Pradip Singh

Molecular microbiologist and structural biologist with over a decade of experience in molecular biology, host-pathogen interaction analysis, antimicrobial discovery, and protein structural analysis. Specialized expertise in cryo-electron microscopy (cryo-EM), high-throughput screening (HTS), and structure-guided drug design, with a focus on Type IV pilus (T4P) biogenesis and virulence pathways. Developed innovative platforms that integrate cell-free protein expression, nanodisc reconstitution, and Artificial Intelligence -based modeling to identify and optimize inhibitors for challenging membrane-bound targets. Skilled at integrating AI-assisted computer programming into research protocols and data analysis. Published research in high-impact, peer-reviewed journals such as mBio, MMBR, and PLoS ONE. Experienced in mentoring graduate and undergraduate researchers, and enthusiastic about expanding skills into academic teaching. I am currently seeking an Assistant Professor position to establish a collaborative research program in microbial pathogenesis and translational microbiology.

• Selected for Cryo-ET training at National Network for Cryo-Electron Tomography (2025) University of Wisconsin-Madison: “Structural Insights into Type IV Pili Machinery of Enteropathogenic E. coli and P. aeruginosa Using Cryo-Electron Tomography”.
• Python for Non-Programmers, LinkedIn | 2023
• The Three Secrets to Effective Time Investment, LinkedIn | 2023
• Teaching skills improvement lessons, LinkedIn | 2024
• Hands on training on handling lab mice at animal house IMTECH, Chandigarh | 2016

• American Society for Microbiology (ASM)
• American Society for Biochemistry and Molecular Biology (ASBMB) 2024 – Spotlight Talk

Publications Under Preparation

• Little, J.1, Singh, P.K.1, Samsó, M., Donnenberg, M.S. Cryo-Electron Microscopy of BfpB Reveals a Type IVb Secretin Multimer Adapted to Accommodate the Exceptionally Wide Bundle-Forming Pilus. (Under revision). [#1 contributed equally]
• Singh, P.K., Samsó, M., Donnenberg, M.S. Cryo-EM Analysis of Pseudomonas aeruginosa PilB T4P Extension ATPase and Its Interaction with PilC protein, a Membrane-Bound Essential Component of the T4P Machine. (Manuscript in preparation).
• Singh, P.K., Escalante, C.R., Donnenberg, M.S. Crystal Structure Analysis of BfpE, a Transmembrane Protein from the T4P Machine of Enteropathogenic Escherichia coli and Its interaction with T4P ATPase BfpD. (Manuscript in preparation).

2025

• Singh, P.K., Donnenberg, M.S. (2025). Revolutionizing Molecular Cloning: Introducing FastCloneAssist, a Streamlined Python Tool for Optimizing Primer Design in Restriction & Ligation-Independent PCR Cloning. PLoS ONE, 20(3): e0306950.
• Patent: Optimizing Primer Design in Restriction and Ligation-Independent Polymerase Chain Reaction (PCR) Cloning – Filed with USPTO, SIN-24-009, March 2025. Inventor: Pradip Kumar Singh. Pending.

2024

• Little, J.I., Singh, P.K., Zhao, J., Dunn, S., Matz, H., Donnenberg, M.S. (2024). Type IV Pili of Enterobacteriaceae Species. EcoSal Plus, eesp-0003.
• Singh, P.K., Samsó, M., Donnenberg, M.S. (2024). Abstract 1095: Structural Divergence of Type IV Pilus Extension ATPases in Pathogenic Bacteria: Cryo-EM Analysis of Pseudomonas aeruginosa PilB. Journal of Biological Chemistry, 300(3).

2023

• Singh, P.K., Donnenberg, M.S. (2023). High-Throughput and Targeted Screens for Prepilin Peptidase Inhibitors Do Not Identify Common Inhibitors of Eukaryotic Gamma-Secretase. Expert Opinion on Drug Discovery, 1–11.

2022

• Singh, P.K., Little, J., Donnenberg, M.S. (2022). Landmark Discoveries and Recent Advances in Type IV Pilus Research. Microbiology and Molecular Biology Reviews, e00076-22.
• Nayak, A.R., Singh, P.K., Zhao, J., Samsó, M., Donnenberg, M.S. (2022). Cryo-EM Structure of the Type IV Pilus Extension ATPase from Enteropathogenic Escherichia coli. mBio, e02270-22.

2020

• Singh, P.K., Johnston, B.D., Johnson, J.R., Donnenberg, M.S. (2020). Draft Genome Sequences of Concurrent Escherichia coli Blood and Fecal Isolates from a Patient with Bacteremia and Diarrhea Belie BioFire-Based Detection of Fecal Enteropathogenic E. coli. Pathogens and Disease, 78(8): ftaa058.

2017

• Nupur, N., Saini, M.K., Singh, P.K., Korpole, S., Tanuku, N.R.S., Takaichi, S., Pinnaka, A.K. (2017). Imhoffiella gen. nov., a Marine Phototrophic Member of the Family Chromatiaceae, Including the Description of Imhoffiella purpurea sp. nov. and the Reclassification of Thiorhodococcus bheemlicus as Imhoffiella bheemlica comb. nov. International Journal of Systematic and Evolutionary Microbiology, 67(6), 1949–1956.
• Gupta, V., Singh, P.K., Korpole, S., Tanuku, N.R.S., Pinnaka, A.K. (2017). Bacillus mangrovi sp. nov., Isolated from a Sediment Sample from a Mangrove Forest. International Journal of Systematic and Evolutionary Microbiology, 67(7), 2219–2224.

2016

• Sharma, P., Verma, N., Singh, P.K., Korpole, S., et al. (2016). Characterization of Heat-Induced Spherulites of Lysozyme Reveals New Insight on Amyloid Initiation. Scientific Reports, 6, 1–13.

2015

• Singh, P.K., Kumari, A., Chawla, N., Pinnaka, A.K., Korpole, S. (2015). Rhodococcus lactis sp. nov., an Actinobacterium Isolated from Sludge of a Dairy Waste Treatment Plant. International Journal of Systematic and Evolutionary Microbiology, 65(Pt 11), 4215–4220.
• Singh, P.K., Solanki, V., Sharma, S., Thakur, K.G., Krishnan, B., Korpole, S. (2015). The Intramolecular Disulfide-Stapled Structure of Laterosporulin, a Class II D Bacteriocin, Conceals a Human Defensin-Like Structural Module. The FEBS Journal, 282(2), 203–214. *Cover page and Editor choice article*.

2014

• Singh, P.K., Sharma, S., Kumari, A., Korpole, S. (2014). A Non-Pediocin Low Molecular Weight Antimicrobial Peptide Produced by Pediococcus pentosaceus Strain IE-3 Shows Increased Activity under Reducing Environment. BMC Microbiology, 14(1), 1–9.

2013

• Baindara, P., Mandal, S.M., Chawla, N., Singh, P.K., Pinnaka, A.K., Korpole, S. (2013). Characterization of Two Antimicrobial Peptides Produced by a Halotolerant Bacillus subtilis Strain SK.DU.4 Isolated from a Rhizosphere Soil Sample. AMB Express, 3(1), 1–11.
• Shalley, S., Singh, P.K., Srinivas, T., Korpole, S., Pinnaka, A.K. (2013). Marinilabilia nitratireducens sp. nov., a Lipolytic Bacterium of the Family Marinilabiliaceae Isolated from Marine Solar Saltern. Antonie van Leeuwenhoek, 103(3), 519–525.

2012

• Singh, P.K., Chittpurna, A., Sharma, V., Patil, P.B., Korpole, S. (2012). Identification, Purification, and Characterization of Laterosporulin, a Novel Bacteriocin Produced by Brevibacillus sp. Strain GI-9. PLOS ONE, 7(3): e31498.
• Sharma, S., Singh, P.K., Korpole, S., Pinnaka, A.K., et al. (2012). Fulvivirga imtechensis sp. nov., a Member of the Phylum Bacteroidetes. International Journal of Systematic and Evolutionary Microbiology, 62(Pt 9), 2213–2217.
• Midha, S., Ranjan, M., Sharma, V., Kumari, A., Singh, P.K., Korpole, S., Patil, P.B. (2012). Genome Sequence of Pediococcus pentosaceus Strain IE-3. American Society for Microbiology Resource Announcement.