Research Publications

Advancing scientific knowledge through cutting-edge research in genomics, bioinformatics, and AI-driven drug discovery

DS

Dr. Dakshinamurthy Sivakumar

Senior Scientist - AI in Drug Discovery & Structural Bioinformatics

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Structural Bioinformatics and Artificial Intelligence Approaches in De Novo Drug Design
D Sivakumar, S Wu
πŸ“š Marvels of Artificial and Computational Intelligence in Life Sciences πŸ“… 2023
SH Jang, D Sivakumar, SK Mudedla, J Choi, S Lee, M Jeon, SK Bvs, et al.
πŸ“š Frontiers in Molecular Biosciences πŸ“… 2022 πŸ”– 9 citations
Classical and Machine Learning Methods for Protein-Ligand Binding Free Energy Estimation
D Sivakumar, S Wu
πŸ“š Current Drug Metabolism πŸ“… 2022 πŸ”– 4 citations
D Sivakumar, S Mudedla, S Jang, H Kim, H Park, Y Choi, J Oh, S Wu
πŸ“š Biomolecules πŸ“… 2021 πŸ”– 7 citations
D Sivakumar, V Kumar, M Naumann, M Stein
πŸ“š Journal of Biological Chemistry πŸ“… 2020 πŸ”– 25 citations
NADH oxidase from Lactobacillus reuteri: A versatile enzyme for oxidized cofactor regeneration
H Gao, J Li, D Sivakumar, TS Kim, SKS Patel, VC Kalia, IW Kim, et al.
πŸ“š International Journal of Biological Macromolecules πŸ“… 2019 πŸ”– 68 citations
Insights into Cell-Free Conversion of CO2 to Chemicals by a Multienzyme Cascade Reaction
RK Singh, R Singh, D Sivakumar, S Kondaveeti, T Kim, J Li, BH Sung, et al.
πŸ“š ACS Catalysis πŸ“… 2018 πŸ”– 132 citations
Identification of 2, 4-dihydroxy-5-pyrimidinyl imidothiocarbomate as a novel inhibitor to Y box binding protein-1 (YB-1) and its therapeutic actions against breast cancer
VP Gunasekaran, K Nishi, D Sivakumar, T Sivaraman, G Mathan
πŸ“š European Journal of Pharmaceutical Sciences πŸ“… 2018 πŸ”– 28 citations
An artificial synthetic pathway for acetoin, 2, 3-butanediol, and 2-butanol production from ethanol using cell free multi-enzyme catalysis
L Zhang, R Singh, Z Guo, J Li, F Chen, Y He, X Guan, YC Kang, JK Lee
πŸ“š Green Chemistry πŸ“… 2018 πŸ”– 86 citations
A review on structures and functions of Bcl-2 family proteins from Homo sapiens
D Sivakumar, T Sivaraman
πŸ“š Protein and Peptide Letters πŸ“… 2016 πŸ”– 15 citations
D Sivakumar, KM Surapaneni, PC Prabu, N Hari, P Thiruvasagam, et al.
πŸ“š RSC Advances πŸ“… 2016 πŸ”– 4 citations
Ultraviolet and 5β€²Fluorodeoxyuridine Induced Random Mutagenesis in Chlorella vulgaris and Its Impact on Fatty Acid Profile
J Anthony, VR Rangamaran, D Gopal, KT Shivasankarasubbiah, et al.
πŸ“š Marine Biotechnology πŸ“… 2015 πŸ”– 45 citations
Screening efficient BH3-mimetics to hBcl-B by means of peptidodynmimetic method
D Sivakumar, B Gorai, T Sivaraman
πŸ“š Molecular BioSystems πŸ“… 2013 πŸ”– 17 citations
In silico methods for designing antagonists to anti-apoptotic members of Bcl-2 family proteins
D Sivakumar, T Richa, S Siva Rajesh, B Gorai, T Sivaraman
πŸ“š Mini Reviews in Medicinal Chemistry πŸ“… 2012 πŸ”– 15 citations
AP

Anoosha Paruchuri

Bioinformatics Scientist - Precision Oncology & AI in Genomics

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Evaluating fibroblast growth factor receptor (FGFR) pathway mRNA expression and protein activation in cholangiocarcinoma tumors
L Stein, JW Reeser, MR Wing, E Samorodnitsky, A Paruchuri, A Smith, et al.
πŸ“š Journal of Clinical and Translational Science πŸ“… 2025
FGFR2-fusions define a clinically actionable molecular subset of pancreatic cancer
L Stein, K Murugesan, JW Reeser, Z Risch, MR Wing, A Paruchuri, et al.
πŸ“š NPJ Precision Oncology πŸ“… 2024 πŸ”– 5 citations
Analytic validation of an FGFR-focused cell-free DNA liquid biopsy assay (FGFR-Dx)
JW Reeser, MR Wing, E Samorodnitsky, T Dao, A Smith, L Stein, et al.
πŸ“š medRxiv πŸ“… 2024 πŸ”– 1 citation
A phase II telemedicine study of pemigatinib in adult patients with unresectable or metastatic pancreas cancer with FGFR2 gene fusions or other FGFR genetic alterations
Z Risch, M Wing, J Reeser, L Stein, T Dao, A Smith, E Samorodnitsky, et al.
πŸ“š Journal of Clinical Oncology πŸ“… 2024
A systematic approach for detection of tumor genomic alterations which alter the immune microenvironment
R Vella, EL Hoskins, JW Reeser, MR Wing, E Samorodnitsky, A Paruchuri, et al.
πŸ“š Cancer Research πŸ“… 2023
Clinical impact of FGFR inhibitors on FGFR2 positive pancreatic cancer
L Stein, JW Reeser, MR Wing, K Murugesan, A Paruchuri, Z Risch, et al.
πŸ“š Cancer Research πŸ“… 2023 πŸ”– 3 citations
Pan-cancer landscape of programmed death ligand-1 and programmed death ligand-2 structural variations
EL Hoskins, E Samorodnitsky, MR Wing, JW Reeser, JF Hopkins, A Paruchuri, et al.
πŸ“š JCO Precision Oncology πŸ“… 2023 πŸ”– 8 citations
Identification of cancer hotspot residues and driver mutations using machine learning
M Pandey, P Anoosha, D Yesudhas, MM Gromiha
πŸ“š Machine Learning in Bioinformatics of Protein Sequences πŸ“… 2023 πŸ”– 3 citations
Identification of potential driver mutations in glioblastoma using machine learning
M Pandey, P Anoosha, D Yesudhas, MM Gromiha
πŸ“š Briefings in Bioinformatics πŸ“… 2022 πŸ”– 22 citations
Pan-cancer landscape and impact of PD-L1 and PD-L2 structural variation
EL Hoskins, E Samorodnitsky, MR Wing, JW Reeser, J Hopkins, A Paruchuri, et al.
πŸ“š Cancer Research πŸ“… 2022
Ppar-responsive elements enriched with alu repeats may contribute to distinctive pparγ–dnmt1 interactions in the genome
A Sharma, F Tobar-Tosse, T Chand Dakal, H Liu, A Biswas, A Menon, et al.
πŸ“š Cancers πŸ“… 2021 πŸ”– 4 citations
Genomic and transcriptomic characterization of relapsed SCLC through rapid research autopsy
HZ Chen, R Bonneville, A Paruchuri, JW Reeser, MR Wing, et al.
πŸ“š JTO Clinical and Research Reports πŸ“… 2021 πŸ”– 20 citations
Characterization of clonal evolution in microsatellite unstable metastatic cancers through multiregional tumor sequencing
R Bonneville, A Paruchuri, MR Wing, MA Krook, JW Reeser, HZ Chen, et al.
πŸ“š Molecular Cancer Research πŸ“… 2021 πŸ”– 7 citations
Research autopsy demonstrates polyclonal acquired resistance in a patient with metastatic GI stromal tumor
A Paruchuri, HZ Chen, R Bonneville, JW Reeser, MR Wing, MA Krook, et al.
πŸ“š JCO Precision Oncology πŸ“… 2020 πŸ”– 2 citations
Quantitative structure–activity relationship in ligand-based drug design: Concepts and applications
V Kanakaveti, P Anoosha, R Sakthivel, SK Rayala, MM Gromiha
πŸ“š Protein Interactions: Computational Methods, Analysis and Applications πŸ“… 2020 πŸ”– 8 citations

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