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{Seminar} @ CDS: 22nd December: “Reconstructing regulatory network in microbes through Machine learning.”

Wed, 22 Dec 21 @ 10:00 AM -- 11:00 AM

Department of Computational and Data Sciences

Department Seminar

SPEAKER     :   Dr. Akanksha Rajput

TITLE            : “Reconstructing regulatory network in microbes through Machine learning”

Date & Time  :  December 22, 2021, 10:00 AM.

Venue              : Online



The Transcriptional Regulatory Network (TRN) plays a critical role in coordinating numerous cellular processes. We extracted and quality controlled all publicly available RNA-sequencing datasets for P. aeruginosa to find 281 high-quality transcriptomes. We produced 83 new RNAseq data sets under critical conditions to generate a comprehensive compendium of 364 transcriptomes. We used this compendium to reconstruct the TRN of P. aeruginosa using independent component analysis (ICA). We identified 104 independently modulated sets of genes (called iModulons), among which 81 (78%) reflect the effects of known transcriptional regulators. We show that iModulons: 1) play an important role in defining the genomic boundaries of biosynthetic gene clusters (BGCs); 2) show increased expression of the BGCs and associated secretion systems in conditions that emulate cystic fibrosis (CF); 3) show the presence of a novel BGC named RiPP (bacteriocin producer) which might have a role in worsening CF outcomes; 4) exhibit the interplay of amino acid metabolism regulation and central metabolism across carbon sources, and 5) clustered according to their activity changes to define iron and sulfur stimulons. Finally, we compared the iModulons of P. aeruginosa with those of E. coli to observe conserved regulons across two gram-negative species. This comprehensive TRN framework covers almost every aspect of the transcriptional regulatory machinery in P. aeruginosa and thus could prove foundational for future research of its physiological functions. Apart from P. aeruginosa, we are working to reconstruct the TRN of Lactobacillus and other important bacterial species.



Dr. Akanksha Rajput is a Postdoctoral scholar at Dr. Bernhard O. Palsson’s lab (Systems Biology Research Group), Department of Bioengineering, University of California San Diego. Her postdoctoral work is focused on bacterial multi-omics data analysis to investigate their antibiotic resistance behavior. She did her Ph.D. from Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India (2012-2018). Her Ph.D. thesis entitled “Development of in-silico resources to study Quorum sensing and Quorum quenching molecules” was awarded as V.C. Vora best thesis award-2018. During her research career, she published various high-impact research articles focused on exploring bacteria, viruses, and archaea through big data analysis approaches. She was also awarded young scientist awards by the Indian Virology Society (IVS) and the BIOinformatics CLUb for Experimenting Scientists (BIOCLUES) Organization for her contribution in the fields of Virology and Bioinformatics respectively. As a researcher, Dr. Rajput is interested in exploring the microbes and their implications in health care (antibiotics resistance, nosocomial infections), as well as in the human body (gut microbiota). The detailed information about Dr. Rajput can be found at https://sites.google.com/view/akanksha-rajput

Host Faculty: Prof. Debnath Pal


Wed, 22 Dec 21
10:00 AM -- 11:00 AM