Dr. Kshitish K Acharya

Dr. Kshitish K Acharya

Faculty Scientist

Research Focus Key Words

‘Biomarker discovery’ ‘Transcriptomics’ ‘Genomics’ ‘Mammalian gene expression regulation’ ‘spermatogenesis’

Background

Kshitish started his research career with wild life studies in the Western ghat forest for an year. He then took to behavioural, histological, physiological and in vitro culture studies. During his post-doctoral work at the University of Virginia (USA), he mainly applied recombinant DNA technology, cell culture and other molecular techniques to characterize a promoter and cognate regulatory proteins. His research mainly used mouse as a model, though he worked on other animals such as bats, hamsters and bonnet monkeys.  He worked on protein purification methods at ‘Yashraj Biotechnology Ltd’ (Mumbai), where he also had his first experience in management and business aspects – for an year. He supervised and guided multiple projects related to metagenomics, genomics, transcriptomics of plants and humans,  as well as microbiomes from various sources, at ‘Shodhaka’ (Bengaluru) – a company he funded and founded. At Shodhaka, his team also developed multiple bioinformatics resources over 10 years, and a bioinformatics global portal (http://www.startbioinfo.com/), in association with BdataA. Apart from teaching, he has guided and supervised a few PhD students and about 100 interns at IBAB. While he has been enjoying a multi-disciplinary research at IBAB as briefed below, transcriptomics and gene expression regulatory mechanisms form a key area of his research.

Education:

PhD: Banaras Hindu University, 1996
MSc: Gulbarga University, 1989
BSc: PoornaPrajna College, Mangalore University, 1983

Professional experience:

Head of research and production units: Yashraj Biotechnology Ltd (2002)
Founder of Shodhaka Life Sciences Pvt. Ltd. in 2008, its director from 2009  till 2019     
Founder of Biological Data Analyzer’s Association (BdataA) in 2016

Current Research Interest

Kshitish’s group has been making combinatorial use of modern approaches in molecular and computational biology, to a) study transcription control mechanisms, b) identify novel markers, for male infertility, and cancer of specific tissues such as prostate, cervix, liver, breast and lung. Addressing reproductive biology at the molecular level, his group first painstakingly compiled gene expression data over multiple years, developed tissue-specific gene expression databases (testis, prostate, & uterus), and found ways to make a better use of existing data. They also developed some of the novel software and computational methods for the analysis of the resulting data to understand the regulatory mechanisms (e.g., GREAM & TIPMaP) or experimental validations (e.g. Ex-Ex Primer). Using RNA-sequencing, his group recently short-listed markers for a type of male infertility, and established novel association of several genes with human spermatogenesis. Currently, they are trying to explore the role of some of the novel genes. Part of his team is also contributing to a nation-wide project that explores the Indian human genome in the context of  hereditary deafness.

Current group members:

1. Mr. Govindkumar Balagannavar completed his master’s in Bioinformatics from Annamalai University in 2009. Though Mr. Govind joined IBAB as a research assistant earlier, he registered for PhD in 2018 with MAHE, Manipal. He has taken a lead role in the transcriptomics exploration of the non-obstructive azoospermia disorder mainly by analyzing the RNA-seq data generated using clinical samples. His work helped to short-list novel markers, which were then experimentally validated. Currently, these molecules are being cloned and expressed.

2. Ms. Kavyashree Basavaraju completed her bachelor’s degree in Biotechnology from M S Ramaiah Insitute of Technology in 2013. She joined IBAB as a research assistant in 2018. She has been involved analyzing interactions among key molecules in the context of the non-obstructive azoospermia. She is also validating gene expression patterns detected by RNA-seq experiments using RT-qPCR, and is attempting to clone and express some of the genes.

3. Ms. Moushumi Goswami completed her MSc in Medical Biochemistry from Kasturba Medical College, MAHE, Manipal. She joined as a research assistant and a potential PhD candidate in 2018, and has been exploring molecular mechanisms related to meiosis and related to mammalian spermatogenesis. She is using both in silico and in vitro procedures in her research work..

4. Ms. Raksha H N completed her masters in Bioinformatics from Visvesvaraya Technological University in 2017. She joined IBAB as a research assistant in 2019. she is maintaining the mammalian gene expression databases and trying to upgrade the same. She is also creating a new gene expression database for the mammalian ovary tissue.

Intern:

1. Mr. Sachin D’Souza joined IBAB as an intern from July 2019. He completed his MSc in Bioinformatics from St. Aloysius college, Mangaluru. He is also working improving the quality and contents of tissue-based mammalian gene expression databases.

Earlier group members:

We are constantly looking for talented new members to join us as interns/PhD students. Please do apply!

1. Dr. Darshan S Chandrashekar, MSc in Bioinformatics from Kuvempu University, Shivamogga, completed PhD (2015) under the guidance of Dr. Kshitish Acharya K by registering at MAHE, Manipal. The title of his thesis was, “Establishing expression-based gene clusters for prediction of mammalian promoters and expression patterns”. He then joined a leading research group in the University of Alabama as a post-doctoral fellow.

2. Dr. Neelima Ch, MSc in Bioinformatics from University of Madras, Chennai, completed her PhD (2016) by registering with IIIT-Hyderabad. She worked on a thesis titled, “Understanding the differences in preliminary stages of gene expression regulation in healthy and unhealthy mammalian tissues, and identification of potential markers” under the guidance of Dr. Kshitish Acharya K. She later turned into an entrepreneur.

3. Mr. Manu S, received the Phi-Psi award by after his MSc in IBAB (2018) and completed a project, conceptualized and initiated by him, on exploring meiotic hotspots in  human populations. He was one of the national toppers in BINC and joined CCMB, Hyderabad to pursue PhD.

4. Dr. Agaz Hussain, an young researcher from Kashmir, worked with our team during his doctorate work at Mangalore University, and continued his collaborative work at IBAB (2019) on new ways of aligning raw NGS reads. He then joined as a post doctoral fellow at University of South Florida.

5. Dr. SreeLakshmi KS, a masters from KMC, MAHE, joined IBAB as a research assistant in a project that involved biocuration of cancer-related gene expression datasets from literature. She went on pursue PhD at IOB, Bengaluru.

6. Mr. Akhilesh Bajpai joined IBAB as a research assistant in a project that involved biocuration of cancer-related gene expression datasets from literature. He then pursed  PhD at VIT, Vellore (& Shodhaka LS Pvt Ltd).

7. Ms. Sravanthi Davuluri joined IBAB as a research assistant in a project that involved biocuration of cancer-related gene expression datasets from literature. She pursued PhD at VIT, Vellore (& Shodhaka LS Pvt Ltd).

8. Dr. Haritha Haridas worked on multiple research projects at IBAB after completing the Laboratory Course in Bio-Techniques (LCBT). Later, she joined the University of Udine, Italy, and completed her PhD.

Over 15 years, about 50 young researchers have worked in IBAB and contributed to our research work, and they include the following: Dr. Kouser Fathima (Chikkamagaluru / University of Mysore), Dr. Sonali (NIRRH, Mumbai), Mr. Siva Arumugam (Tenkasi), Ms. Krishna Patel (Vyara), Mr. Rushiraj M (VTU/Gujarat), Mr. Lijo Thomas K (Thrissur, Kerala), Ms. Deepthi H (Bengaluru), Dr. Pranami Bora (Guahati), Ms. Leena Rao (Udupi), Mr. Nagaraj Naik (Shivamogga), Dr. Kalesh S (Coimbatore), Ms. Praveena Komali (Andhra Pradesh), Mr. Sunilkumar (Shivamogga), Mr. Sudhir (Bengaluru), Mr. Ramkumar Pullata (Andhra Pradesh), Mr. Mohammed Farouk (Madurai), Mr. Himadri Singh (Munger, Bihar), Ms. Ilakya S (Tiruchirapalli), Ms. Meena N (Tiruchirapalli), Mr. Varun Malhotra (Delhi), Mr. Hardik Shah (DYPatil College/Gujarat), Ms. Deepa Raj Paul (VIT/Kerala),  Ms. Shruti (IBAB) and Ms. Greta Kasliwal (IBAB/Indore) and Dr. Kuljeet Singh Sandhu (IBAB/Punjab). Dr. Kshitish’s group at IBAB also provided an opportunity for about 50 young interns to get trained in projects involving programming, biocuration, recombinant DNA technology and/or gene expression, NGS as well as other types of data analysis. A good proportion of interns and research assistants contributed to biocuration work. All efforts and contributions by the interns and research assistants/associates and PhD students is highly appreciated.

Collaborators

Dr. Vasan S [Ankur-Manipal hospitals, Bengaluru]
Dr. Mahale SD & Dr. Parte P [NIRRH, Mumbai]
Researchers of R & D unit of the Shodhaka LS Pvt. Ltd., Bengaluru
Members of BdataA [Biological data Analyzers’ Association – a virtual organization]
Dr. Jayashree RS & Dr. Mahua S [KMIO, Bengaluru]

Major contributions/findings

A. Reproductive biology

A1. Identified 19 candidate marker molecules for differentiating 2 types of male infertility, and identifying spermatogenesis failure (being published).
A2. Specific regulatory region that play a key role in spermatid-specific transcription of a gene (acrv1), and the cognate potential regulatory proteins were also identified.
A3. Tissue-specific databases have been developed to aid researchers working on testis, and uterus. Prostate and ovary databases are being developed.

B. Cancer

B1.Identified gender-based candidate markers for a specific type of lung cancer (being published).
B2.Identified new candidate markers for liver cancer (to be published)

C. Bioinformatics and data analysis methods

C1. Compiled 375 protein-protein interaction databases and tools, short-listed top 16 of them and compared systematically from a user’s perspective.
C2. On an average, about 35% of relevant citations can be lost when using any one of the top literature search engines.
Literature search being so fundamental any researcher, it was also important to catalog all tools, and recommend tools for specific applications.
C3. Compiled thousands of bioinformatics resources systematically in one place and catalogued them based on type of applications (see http://www.startbioinfo.com/).
C5. Such meta analysis methods could be applied to a variety of gene expression data, including RNA-seq data. These methods can produce a hierarchical list of molecules associated with any specific disorder or other condition of interest.
C6. A software for exon-exon junction-specific primer designing.
C7. A software for genome-wide repeat element analysis.
C8. A database to promote endometrial receptivity studies.

D. Genomics and transcriptomics

Guided and supervised complete analysis of NGS data in more than a dozen projects that included metagenomics of microbiomes of soil and human gut, new species genome establishment and annotations, and transcriptomics of human tissues, and tissues of certain animals and plants.

E. Olfaction in animals

E1. A female mouse can remember the urinary pheromones of her mate for 7 days after insemination, but not more than that [note: such pheromones are key to protect the pregnancy triggered by him, & understanding such pheromonal communications may be important for controlling rodent pests].
E2. Despite being equipped with abilities to see, hear, and locate things using echoes, bats use smells to find fruits in the night.

Representative publications

  1. Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K Acharya (2018)
    How helpful are the protein-protein interaction databases and which ones? https://www.biorxiv.org/content/10.1101/566372v1
  2. Manu S, Acharya KK, Thiyagarajan S (2018) 
    Systematic analyses of autosomal recombination rates from the 1000 genomes project uncovers the global recombination landscape in humans.  https://www.biorxiv.org/content/early/2018/01/12/246702.
  3. Adurthi S, Kumar MM, Vinodkumar HS, Mukherjee G, Krishnamurthy H, Acharya KK, Bafna UD, Uma DK, Abhishekh B, Sudhir Krishna, Parchure A, Murali A, and Jayshree RS (2017) 
    Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer. Scientific Reports 77(1):17289.
  4. Narayanaswamy PB, Baral TK, Haller H, Dumler I, Acharya KK and Kiyan Y (2017) 
    Transcriptomic pathway analysis of urokinase receptor silenced breast cancer cells: a microarray study. Oncotarget 8(60): 101572-101590. 
  5. Pathak BR, Breed AA, Apte S, Acharya KK, Mahale SD. (2016)
    Cysteine-rich secretory protein 3 plays a role in prostate cancer cell invasion and affects expression of  PSA and ANXA1. Mol Cell Biochem. 411(1-2):11-21. 
  6. Chandrashekar DS, Dey P, Acharya KK (2015) 
    GREAM: A web server to short-list the potentially important genomic repeat elements based on over-/under-representation in specific chromosomal locations such as the gene neighborhoods within or across 17 mammalian species. PLOS One  Jul 24;10(7):e0133647.
  7. Bhagwat S, Dalvi V, Chandrasekhar DS, Matthew T, Acharya KK, Gajbhiye R, Kulkarni V, Sonawane S, Ghosalkar M, Parte P (2014)
    Acetylated alpha tubulin is reduced in individuals with poor sperm motility.Fertility & Sterility 101(1):95-104.e
  8. Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS and Acharya KK (2013). 
    TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes. BMC Genomics 14: 922
  9. Bhagwat SR, Chandrashekar DS, Kakar R, Davuluri S, Bajpai AK, Nayak S, Bhutada S, Acharya KK, Sachdeva G (2013) 
    Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PLOS One 8(3), e58419
  10. Acharya KK, Chandrashekar DS, Chitturi N, Shah H, Malhotra V, Sreelakshmi KS, Deepti H, Bajpai A, Davuluri S, Bora P, Rao L. (2010)
    A novel tissue-specific meta-analysis approach for gene-expression predictions, initiated with a mammalian gene expression testis database. BMC Genomics, 11: 467 
  11. Kshitish K Acharya, Greta K & Harita H (2008) 
    How do you choose your search engine(s)? Nature Precedings (pre-print; highly voted for) http://precedings.nature.com/documents/2101/version/2

Address

Institute of Bioinformatics and Applied Biotechnology
Biotech Park, Electronic City Phase I,
Bengaluru 560100,
India

Phone

080 285 289 00/01/02, extension 104

Email

kshitish@ibab.ac.in