechanistic study, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1870, Issue 4, 2022, 140766, ISSN 1570-9639

https://doi.org/10.1016/j.bbapap.2022.140766

Pre-prints

-Zhou, S., Lizarazo, S., Mouli, L., Chorghade, S., Cheng, R., Rajendra, K. C., Kalsotra, A., Van Bortle, K. (2024). Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. bioRxiv.

https://doi.org/10.1101/2024.07.02.601767

Relevant Courses

Departmental courses: Bioinformatics*, Computational Structural Biology, Protein Engineering, Introduc- tion to System Biology, Biochemistry*, Analytical Biochemistry Laboratory, Genetics, Gene Expression, Microbiology*, Cell and Molecular Biology*, Biochemical Reaction Engineering*, Immunology, Advanced Immunology and Immunotherapeutics, Cancer Biology, Neurophysiology, Animal Cell Culture and Im- munotechnology*, Secondary Metabolism in Plants and Microbes, Plant Cell and Tissue Culture*, Environ- mental Biotechnology, Science of Living System, Bioprocess Technology, Bioinformatics, Physical Chemistry II(CHEM 444), Introduction to Biophysics (BIOP 401), Experimental Biophysics (PHYS 498 EBP) Inter-disciplinary courses: Programming and Data Structure*, Probability and Statistics, Partial Differen- tial Equations, Mathematics-I, Mathematics-II, Physics*, Chemistry*, Engineering Drawing and Computer Graphics, Mechanics, Mass Transfer*, Methods of Data Science (IS 517)

* : includes Lab components

Academic Distinctions

Received ” Best B. Tech Project Award ” at Department of Biotechnology and Biochemical Engineering, IIT Kharagpur .

Selected for SHE scholarship under INSPIRE, upon being in top 1% of students in Maharashtra board exam (12th standard).

Secured Rank-1 in school

Qualified IIT-JEE (Main)-2015 and IIT-JEE (Advanced)- 2015 Competitions/Certifications

Got A+ grade in short term course on “Object Oriented Programming and Algorithm Design in Java” organized by CEP, IIT Kharagpur.

Successfully qualified Code-Fun-Do, a coding marathon conducted by Microsoft upon successfully making a ”Virtual Periodic Table” application for Windows platform.

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