Basic Details:
Email ID: manan@bioinformatics-india.dev
Year of Birth: 1992
Country (Nationality): India
Country (Residence): Germany
Languages
English (Native)
Hindi (Native)
Gujarati (Mother Tounge)
German (A2)
My Objective
John Naisbitt once said “We are drowning in Information but starved for Knowledge” which is true. Everyday we are generating so much data, but our ability to translate that data into something useful is severly compromised by our current lack of technology and sufficient workforce skilled to make sense of that information. My objective is to contribute to solving this problem by creating smart tools that can translate this information to knowledge and at the same time become competent enough to interpret this information. My field of choice is Biology because I was intreguied by how just ‘ATGC’ these four bases create the most complex systems in form of organisms.
Qualifications
| Program | Institute/College |
|---|---|
| PhD in Biodiversity and Bioinformatics (2025) |
University of Duisburg-Essen, Essen, Germany |
| Python Certification Training | TryCatch Institute, Mumbai |
| Masters in Bioinformatics | Bioinformatics Centre, Pune University |
| Bachelors in Biotechnology | Jai Hind College, Mumbai University |
| Diploma in Basic Web designing | Computer station Inc., Mumbai |
| Higher Secondary Schooling(Science) | Shri Tikamdas Bhatia College Of Science, Maharashtra Boards |
| Secondary Schooling | Rustomjee International School, Maharashtra Board |
Core Skills
| 🔬 Bioinformatics | 🧬 Sequencing | 🖥️ Computing | 🧪 Wet Lab |
|---|---|---|---|
| Metagenomics, Metatranscriptomics, Genomics, Programming (Python, R, Perl, Snakemake) | Illumina, Nanopore, Sanger | Linux (HPC), Windows, Virtual Machines, Databases, Web-servers, Automation | Mesocosms, Sampling, DNA extraction, Library prep, Sequncing |
Work Experience
| Company/Institute | Designation | Duration |
| Persistent Systems Ltd. | Trainee | 3 Months (2015) |
| Persistent Systems Ltd. | Domain Analyst | 9 Months (2015-2016) |
|
Worked in the support team for bioinformatics and clinical research platforms, including CaTissue (Bio-Banking), InfoEd (Electronic Research Administration), Oncore (Oncology Clinical Research Management), and InForm (Electronic Patient Data Collection). I was also involved in testing and quality assurance for OncDRS (Clinical Data Retrieval System). My responsibilities included application administration, database management, and ensuring smooth operation and support for end users across multiple clinical and research platforms. |
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| Company/Institute | Designation | Duration |
| National Collection of industrial Micro-organisms (CSIR-NCL) |
Project Assistant II | 2+ years (2016-2018) |
|
Worked under the guidance of Dr. Mahesh Dharne on projects involving microbial genomics and environmental sequencing. I was responsible for the analysis of multiple next-generation sequencing datasets, including 16S/18S/ITS amplicons, shotgun metagenomes, and whole genomes (bacteria and viruses), using platforms such as Illumina MiSeq/HiSeq and Oxford Nanopore MinION. My work also involved sampling, DNA extraction, library preparation, and sequencing of samples collected from diverse and extreme environments such as hot springs, rivers, hypersaline lakes, and glaciers. Additionally, I set up and maintained a Linux-based high-performance computing (HPC) infrastructure, developed custom bioinformatics pipelines using Python, R, and Perl, and contributed to the maintenance of internal databases. I also provided support to doctoral researchers by advising on bioinformatics methodologies and developing custom scripts to assist their research. |
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| Company/Institute | Designation | Duration |
| PierianDx India Pvt. Ltd. | Bioinformatician | 2 Months (2019) |
| Customizing Directed Acyclic Graphs for use in PierianDx’s Clinical Genomics Workbench to suite the institute’s/hospital’s needs. | ||
| Company/Institute | Designation | Duration |
| University of Duisburg-Essen | Doctoral Researcher | 5 years (2020-2025) |
|
Pursued a PhD under the supervision of Prof. Dr. Jens Boenigk and Prof. Dr. Daniela Beisser, supported by a scholarship from the Bauer-Stemmler Stiftung. My thesis, titled “Hidden Signals: Employing Taxonomy and Functions to Reveal Freshwater Ecosystem Resilience Using Meta-Omics Methods”, explored the use of metabarcoding, metatranscriptomics, and metagenomics to investigate microbial responses to environmental stressors in freshwater ecosystems. The research involved designing and running mesocosm experiments, generating RNA/DNA sequencing data, and developing bioinformatics workflows to uncover patterns in both taxonomic and functional resilience. In parallel, I contributed to the CRC-RESIST project as a Research Data Manager, responsible for the organization, structured storage, and long-term infrastructure supporting large-scale research data. |
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| Company/Institute | Designation | Duration |
|
Bioinformatician | ongoing since 2025 |
|
With the transition of CRC-RESIST into its second phase, for INF sub-project, I continue to manage research data and now also lead initial analysis of amplicon sequencing (metabarcoding) datasets. In parallel, I have joined the Genomics Core Facility, where I contribute to implementing automation tools for high-throughput liquid handling systems, and improving data delivery pipelines via platforms such as eLab (protocol and metadata management) and Dataverse (sequencing data dissemination). |
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Public Tools
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- Github: mbshah (Vairous scripts created while pursuing research at NCIM and UDE)
- GitLab (UDE): CRC-RESIST related internal tools: eLabFTW-ude-cli, Dataverse Batch Uploads
- PAIS database: Coming Soon
Publications
- Breaking the Standard: Can Oxford Nanopore Technologies Sequencing Compete With Illumina in Protistan Amplicon Studies?
- Authors: Dana Bludau, Guido Sieber, Manan Shah, Aman Deep, Jens Boenigk, Daniela Beisser.
- Journal: Environmental DNA (2025)
- DOI: 10.1002/edn3.70084
- Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes
- Authors: Manan Shah, Till L. V. Bornemann, Julia K. Nuy, Martin W. Hahn, Alexander J. Probst, Daniela Beisser, Jens Boenigk.
- Journal: Environmental Microbiology (2024)
- DOI: 10.1111/1462-2920.16634
- Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater
- Authors: Guido Sieber, Felix Drees, Manan Shah, Tom L. Stach, Lotta Hohrenk-Danzouma, Christina Bock, Maryam Vosough, Mark Schumann, Bernd Sures, Alexander J. Probst, Torsten, C. Schmidt, Daniela Beisser, Jens Boenigk.
- Journal: Science of The Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.167457
- Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater
- Authors: Tom L. Stach, Guido Sieber, Manan Shah, Sophie A. Simon, André Soares, Till L. V. Bornemann, Julia Plewka, Julian Künkel, Christian Becker, Folker Meyer, Jens Boenigk, Alexander J. Probst.
- Journal: MicrobiologyOpen (2023)
- DOI: 10.1002/mbo3.1347
- The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release
- Authors: M.Voss, CRC-RESIST Consortium, B. Suers.
- Journal: Science of the Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.162196
- Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India
- Authors: Rachel Samson, Vinay Rajput, Rakeshkumar Yadav, Manan Shah, Mahesh Dharne.
- Journal: Science of The Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.162125
- Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion
- Authors: G. Sieber, D. Beisser, J. L. Rothenberger, M. Shah, M. Schumann, B. Sures & J. Boenigk.
- Journal: Scientific Reports (2022)
- DOI: 10.1038/s41598-022-22906-6
- Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities
- Authors:Rachel Samson, Vinay Rajput, Manan Shah, Rakeshkumar Yadav, Priyanka Sarode, Syed G Dastager, Mahesh S Dharne, Krishna Khairnar.
- Journal: Chemosphere (2020)
- DOI: 10.1016/j.chemosphere.2020.126507
- Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India
- Authors: Jaya Chakraborty, Vibhavari Sapkale, Vinay Rajput, Manan Shah, Sanjay Kamble, Mahesh Dharne.
- Journal: Ecotoxicology and Environmental Safety
- DOI: 10.1016/j.ecoenv.2020.110443
- Metagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India
- Authors: Jaya Chakraborty, Vibhavari Sapkale, Manan Shah, Mahesh Dharne.
- Journal: Ecological Indicators (2019)
- DOI: 10.1016/j.ecolind.2019.105827
- Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges
- Authors: Rachel Samson, Manan Shah, Rakeshkumar Yadav, Krishna Khairnar.
- Journal: Science of The Total Environment (2019)
- DOI: 10.1016/j.scitotenv.2019.04.166
- Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India
- Authors: Gajanan Mehetre, Manan Shah, Syed Dastager, Mahesh Dharne.
- Journal: Archives of Microbiology (2018)
- DOI: 10.1007/s00203-018-1484-4