Molecular mechanisms and chromatin regulation
Structure–function reasoning, construct and variant design, molecular cloning, targeted mutagenesis and mechanistic interpretation.
Research scientist · Life sciences
Hari Raj Singh PhD
Molecular Cell Biologist · Scientific Programme Builder · Bio × AI
I study how molecular mechanisms shape cellular organisation, and build experimental, quantitative and computational systems that make those relationships testable.
16 worksDirectly linked research, reviews, tools and commentaries
15+ yearsInternational scientific experience
Cross-scaleMolecules · cells · data · evidence
TRIMCodeTRIM-family mesoscale-biology programme
Scientific profile
Scientific practice across scales.
Mechanistic discovery, quantitative cell biology and reusable research systems brought together through rigorous experimental and computational work.
Questions move from molecular control to cellular organisation—and from evidence to responsible scientific translation.
Hari Raj Singh is an interdisciplinary molecular and cellular biologist whose work connects mechanistic discovery, quantitative imaging, human genetics, mesoscale cellular organisation, AI-enabled prediction and scientific platform development. His record spans chromatin regulation, protein structure, TRIM-family biology, biomolecular condensates, nucleic-acid systems, scientific communication and evidence-aware research infrastructure.
Mechanistic cell biologyMesoscale organisationQuantitative bioimagingHuman geneticsPredictive biology & AIMolecular bioengineeringScientific communicationProgramme stewardship
Research practice
Questions connected across biological scales.
Quantitative cellular organisation
Live-cell fluorescence microscopy, high-content imaging, FRAP, localisation, morphology and mesoscale phenotype analysis.
Predictive biology and AI
Structured biological data, feature engineering, leakage-aware evaluation, multimodal integration and calibrated evidence reporting.
Scientific platforms and translation
Reusable schemas, provenance, limitations and modular research systems connect observations with testable hypotheses.
Selected scientific and programme impact
Evidence across mechanism, organisation and prediction.
Three examples connect biological questions to experimental systems, quantitative analysis and reusable evidence.
PICNIC — Predictive Biology
- Problem
- Predict which proteins form biomolecular condensates across organisms and structural classes.
- Contribution
- As co-first author and experimental co-developer, I connected biological feature design, machine-learning prediction and prospective cellular validation.
- Impact
- Nature Communications publication and an accessible prediction platform.
TRIMCode — Programme Building
- Problem
- Explain how modular TRIM-family architecture produces cellular organisation and disease-associated states.
- Contribution
- As founder and scientific programme lead, I connected protein architecture, quantitative imaging, human genetics, cellular organisation and predictive research.
- Impact
- A family-scale biological atlas, disease mechanism and reusable research framework.
ALC1 — Mechanistic & Translational Biology
- Problem
- Determine how PAR signalling activates the oncogenic chromatin remodeller ALC1.
- Contribution
- As single first author, I established the mechanism connecting PAR signalling, autoinhibition and chromatin remodelling.
- Impact
- A Molecular Cell mechanism with relevance to subsequent ALC1-focused therapeutic development.
Research programme
TRIMCodeTRIM-family mesoscale biology.
TRIMCode examines how molecular sequence and modular protein architecture shape cellular organisation through quantitative experiments, predictive models and reusable research tools.
Guiding questions
- 01
When does cooperativity explain mesoscale organisation?
- 02
When does condensation add explanatory power?
Organisation, function and disease
Resolve how changes in TRIM proteins reshape mesoscale organisation, molecular activity and cellular phenotype.
Quantitative organising principles
Connect protein architecture, interaction patterns, condensate dynamics and spatial behaviour across cellular contexts.
Predictive research tools
Combine structured experimental records, interpretable modelling and iterative validation into an evidence-aware framework.
Media & community
What is a mesoscale?
A short, original explainer on the organisational level between single molecules and whole cells that TRIMCode is built to study.
Where does it come from?
A short, original explainer tracing mesoscale organisation back to the molecular systems it emerges from.
Career
Academic and professional history.
Founder and Lead — TRIMCode Research Programme
TRIM-family architecture and cellular organisation
Mesoscale Cell Biology framework
Bio × AI
Germany
Data Science & AI · Full-time Training
neue fische
Bio × AI focus: Python & SQL · Machine Learning Engineering · Deep Learning · Time Series · LLMs & AI Agents.
Delivery: Model Deployment · Agile Project Coordination · Stakeholder Communication.
Germany
Senior Postdoctoral Scientist / Experimental Platform Lead
Max Planck Institute of Molecular Cell Biology and Genetics
Professor · Tony Hyman · Director General, EMBL
Interdisciplinary programme building across molecular and cell biology, human genetics, quantitative imaging, computational analysis and translational disease research · TRIMCode · TRIM8 syndrome · PICNIC.
Dresden, Germany
Postdoctoral Scientist, Synthetic Biology and Nucleic Acid Systems
Technical University of Munich
Professor · Fritz Simmel · Chair of Physics of Synthetic Biological Systems, TUM
Intracellular information processing and recording systems.
Munich, Germany
Doctoral Researcher, Molecular Cell Biology
Ludwig-Maximilians-Universität München
Professor · Andreas Ladurner · Physiological Chemistry, BMC, LMU
Founder · Eisbach Bio GmbH
Interdisciplinary doctoral research across molecular biology, structural biology, chromatin mechanisms and biophysics · ALC1 modular allostery and PARP-dependent activation · CRY1 structural biology · H3–NASP chromatin biology.
Munich, Germany
Junior Research Fellow, Chromatin and Stem Cell Biology
Jawaharlal Nehru Centre for Advanced Scientific Research
Professor · M. R. S. Rao · Former President, JNCASR
Chromatin dynamics, epigenetic regulation and stem cell biology.
Bengaluru, India
Master's Thesis Researcher
National Centre for Cell Science
Professor · Yogesh Shouche · Director, SKAN Research Trust
Founding Lead · National Centre for Microbial Resource · Former NCCS PI
Professor · W. N. Gade · Head, Department of Biotechnology · Former Vice-Chancellor, University of Pune
Microbial synthesis of silver nanoparticles and operon mapping in Morganella sp.
Pune, India
Education and development
Formal education and international scientific training.
Data Science & Artificial Intelligence
IHK-certified professional programme · neue fische / SPICED Academy · Germany
PhD (Dr. rer. nat.) · Molecular Biology
Ludwig Maximilian University Munich · Germany
M.Sc. Biotechnology · First Class
University of Pune / National Centre for Cell Science · India
B.Sc. (Hons.) Biochemistry · First Class
Aligarh Muslim University · India
Selected training and scientific exchange.
Epigenetic Regulation and Genome Control
16–18 December 2009 · CCMB · Hyderabad, India
Chromatin and Systems Biology
30 August–5 September 2013 · Spetses, Greece
International Synthetic and Systems Biology Summer School
5–9 July 2015 · Taormina, Sicily, Italy
Quantitative Principles in Biology
2–4 November 2017 · EMBL Heidelberg, Germany
Startup Weekend Munich
28–30 April 2017 · Munich, Germany
Grant Writing
14–15 November 2017 · LMU Munich, Germany
Physical Biology of the Cell
3–7 October 2022 · MPI-CBG, Dresden · Rob Phillips, Caltech
Quantitative Bio-Image Analysis with Python
17–21 October 2022 · MPI-CBG, Dresden · Robert Haase
Antibody Engineering & Display Technologies
14–28 October 2024 · Cold Spring Harbor Laboratory, New York, USA
From Single Cells to Entire Organisms
10–14 February 2025 · Multiscale Imaging Workshop · Tübingen, Germany
Protein Quality Control, Ageing and Disease
18–23 May 2025 · EMBO Workshop · TRIM-family condensatopathy presentation
SEB Annual Conference Antwerp
8–11 July 2025 · Antwerp, Belgium · TRIM proteins and human condensatopathies
Publications and research outputs
A connected research record.
16 outputs
The record spans chromatin regulation, structural biology, biomolecular condensates, human genetics, molecular bioengineering, scientific databases and predictive biology.
Single first author
ALC1 autoinhibition
Contribution
A poly(ADP-ribose) trigger releases ALC1 autoinhibition
Mechanistic discovery connecting ADP-ribose signalling, chromatin remodelling, protein allostery and oncology.
Molecular Cell · 2017Co-first author
PICNIC Predictive Biology
Contribution
PICNIC Accurately Predicts Condensate-Forming Proteins Regardless of Their Structural Disorder across Organisms
Co-developed and experimentally anchored a predictive-biology framework with proteome-scale application and in-cell validation.
Nature Communications · 2024Co-first author
TRIM Mesoscale Landscaping
Contribution
Mesoscale Landscaping of the TRIM Protein Family Reveals a Novel Human Condensatopathy
Atlas-scale imaging and human-genetics research linking sequence variation, cellular phenotypes and condensatopathy.
bioRxiv · 2025Collaborative co-author
Cryptochrome Structure
Contribution
Structures of Drosophila Cryptochrome and Mouse Cryptochrome1 Provide Insight into Circadian Function
Structural and mechanistic work connecting protein architecture, interactions and signalling function.
Cell · 2013Collaborative co-author
sNASP–Histone Recognition
Contribution
The Histone Chaperone sNASP Binds a Conserved Peptide Motif within the Globular Core of Histone H3 through Its TPR Repeats
Protein-interaction and chromatin-assembly research linking sequence motifs to molecular recognition.
Nucleic Acids Research · 2016Collaborative co-author
Nucleic-Acid Strand Displacement
Contribution
Principles and Applications of Nucleic Acid Strand Displacement Reactions
Connects nucleic-acid chemistry, molecular computation, sensing and synthetic biology.
Chemical Reviews · 2019Collaborative co-author
PAR Signalling in DNA Repair
Contribution
Poly-ADP-Ribosylation Signalling during DNA Damage Repair
Integrates ADP-ribosylation, chromatin dynamics and DNA-damage-response mechanisms.
Frontiers in Bioscience · 2015Collaborative co-author
ALC1 Chromatin Relaxation
Contribution
The Poly(ADP-Ribose)-Dependent Chromatin Remodeler Alc1 Induces Local Chromatin Relaxation upon DNA Damage
Live-cell imaging and mechanistic chromatin biology linking molecular signalling to cellular structural change.
Molecular Biology of the Cell · 2016Collaborative co-author
PICNIC Web Server
Contribution
PICNIC Web Server for Predicting Proteins Involved in Biomolecular Condensates
Transforms a machine-learning method into an accessible hypothesis-testing interface.
Bioinformatics · 2026 issue · online 2025Collaborative co-author
CD-CODE 2.0 Knowledgebase
Contribution
CD-CODE 2.0: An Enhanced Condensate Knowledgebase Integrating Pathobiology, Condensate-Modulating Drugs, and Host–Pathogen Interactions
Contributes to connected scientific-data infrastructure for condensate biology and translational hypothesis generation.
Nucleic Acids Research · 2026 issue · online 2025First author
Nucleosome Plasticity
Contribution
Remodelers Tap into Nucleosome Plasticity
Commissioned-style scientific interpretation connecting structural mechanism to broader chromatin biology.
Nature Structural & Molecular Biology · 2017First author
ACF & Nucleosome Spacing
Contribution
ACF Takes the Driver's Seat
Concise mechanistic commentary on nucleosome organisation and remodeler regulation.
Molecular Cell · 2014First & corresponding author
Phase Separation & Gene Transcription
Contribution
Post-Translational Modification, Phase Separation, and Robust Gene Transcription
Scientific synthesis across gene regulation, condensate biology and reversible molecular control.
Trends in Genetics · 2019First & corresponding author
Epigenetic Editing
Contribution
Epigenetic Editing: Repurposing for Rescue
Connects genome engineering, chromatin regulation, therapeutic possibility and explicit limitations.
Trends in Biochemical Sciences · 2018First & corresponding author
DNA Nanorobot & Cancer
Contribution
A DNA Nanorobot Uprises against Cancer
Connects DNA nanotechnology, molecular sensing, oncology and responsible therapeutic engineering.
Trends in Molecular Medicine · 2018First & corresponding author
TET2, Cancer & Diabetes
Contribution
Glucose-Regulated TET2 Activity Links Cancer to Diabetes
Cross-domain commentary linking cancer metabolism, epigenetics and protein regulation.
Trends in Cancer · 2019Research translation
Mechanism with a translational trajectory.
Hari Raj Singh's 2017 single-first-author study established how PAR releases ALC1 auto-inhibition, connecting protein allostery, chromatin remodelling and oncology. The published mechanism forms part of the scientific lineage of later ALC1-focused therapeutic development.
Open the Molecular Cell study ↗Methods and capabilities
Experimental depth with quantitative reach.
Experimental systems
Molecular cloning, construct and variant design, targeted mutagenesis, mammalian cell culture, protein and nucleic-acid characterisation, biochemical and structure–function analysis.
Quantitative cell biology
Live-cell fluorescence microscopy, high-content imaging, FRAP, condensatography, image feature extraction, localisation and morphology phenotyping.
Data and AI
Python, structured data analysis, statistics, feature engineering, model evaluation and interpretation, multimodal integration, traceable metadata and analysis-ready datasets.
Scientific delivery
Experimental design, controls, reproducibility, protocols, evidence evaluation, scientific writing, interdisciplinary coordination and mentoring.
Scientific leadership & programme building
Multidisciplinary work delivered as one scientific system.
I build research environments in which experimental biology, quantitative analysis and computational methods work as one scientific system.
My leadership spans programme design, experimental-platform development, interdisciplinary coordination, mentoring, scientific communication and evidence-based decision-making.
Questions, milestones and direction
Define research questions, decision points, milestones, dependencies and long-term scientific direction while keeping the biological problem central.
Evidence: TRIMCode programme architecture and reusable research frameworkCross-functional programme execution
Coordinate molecular biology, live-cell and high-content imaging, human genetics, quantitative analysis and external expertise; track progress and review technical risks.
Evidence: MPI-CBG experimental-platform delivery across TRIM, TRIM8 and PICNIC workReproducible scientific practice
Mentor researchers, troubleshoot complex experimental projects and strengthen protocols, documentation, quantitative interpretation and reproducibility.
Evidence: research-led mentoring and platform troubleshooting across academic levelsEvidence shared across boundaries
Connect collaborators, disease communities, technology platforms and scientific outputs through clear stakeholder communication and evidence-aware decisions.
Evidence: human-genetics, cellular-phenotyping and predictive-biology collaborationsExperimental-platform and quantitative-imaging leadership
Imaging-intensive workflows, shared experimental systems, technical-risk review and continuous scientific readiness.
TRIMCode and MPI-CBG programme evidence
Programme building and cross-functional delivery shown through linked publications, methods, platforms and research outputs.
Contact
Ideas, collaborations and conversations.
I welcome conversations across experimental biology, quantitative imaging, scientific programmes, publishing and communication, research platforms and Bio × AI—where careful evidence and ambitious questions can lead to useful work.
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