Dr. Siddharth Sinha
Cancer Genomics • Computational Structural Biology • Molecular Dynamics • AI/ML in Biomedicine
An enthusiastic researcher with expertise in cancer genomes, big data analytics, bioinformatics, drug design, and computational structural biology. Focused on protein structure–based evaluation, MD simulations, free energy estimation, ligand binding, and conformational analysis for variant classification and target discovery.
Macau, Macao S.A.R.
University of Macau
Open to opportunities
Skills
Biomedical • Computational • ProgrammingBiomedical & Genomics
- Cancer genomics; Variant Calling, Joint Genotyping (GATK), WES, sRNA‑seq, NGS
- Clinical data analysis; DNA damage repair genes (BRCA1/2, PTEN, TP53, MLH1, MSH2)
- Molecular biology: Western Blot, ELISA, SDS‑PAGE, PCR
Computational Structural Biology
- Molecular Dynamics (all‑atom & CG), REMD, Free‑energy calculations
- Protein–ligand modeling: Homology & Pharmacophore modeling, Docking
- 3D & G‑QSAR, QM/MM (semi‑empirical)
Data & Software
- Big Data Analytics; AI & Machine Learning in biosciences
- Python, R, C++; High‑performance computing (HPCC)
- Statistics for biomedicine; Deep learning (autoencoders for MD)
Achievements & Highlights
Publications
24 peer‑reviewed articles spanning computational structural bioinformatics, drug design, and cancer genomics.
Awards
- Silver Prize (Poster), Apr 2023
- Oral Speaker – Honorable Mention, May 2020
- First Prize (Poster), Apr 2013
Funding & Service
- Post‑doc projects on BRCA1/2, PTEN, TP53, MLH1 accepted for extramural funding
- Professional associations: FENS, ISCB
Publications
Grouped by year • Field shown2024
| Year | Field | Citation / Link |
|---|---|---|
| 2024 | Computational Structural Bioinformatics | Comprehensive classification of TP53 somatic missense variants based on structural stability. Brief. Bioinf. |
| 2024 | Genomics | Portuguese BRCA pathogenic variation & admixture impact. BMC Genomics |
| 2024 | Genomics | Pathogenic variants in DNA damage repair genes arose in recent history. BMC Cancer |
| 2024 | Computational Structural Bioinformatics | MLH1 VUS classification using protein structure‑based DL + Ramachandran + MD. IJMS |
2023
| Year | Field | Citation / Link |
|---|---|---|
| 2023 | Computational Structural Bioinformatics | Classification of PTEN missense VUS through exascale simulations. Brief. Bioinf. |
| 2023 | Genomics | Asian BRCA variation: ethnic specificity & deleteriousness from 7,500+ variants. Int J Cancer |
2022
| Year | Field | Citation / Link |
|---|---|---|
| 2022 | Review / Methods | Applications of molecular dynamics simulation in protein study. Membranes |
| 2022 | Computational Structural Bioinformatics | BRCA2 BRC4 deleterious VUS via MD. Brief. Funct. Genom. |
| 2022 | Virology / Structural | SARS‑CoV‑2 RBD double mutations increase transmissibility via enhanced ACE2 interaction. Viruses |
2021–2018
| Year | Field | Citation / Link |
|---|---|---|
| 2021 | Computational Structural Bioinformatics | Deleterious TP53 missense VUS via structural stability. IJMS |
| 2020 | Methods | Ramachandran + MD for variant classification; TP53 model. CSBJ |
| 2020 | Computational Structural Bioinformatics | BRCA1 BRCT VUS classification by MD. CSBJ |
| 2019 | Cancer Genomics | TNBC: DNA methylation + transcription biomarkers & targets. Cancers |
| 2019 | Genomics | BRCA1/2 germline variation in 30k+ Chinese HBOC patients. Int J Cancer |
| 2018 | Neurogenetics | ATXN2 nsSNPs: simulation & structural consequences in SCA2. J Cell Biochem |
2017–2011 (Drug Design & Methods)
| Year | Field | Citation / Link |
|---|---|---|
| 2017 | Enzyme Inhibition | Chymase inhibition: free energy & decomposition. Gene |
| 2017 | TB Resistance | Rifampicin resistance in M. tuberculosis RNAP β mutants. J Cell Biochem |
| 2017 | HDAC Inhibitors | Class IIa HDAC inhibitors toward SCA2: 3D‑QSAR & pharmacophore. Front Neurosci |
| 2016 | HDAC Inhibitors | Hydroxamic‑based HDAC inhibitors: fragment G‑QSAR & MD. J Biomol Struct Dyn |
| 2015 | Immunology | H. pylori NAP as potential Treg modulator in asthma. Front Microbiol |
| 2011 | MMP9 Inhibitors | Structural insights into MMP9 inhibitor binding. Bioinformation |
Full publication list available on Google Scholar, ResearchGate, and ORCID (see Profile Links below).
Experience
Postdoctoral Fellow — University of Macau (Nov 2017 – Apr 2024)
Cancer predisposition genes; MD simulations (REMD), WES/TAS/RNA‑seq analytics; target design across enzymes, ion channels & receptors.
Senior Research Fellow — Jawaharlal Nehru University, Delhi (Feb 2015 – Oct 2017)
Drug repurposing for Class IIa HDAC; HTS with pharmacophore + QSAR; designed/validated HIC & DHC on SH‑SY5Y and IMR‑32.
Senior Programmer — Bioinformatics Center, Biotech Park, Lucknow (Dec 2012 – Jul 2013)
Bioinformatics software validation; training & workshops; Python, R, C++.
Trainee Scientist — ACS bioINFORMATICS, Lucknow (Aug 2008 – Oct 2012)
Course design; industry training; collaborations; MMP9 inhibitor research.
Education
Ph.D., Applied Health Sciences (Computational Structural Bioinformatics)
TERI School of Advanced Studies, New Delhi — 2018
Thesis on histone deacetylase (HDAC) in SCA2 using homology modeling, docking, pharmaco‑informatics, MD, 3D/G‑QSAR and in‑vitro validation.
B.Tech, Biotechnology
Amity University, Delhi (NCR) — 2010
Teaching, Conferences & Professional Associations
Teaching & Supervision
- Supervised 50+ MSc dissertations (University of Macau)
- Teaching Fellow: Biomedical Statistics & Big Data in Cancer Biology (2019, 2020, 2022, 2023)
- TERI University: Bioinformatics lab (2016–2017), lectures for MSc (2015)
Conferences (Selected)
- Advanced Methods in MD, Copenhagen — Oral (Dec 2023)
- EMBO Workshop on Computational Structural Biology, Heidelberg (Dec 2023)
- Basel Computational Biology Conf. — BRCA2 BRC4 (Sep 2021)
- 4th Symposium on Biomedical Sciences — BRCA1 BRCT (May 2020)
Professional Associations
Federation of European Neurosciences Society (FENS); International Society for Computational Biology (ISCB)
Profile Links
- Google Scholar — QiN‑Z78AAAAJ
- ResearchGate — Profile
- LinkedIn — @siddharth-sinha
- ORCID — 0000‑0003‑3868‑1967
Tip: Use the Find (Ctrl/⌘+F) in your browser to search titles, authors, or keywords.