Pyaree Mohan DashBioinformatics · AI · Genomic medicine

I read the genome
between the lines.

Bioinformatics analyst, developer, and scientist turning genomic complexity into models, reproducible systems, biological evidence, and decisions.

I connect predictions to biological signals and turn complex data into clear decisions.

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Portrait of Pyaree Mohan Dash
Pyaree Mohan DashGermany · Open to global collaboration
REGULATORY LANDSCAPE / MPRA SIGNALMove your pointer across the track →
A T G C C A T T A G G C A A C G T C C T A G A A T G C G G A C T A A C G T T A

Regulatory genomicsVariant-effect prediction, MPRA, and interpretable genomic AI.

Reproducible systemsResearch workflows that move from raw reads to usable evidence.

Translational thinkingComputational prioritization designed for experimental follow-through.

01 / About

Three roles.
One connected practice.

My work sits where computational method, biological interpretation, and reliable delivery meet. I can investigate the question, build the system, and explain what the result means.

A / 01

Analyst

I make complex biological data legible, comparable, and decision-ready.

  • Connected model predictions to biologically meaningful regulatory signals.
  • Identified GPCR ligand-binding residues through integrated structural analysis.
  • Used time-series disease simulations to surface candidate biomarkers.
D / 02

Developer

I turn one-off analyses into reproducible tools, pipelines, and research infrastructure.

  • Co-built MPRAsnakeflow for quality-controlled analysis of 240,000 variants.
  • Built an integrated GPCR structure-drug-ligand knowledge base.
  • Work across Python, R, Bash, workflow engines, containers, APIs, and cloud.
S / 03

Scientist

I design focused computational strategies that survive biological and experimental scrutiny.

  • Improved variant-effect prediction correlation by 60% with a focused CNN.
  • Prioritized heart-targeting candidates validated in mice and pigs.
  • Reconstructed FPR receptor evolution across 19 species.

02 / Experience

Research experience

A trajectory from systems biology and receptor evolution to scalable genomics, AI, and translational gene delivery.

2025Present

Research Assistant · Part-time

University Hospital Heidelberg

Heidelberg, Germany

Precision cardiac gene delivery

  • Developed a multimodal framework to identify heart-targeting gene-delivery candidates with strong translational potential; leading candidates were successfully validated in mice and pigs.
  • Elucidated candidate biological drivers, providing a reusable strategy to prioritize next-generation delivery vectors.
20212025

Bioinformatics Scientist

Berlin Institute of Health at Charité

Berlin, Germany

Variant effects · High-throughput genomics

  • Designed a scalable variant-effect prediction framework spanning linear, ensemble, and large DNA foundation models; a task-specific CNN improved Pearson correlation by 60% over the larger models.
  • Developed interpretation algorithms connecting predictions to biologically meaningful regulatory signals, strengthening candidate selection and downstream validation.
  • Co-built MPRAsnakeflow, converting raw Illumina data into quality-controlled measurements, reports, and visualizations for 240,000 variants.
  • Led pilot studies establishing an AI-guided framework for disease-relevant variant design and analysis, laying groundwork for adoption within NHGRI-IGVF.
  • Built a model-guided framework ranking enhancers and variants by predicted effect size and delivering experiment-ready candidates for targeted gene-delivery studies.
20182021

Graduate Research Assistant

CIPMM Homburg · HS-KL

Saarland, Germany

Immune receptor evolution and function

  • Reconstructed the evolutionary landscape of bacterial FPR immune-receptor families across 19 species and traced how diversification shaped immune-signaling roles.
  • Combined high-throughput cellular screening and bio-imaging analysis to identify novel receptor-specific peptide binders.
20192020

Graduate Research Assistant

Helmholtz Institute for Pharmaceutical Research Saarland

Saarbrücken, Germany

Drug bioinformatics

  • Built an integrated GPCR structure-drug-ligand knowledge base for graph-based receptor-ligand analysis and drug-target discovery.
  • Identified key amino-acid residues governing GPCR ligand binding through integrative structural analysis.
20152015

Research Intern

Amrita University · School of Biotechnology

Kerala, India

Sanitation biotechnology

  • Contributed to a Bill & Melinda Gates Foundation-funded project developing biocontrol-based disinfection technologies for regions facing sanitation and wastewater challenges.

03 / Impact atlas

Work translated into
usable results.

Filter the atlas by the kind of problem solved. Each card represents a concrete result from my research or academic projects.

Gene delivery01

Heart-targeting candidates advanced to in-vivo validation.

Multimodal prioritization produced candidates with strong translational potential, successfully validated in mice and pigs.

Biological insight02

Explained candidate performance.

Biological drivers became a reusable strategy for selecting next-generation delivery vectors.

Variant effects03
+60%

Focused model design beat scale.

A task-specific CNN improved correlation over larger DNA foundation models.

Explainable AI04

Predictions became biological signals.

Interpretation algorithms sharpened candidate selection and downstream experimental validation.

High-throughput genomics05
240K

Reproducible MPRA analysis at scale.

MPRAsnakeflow converts raw Illumina reads into QC measurements, reports, and visualizations.

Consortium science06

AI-guided variant design for IGVF.

Pilot studies laid the groundwork for consortium-wide disease-variant design and analysis.

Experimental design07

Experiment-ready enhancers and variants.

An end-to-end framework ranked candidates by predicted effect size for targeted studies.

Evolution08
19 species

The FPR receptor landscape reconstructed.

Evolutionary analysis traced functional diversification across immune-receptor families.

Cell screening09

Novel receptor-specific peptide binders.

High-throughput cellular screening combined with mammalian-cell bio-imaging analysis.

Knowledge systems10

A graph-ready GPCR knowledge base.

Integrated structure, drug, and ligand evidence for receptor analysis and discovery.

Structural analysis11

Binding residues identified.

Integrative analysis isolated key amino acids governing GPCR ligand binding.

Public health12

Biocontrol research for sanitation.

Contributed to Gates Foundation-funded work on disinfection and wastewater challenges.

Peptide design13
75%

More than 90% less screening burden.

Ensemble learning accelerated FPR peptide-binder prioritization while retaining precision.

Functional biology14

Specialization within the FPR family.

Distinct receptor features guided receptor-specific peptide design.

Disease modelling15

Parkinson's pathways connected.

An integrated mathematical model enabled system-level analysis of disease progression.

Biomarkers16

Early-progression signals surfaced.

Time-series simulations identified candidate biomarkers associated with early disease progression.

04 / Skills

Tools for the full lifecycle

From exploratory analysis and model development to reproducible execution and research-facing delivery.

01

Programming

PythonBashRC++SQL
02

Machine learning

scikit-learnKerasTensorFlowPyTorchHugging FaceSHAPLangChain
03

Web & workflows

AWSGoogle CloudDockerSnakemakeNextflowFastAPIFlask
04

Bioinformatics

BWA-MEMbcftoolsVEPbedtoolsFastQCpysamBiopython
05

Scientific focus

Regulatory genomicsVariant effectsMPRAGenomic AIGene deliveryGPCR biologySystems modelling
06

Languages

EnglishFull professional proficiency · C1

GermanLimited working proficiency · A2

05 / Education & projects

Scientific foundations

2017—2021

Master of Science

Bioinformatics

Saarland University · Germany

GPA 1.7 · Advisor: Prof. Dr. Volkhard Helms

Machine Learning-Guided Peptide DesignEnsemble learning achieved 75% precision while reducing the screening burden by more than 90%.
2014—2017

Bachelor of Science

Biotechnology

Amrita University · India

GPA 9.2/10 · German equivalent 1.3

Biochemical Systems Theory in Parkinson's DiseaseIntegrated mathematical modelling connected cell-death pathways and candidate early biomarkers.

06 / Publications

Work in the
scientific record.

Regulatory genomics, reproducible MPRA analysis, and systems biology across leading journals and conferences.

2026Massively parallel characterization and predictive modelling of neuronal regulatory variationSalomon, Deng, Dash, Chalkiadakis, Li, Chen, et al.bioRxiv↗ 2026Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflowRosen, Salomon, de Lange, Dash, Keukeleire, et al.Genome Research↗ 2025Massively parallel characterization of transcriptional regulatory elementsAgarwal, Inoue, Schubach, Penzar, Martin, Dash, et al.Nature↗ 2017Computational modelling of apoptosis in Parkinson's disease using biochemical systems theorySasidharakurup, Dash, et al.IEEE · ICACCI↗

07 / Selected talks

Presented to the community

Invited and selected work at international computational-biology conferences.

2024RSG Chair

ISMB · RSGDREAM

Accelerating high-throughput characterization of regulatory variants with deep learning.

Dash, Deng, Shendure, Ahituv, Schubach & Kircher

2023MLCSB Chair

ISMB / ECCB

Massively parallel characterization of transcriptional regulatory elements.

Agarwal, Inoue, Schubach, Penzar, Martin, Dash, et al.

08 / Recognition & service

Contribution beyond the analysis

2022

Honorable mention

Invited poster at the ISCB RSG conference with DREAM Challenges.

2021

Featured research

Master's thesis featured at the Upper-Rhine Artificial Intelligence Symposium.

2016 · 2017

Research fellowship

Indian Academy of Science fellowship; approximately 250 students selected across India.

2023 · 2024

Peer reviewer

Reviewer for Bioinformatics and Bioinformatics Advances, Oxford University Press.

2024

Workshop organizer

Co-organized an international IGVF workshop on MPRA design for AI applications.

2018 · 2021

Mentorship

Co-supervised two bachelor's students and one master's student at CIPMM.

09 / Contact

Bring me a hard
biological problem.

Available for selected roles and consulting collaborations across bioinformatics analysis, genomic AI, workflow development, research strategy, and scientific communication.

Emailpyareemohandash@gmail.com↗LinkedInlinkedin.com/in/pmdash↗GitHubgithub.com/pyareedash↗Curriculum vitaeView full CV↗