CV

Education

• B.Sc. in Biotechnology, Marwari College, Bhagalpur, Tilka Manjhi Bhagalpur University, 2013
• M.Sc. in Bioinformatics, Central University of South Bihar, 2016
• Ph.D in Bioinformatics, International Institute of Information Technology (IIIT) - Hyderabad, 2023

Work experience

• July 2024- June 2025: Post‑doctoral Fellow
  • Lehigh University,Bethlehem, Pennsylvania, United States
  • Biomolecule simulation. Ligand interaction and stability with URAT1 using atomistic molecular dynamics simulation.
  • Studying the state transition of the Organic Cation Receptor1 (OCT1) using the enhanced sampling method.
  • Integrated MDAnalysis-based analysis modules (RMSF, radius of gyration, position vs time, and helix analysis) into \href{https://github.com/nk53/stanalyzer}{stanalyzer}
• Sept 2023‑ March 2024: Post‑doctoral Fellow
  • IIT Delhi & IHub‑Data IIIT Hyderabad
  • Soft matter simulation. Aggregation of pseudoisocyanine chloride (PIC) in the presence of crowder at multiple temperatures.
  • Interaction of model mini peptide with eukaryotic model membrane.
• Oct 2016‑ June 2017: Project Assistant
  • CSIR‑IGIB, New Delhi,
  • Membrane binding and targeting of peripheral proteins: Finding molecular address using in silico studies.

Skills

• Programming Skills
  • Python, Unix/Linux, Shell scripting, R (statistical software), LaTeX, Basic of C, C++, Perl, PHP, HTML.
  • Related Courses
    • Qualified Computer Teacher Training Course (CTTC) and (DCA) from SITD (Society for Information Technology Development) (secured 84.8%).
    • Qualified Linux test conducted by IIT Bombay, funded by MHRD, Gov. of India.
• Bioinformatics Skills
  • Visualization tools: Chimera, VMD, Pymol, Discovery Studio, Desmond, Paraview.
  • Molecular Dynamics tool (Atomistic and Coarse Grained Simulation): Gromacs, Desmond (Schrödinger), AMBER (basic).
  • Protein structure prediction: Homology moldeling (Modeller, SWISS MODEL), Fold recognition (I‐TASSER, MUSTER, Phyre and Phyre2), Ab‐initio (ROBETTA).
  • Chemical Structure Drawing tools: ChemDraw, Chem Ultra, MarvinSketch.
  • Other tools and servers: Inkscape, Xmgrace, CHARMM‐GUI Input Generator, MDAnalysis, MDTraj, FATSLiM, stanalyzer, LAMMPS (basic).
• Languages
  • English and Hindi (can read, write and speak)

Publications

• Y Suo†, J G. Fedor†, H Zhang, K Tsolova, X Shi, K Sharma, S Kumari, M Borgnia, P Zhan, W Im, S Lee* Molecular basis of the urate transporter URAT1 inhibition by gout drugs. bioRxiv.
• S. Kumari, A. Mitra, and G. Bulusu, “Putative Role of cholesterol in shaping the structural and functional dynamics of Smoothened (SMO)”, The Journal of Physical Chemistry B, 127(44), 9476-9495.
• S. Kumari, A. Mitra, and G. Bulusu, “Structural dynamics of Smoothened (SMO) in the ciliary membrane and its interaction with membrane lipids.”, Biochimica et Biophysica Acta (BBA)-Biomembranes, 1864(8), 183946.

Conferences and Workshops Attended

• Poster presentation at the conference
  • S. Kumari, A. Mitra, and G. Bulusu. “A Journey into the Structure and Dynamics of Smoothened (SMO) in Hedgehog (HH) Signaling Pathway”. JNCASR‑CECAM Conference MD@60, organized by Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India. (February 26‑29, 2024).
  • S. Kumari, A. Mitra, and G. Bulusu. “Investigating cholesterol binding to cholesterol‐binding motifs of SMO‐TMD”. 44th Indian Biophysical Society Meeting (IBS 2022) 2022, organized by the National Centre for Biological Sciences (NCBS), Bangalore, India. (March 27‐29, 2023).
  • S. Kumari, A. Mitra, and G. Bulusu. “Structural variations of different cholesterol‐bound states of Smoothened (SMO)”. MBU50 Symposium 2022, organized by the Indian Institute of Science (IISc), Bangalore, India. (January 23‐25, 2023).
  • S. Kumari, A. Mitra, and G. Bulusu. “Investigating cholesterol binding to cholesterol‐binding motifs of SMO‐TMD”. 44th Indian Biophysical Society Meeting (IBS 2022) 2022, organized by ACTREC, Tata Memorial Centre, Navi Mumbai, India. (March 30‐31 and April 1, 2022).
  • S. Kumari, A. Mitra, and G. Bulusu. “Structural modulation in Smoothened (SMO) in ciliary membrane and its interaction with membrane lipids”. Molecular Modeling (MM) 2021. Organized by the Association of Molecular Modelers of Australasia (December 6‐8, 2021) (Virtual).
  • S. Kumari, A. Mitra, and G. Bulusu. “Structural modulation in Smoothened (SMO) in ciliary membrane and its interaction with membrane lipids”. EMBO Workshop, Advances and Challenges in Biomolecular Simulations 2021. Organized by Alexandre Bonvin, Utrecht University, NL. (October 18–21, 2021) (Virtual).
  • S. Kumari, A. Mitra, and G. Bulusu. “Structural modulation in Smoothened (SMO) in ciliary membrane and its interaction with membrane lipids”. HySci 2020. Organized by CCMB Hyderabad, India. December 17‐18 (Virtual).
  • S. Kumari, F. Khan. ”Clustering method development for screening of Sesquiterpenoids as Anti‐cancer Natural Lead against Human DNA Topoisomerase II alpha”. 1st International conference on human implication of biotechnology (ICHIB), Organized by Central University of South Bihar, Patna, India (February 12‐14, 2016).
• Workshop and symposium attended
  • Participated in National Supercomputing Mission (NSM) on Multiscale Modelling using exascale computing: Membrane Protein Interactions organized by Indian Institute of Science (IISc), Bengaluru, India. (July 6‐15, 2023).
  • 2021 Online Martini Workshop, Organized by the University of Groningen, September 1‐3, 2021.
  • Machine Learning for Science (ML4Science). International Institute of Information Technology (IIIT), Hyderabad, India. (November 29‐30, 2019).
  • Indo‐German workshop on Computing in Chemistry, Biology and Medicine. International Institute of Information Technology (IIIT), Hyderabad, India. (November 29‐30, 2017).

Teaching

• Advanced Biomolecular Architecture.
  • The responsibilities were to conduct weekly tutorial/lab sessions and evaluations of assignments, examination answer scripts.
• Biomolecular Structure Interaction and Dynamics.
  • The responsibilities were to conduct weekly tutorial/lab sessions and evaluations of assignments, examination answer scripts.
• Computing Tools.
  • The responsibilities were to conduct weekly tutorial/lab sessions, evaluations of assignments and final projects, and invigilation of exams.
• Selected topics in Instrumental Analysis.
  • The responsibilities include evaluations of assignments and examination answer scripts.
• Topics in Nanosciences.
  • The responsibilities included the evaluations of assignments, examination answer scripts, and the final project.

Awards & Fellowships

• Best poster award, JNCASR‑CECAM Conference MD@60 organized by organized by Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India (2024).
• Fee waiver, virtual EMBO Workshop‐Advances and Challenges in Biomolecular Simulation (2021).
• Best poster award, HySci 2020, organized by CSIR–Centre For Cellular And Molecular Biology (CCMB) (2020).
• Selected conference travel grant, IBS (2020).
• DST INSPIRE Fellowship, Govt. of India (2017‐2022, Five years fellowship for pursuing Ph.D.).
• 1st rank, M.Sc. Bioinformatics in Central University of South Bihar (2014‐2016).

Scientific Meetings Organised

• Volunteer, Machine Learning for Science: Symposium and Discussion Meeting (29‐30th November, 2019), Tutorials and Hands‐On Sessions (1st December, 2019). IIIT, Hyderabad (2019).
• Volunteer, INDO‐GERMAN Workshop on Computing in Chemistry, Biology and Medicine (CCBM 2017), 29‐30th, November 2017. IIIT, Hyderabad (2017)
• Volunteer, 1st International conference on human implication of biotechnology (ICHIB), Organized by Central University of South Bihar, Patna, India (February 12‐14, 2016).

Other Position(s)/ Responsibility

• Director of Communication and Events, Lehigh Postdoctoral Association, Lehigh University (August 2024- January 2025)
• Core volunteer, Campus-wide COVID‐19 screening on IIIT, Hyderabad campus (2021).
• Core volunteer, Social service‐ community kitchen on IIIT, Hyderabad campus during 1st wave of COVID‐19 (2020).
• Mess Representative, Worked in a team of 3 members (Mess committee) to run the IIIT, Hyderabad mess during 1st wave of COVID‐19 (2020).
• Mess Representative, Central University of South Bihar, Gaya (2015‐2016)