Graduation Level Topics

·  Expression Analysis of a Stress-Responsive Gene by qPCR (Data/Design Project)
Aim: evaluate expression patterns of a candidate stress gene across tissues or treatments using qPCR principles. Approach: design primer-validation strategy conceptually, select reference genes and outline sample grouping. Validation: demonstrate fold-change calculations, melt-curve checks and replicate consistency. Relevance: trains students in gene-expression experimental design and interpretation for crop/medical contexts in India. Deliverable: full methods abstract and data-analysis pipeline.

·  In-silico Promoter Analysis and Cis-Element Mapping for a Plant Gene
Aim: identify regulatory motifs in a promoter region relevant to abiotic stress tolerance. Approach: use public genome databases and motif-finding tools to annotate conserved elements and predict transcription-factor binding. Validation: propose reporter-assay follow-ups conceptually and comparative promoter conservation across cultivars. Relevance: informs promoter choice for expression-control studies in Indian crop research. Output: annotated promoter map and experiment plan.

·  Molecular Identification of Unknown Bacterial Isolates by 16S rRNA Sequencing (Concept + Reporting)
Aim: characterize culturable isolates from soil/water using 16S sequence-based taxonomy. Approach: outline Sanger/NGS sequence quality checks, alignment and phylogenetic placement. Validation: species-level vs genus-level assignment criteria and reporting of percent identity thresholds. Relevance: supports environmental microbe studies and simple diagnostics in India. Deliverable: identification report template.

·  Design and Interpretation of an RNA Interference (RNAi) Knockdown Study (Proposal Level)
Aim: draft a conceptual RNAi project to silence a target gene and predict phenotypic outcomes in a model organism. Approach: justify target selection, propose controls and outline phenotypic assays and off-target assessment conceptually. Validation: propose qPCR/phenotype concordance checks and rescue experiments as interpretation safeguards. Relevance: prepares students for functional genetics studies in Indian labs under supervision. Output: non-actionable experimental plan and risk assessment.

·  Comparative Analysis of DNA Extraction Methods for Challenging Samples
Aim: review extraction strategies for degraded or inhibitor-rich samples (hair, soil) and propose decision criteria. Approach: compile method pros/cons, QC checkpoints and DNA-quantity/quality metrics to prioritize methods. Validation: simulate downstream PCR success rates conceptually and propose a kit-selection matrix. Relevance: practical guidance for diagnostic and field-sampling work in India. Deliverable: selection checklist and validation plan.

·  Designing a Primer-Pair Validation Pipeline for Student PCR Projects
Aim: create a robust plan for primer design, in-silico specificity checks and validation without bench protocols. Approach: outline primer properties, BLAST-checks and expected amplicon verification steps. Validation: simulation of primer performance on reference sequences and criteria for acceptance. Relevance: essential skills for molecular projects across Indian universities. Output: primer-validation SOP (non-procedural).

·  Comparative Mitochondrial vs Nuclear Markers for Population Genetics (Conceptual Study)
Aim: evaluate marker choice for studying genetic diversity in a local species (fish/plant/insect). Approach: compare inheritance, mutation rates and resolution of mtDNA and nuclear markers; outline sampling schemes. Validation: propose statistical metrics (haplotype diversity, Fst) and power analysis. Relevance: informs conservation genetics and resource management in India. Deliverable: marker-selection guidance and analysis plan.

·  Designing a Molecular Diagnostic Workflow for a Hypothetical Local Pathogen (Non-Operational)
Aim: propose an evidence-based diagnostic algorithm integrating molecular and serologic tests for a target pathogen. Approach: outline test selection criteria, sample priorities and result interpretation rules. Validation: include decision thresholds, confirmatory testing cascades and reporting language for clinicians. Relevance: prepares students for translational diagnostic thinking relevant to Indian healthcare. Output: diagnostic algorithm abstract.

·  Molecular Cloning Project — Construct Design and In-silico Verification
Aim: design a cloning strategy on paper: vector choice, insert design and expression tags, without hands-on steps. Approach: annotate map features, restriction or seamless cloning rationale and in-silico verification checks. Validation: propose sequencing checks and functional readouts conceptually. Relevance: builds design and troubleshooting skills needed in Indian molecular labs. Deliverable: annotated construct file and QC plan.

·  SNP Discovery and Validation Using Publicly Available Sequence Data (Bioinformatics Project)
Aim: mine public datasets to identify candidate SNPs in a gene of interest and design validation experiments. Approach: variant-calling workflow, filtering criteria and annotation for consequence prediction. Validation: propose genotyping strategies and population-frequency assessments tied to Indian germplasm or cohorts. Relevance: inexpensive route to genetic-marker discovery for local research. Output: candidate-SNP list and validation roadmap.

·  Molecular Basis of Antimicrobial Resistance: Gene Detection and Reporting Strategy
Aim: create a lab-agnostic framework to detect and interpret common resistance genes in clinical isolates. Approach: outline target panels, interpretation of gene presence vs phenotype and reporting caveats. Validation: concordance checks with phenotypic data and recommended QC steps. Relevance: addresses AMR surveillance and stewardship in Indian hospitals. Deliverable: reporting template and interpretation guide.

·  Designing a Comparative Transcriptomics Study from Public RNA-seq Datasets
Aim: formulate a comparative transcriptome analysis to identify differential pathways under two conditions (stress vs control). Approach: define sample selection, normalization, DEG calling and pathway-enrichment steps conceptually. Validation: propose validation via qPCR and biological replication considerations. Relevance: equips students to leverage open data for hypothesis generation in India. Output: analysis pipeline and interpretation plan.

·  Molecular Markers for Plant Variety Identification — Selection and Utility
Aim: propose sets of microsatellites/SNPs to discriminate cultivars of a regional crop. Approach: rationale for marker types, required resolution and sampling strategy. Validation: simulation of discriminatory power and reporting genotype-matching thresholds. Relevance: supports seed-certification and IP considerations in Indian agriculture. Deliverable: marker panel proposal and validation metrics.

·  Designing a Non-Destructive DNA Sampling Strategy for Wildlife Conservation Studies
Aim: outline ethical sampling (scat, hair) and molecular approaches to maximize DNA recovery while minimizing disturbance. Approach: recommend sampling densities, preservation considerations and marker choices. Validation: propose success-rate metrics (amplification, genotyping completeness) and contamination controls. Relevance: practical for Indian conservation research with regulatory sensitivity. Output: field-sampling SOP concept and QC plan.

·  Molecular Detection Strategies for Food Allergen Traces in Processed Foods (Conceptual)
Aim: design a DNA-based assay plan to complement protein-based allergen detection in complex matrices. Approach: choose genetic targets, discuss sensitivity/specificity trade-offs and validation panels. Validation: propose orthogonal confirmation with protein assays and spike–recovery studies. Relevance: supports food safety surveillance and consumer protection in India. Deliverable: assay selection and validation plan.

·  Introductory Epigenetics: Bisulfite Data Interpretation and Methylation Mapping (Data Project)
Aim: interpret public bisulfite sequencing data to map methylation changes associated with a condition. Approach: discuss mapping, methylation calling, and DMR identification conceptually. Validation: propose qPCR-bisulfite confirmation strategies and biological interpretation heuristics. Relevance: introduces epigenomic thinking for disease or stress studies in India. Output: analysis outline and interpretation checklist.

·  Designing a Molecular Forensics Mini-Project: STR Panel Selection and Reporting
Aim: select an STR marker panel for identity testing in a mock forensic scenario with reporting considerations. Approach: justify marker choice, explain match-statistics concepts and chain-of-custody implications (conceptual). Validation: simulate match probabilities and conservative reporting language for courts. Relevance: training for forensic lab collaborations in India. Deliverable: panel rationale and reporting template.

·  In-silico Protein Structure Prediction and Domain Mapping for a Hypothetical Protein
Aim: predict domain architecture and potential functional sites from sequence data using public tools. Approach: integrate secondary/tertiary prediction, conserved motif searches and functional inference. Validation: propose mutational or binding assays conceptually to test hypotheses. Relevance: bridges sequence data to mechanistic hypotheses for Indian research projects. Output: annotated structure-report and experimental follow-ups.

·  Designing an Educational Module on Molecular Diagnostic Quality Control for Labs
Aim: produce a teaching module focusing on controls, contamination avoidance and interpretation of molecular test QC. Approach: include decision trees for control failure scenarios and recommended corrective actions. Validation: assessment templates and mock-run analyses for student evaluation. Relevance: enhances lab reliability across Indian teaching hospitals. Deliverable: module outline and assessment rubric.

·  Molecular Epidemiology: Phylogeographic Analysis Plan Using Public Sequences
Aim: draft a phylogeographic study to trace spread patterns of a pathogen using sequence data. Approach: sequence selection, alignment, tree inference and temporal/ geographic mapping conceptually. Validation: sensitivity checks to sampling bias and recommendations for robust interpretation. Relevance: useful for outbreak retrospective studies in India. Output: analytical plan and caveat list.

·  Molecular Characterization of Plant Viral Isolates Using Partial Genome Sequencing
Aim: propose a sequencing-based characterization approach to classify and monitor plant virus variants. Approach: target region selection, sequence QC and variant annotation strategies. Validation: phylogenetic placement and implication assessment for resistant cultivars in India. Relevance: informs extension services and crop management. Deliverable: surveillance plan and reporting standards.

·  Designing a CRISPR Off-Target Bioinformatics Assessment for Guide Selection
Aim: prepare a computational workflow to evaluate off-target potential of candidate guides in a reference genome. Approach: ranking metrics, mismatch tolerance considerations and annotation of potential functional off-targets. Validation: recommend experimental validation cascades and conservative interpretation for project proposals. Relevance: responsible gene-editing planning in Indian labs. Output: guide-selection pipeline spec.

·  Comparative Assessment of Mitochondrial DNA vs Nuclear Markers for Forensic/Archaeological Samples
Aim: evaluate marker suitability for degraded samples from archaeological contexts. Approach: discuss copy-number advantages, contamination risks and interpretational limits. Validation: propose decision-tree for marker application and reporting constraints. Relevance: aids forensic and heritage projects in India where samples may be degraded. Deliverable: marker-use guidance and evidence-reporting notes.

·  Sequence-Based Detection of Transgenes in Crops: Designing a Surveillance Strategy
Aim: outline a molecular surveillance plan for detecting specific transgene insertions in seed lots. Approach: select unique junction/insert targets, assay sensitivity considerations and sampling logistics. Validation: propose false-positive/negative mitigation and confirmatory workflows. Relevance: seed quality control and regulatory compliance in India. Output: surveillance SOP concept.

·  Design of a Molecular Lab Notebook Template Emphasizing Reproducibility
Aim: create a template that captures essential metadata for molecular experiments enabling reproducibility. Approach: required fields, versioning, sequence/primer inventories and data links concept. Validation: pilot with student projects and iterate based on usability. Relevance: promotes good scientific practice in Indian labs. Deliverable: template and instruction guide.

·  In-silico Identification of microRNA Targets for a Candidate microRNA
Aim: predict and prioritize mRNA targets of a miRNA implicated in stress or disease. Approach: combine target-prediction algorithms, conservation filters and pathway enrichment for candidate selection. Validation: design conceptual reporter assays and expression correlation studies. Relevance: hypothesis generation for functional molecular projects in India. Output: ranked target list and validation roadmap.

·  Designing a Sample Randomization and Blocking Scheme for Molecular Experiments
Aim: construct robust experimental designs to control batch effects and confounders in molecular assays. Approach: randomization, blocking variables, and replication planning conceptually. Validation: propose statistical models to adjust for batch effects and QC metrics. Relevance: critical for reliable molecular studies in Indian labs. Deliverable: experimental design template and analysis notes.

·  Conceptual Project: Molecular Barcoding to Track Multiple Clones in a Competition Assay
Aim: design a barcoding scheme to track relative abundances of strains in pooled experiments. Approach: barcode design principles, sequencing-depth planning and error-correction concepts. Validation: simulation of barcode collision rates and interpretation rules. Relevance: modern experimental designs scalable for Indian research groups. Output: barcoding plan and QC thresholds.

·  Design of a Non-Invasive Molecular Biomarker Study Using Saliva or Urine
Aim: plan a biomarker discovery/validation pipeline using non-invasive matrices suited to community studies. Approach: sample handling, target selection, normalization and confounder control conceptualization. Validation: proposed pilot cohorts and orthogonal confirmation strategies. Relevance: enhances field-friendly molecular studies in India. Deliverable: study protocol abstract.

·  Comparative Guide: When to Use qPCR vs Digital PCR for Low-Abundance Targets
Aim: create a decision framework guiding assay choice based on sensitivity, quantitation needs and resources. Approach: discuss partitioning, dynamic range, cost trade-offs and reporting formats. Validation: propose pilot comparisons and acceptance thresholds for labs. Relevance: optimal assay selection for Indian diagnostic or research labs. Output: decision tool and pilot plan.

·  Designing a Molecular Assay Validation Plan for Academic Labs Pursuing Clinical Studies
Aim: draft validation endpoints (sensitivity, specificity, LOD) and acceptable evidence for translational studies. Approach: define sample panels, inter-run reproducibility criteria and documentation standards. Validation: propose phased validation with escalating complexity. Relevance: bridges academic work to translational applications in India. Deliverable: validation framework and checklist.

·  In-silico Comparative Genomics to Identify Candidate Drug Targets in a Pathogen
Aim: use comparative approaches to find pathogen-specific, conserved proteins suitable as therapeutic targets. Approach: subtractive genomics, essentiality inference and host-homology avoidance filters. Validation: propose experimental target engagement strategies and resistance-risk assessment. Relevance: early-stage drug-discovery input relevant to regional pathogens in India. Output: prioritized target list and follow-up plan.

·  Design of a Molecular Surveillance Dashboard Using Sequencing Metadata
Aim: conceptualize a dashboard that integrates sequence QC metrics, lineage calls and epidemiological annotations. Approach: metadata standards, visualization priorities and alert thresholds conceptually defined. Validation: pilot dataset to test signal detection and reporting pipelines. Relevance: actionable surveillance tools for Indian public-health labs. Deliverable: dashboard spec and data ingestion plan.

·  Exploratory Project: Use of DNA Barcoding for Market Fish Species Authentication
Aim: design a protocol for species ID of seafood samples to detect mislabeling using mitochondrial barcodes. Approach: marker selection, reference database matching and threshold criteria. Validation: blind-testing plan and reporting language for consumer protection. Relevance: supports seafood traceability and market regulation in India. Output: plan and interpretation framework.

·  Designing an Educational Module on Sequence Data Management and FAIR Principles
Aim: create curriculum content teaching students about data formats, metadata and FAIR (Findable, Accessible, Interoperable, Reusable) standards. Approach: practical examples, data deposition workflows and ethical considerations. Validation: assessment rubrics and sample student assignments. Relevance: builds data stewardship skills for Indian researchers. Deliverable: module and evaluation rubric.

·  Conceptual Project: Allele-Specific Expression Analysis for Imprinted Genes
Aim: design a study to detect allele-biased transcription using RNA-seq information and genotypes. Approach: read-mapping strategies, allelic count methods and statistical testing concepts. Validation: propose orthogonal validation (pyrosequencing) and sample size considerations. Relevance: introduces students to regulatory genetics questions in India. Output: analysis plan and validation steps.

·  Designing a Molecular Workflow to Monitor GMO Presence in Seed Lots (Non-Operational)
Aim: outline an evidence-based approach to screen and confirm genetically modified insertions in seed consignments. Approach: sampling strategy, primary screening method and confirmatory sequencing considerations. Validation: define limits of detection and false-positive management. Relevance: seed certification and regulatory compliance in India. Deliverable: surveillance SOP and interpretation template.

·  Comparative Analysis Plan for CRISPR-Cas Variants and Their Applications
Aim: review Cas variants (nickases, base editors, prime editors) and map applications and limitations for graduate projects. Approach: summarize editing scope, efficiency expectations and off-target concerns conceptually. Validation: propose in-silico off-target assessment and control design for project proposals. Relevance: informed choice of editing tools for Indian labs. Output: comparative brief and recommendation matrix.

·  Designing a Small-Scale Population Genomics Study Using Reduced-Representation Sequencing
Aim: plan RAD/GBS-style study for population structure in a regional organism with budget constraints. Approach: sampling numbers, marker density trade-offs and downstream analysis pipelines conceptually outlined. Validation: power calculations and pilot-sample sequencing plan. Relevance: accessible population genomics for Indian biodiversity studies. Deliverable: study plan and expected outputs.

·  Molecular Quality Assurance: Designing Controls for RNA Integrity in Transcriptomics
Aim: propose practical criteria and control strategies to assess RNA integrity and its impact on downstream data. Approach: RNA-quality metrics, sample exclusion criteria and normalization approaches conceptually defined. Validation: pilot analyses illustrating bias mitigation and reporting standards. Relevance: improves robustness of Indian transcriptomics projects. Output: QA checklist and reporting templates.

·  In-silico Design of Fusion-Protein Constructs for Functional Studies (Non-Operational)
Aim: design conceptual fusion constructs (reporter, localization tags) with considerations for linker choice and frame maintenance. Approach: annotate functional domains, codon optimization rationale and predicted expression outcomes. Validation: sequencing-confirmation and planned assays for function/localization. Relevance: common requirement in cell-biology projects in India. Deliverable: construct designs and validation plan.

·  Designing a Molecular Project to Track Horizontal Gene Transfer in Environmental Samples
Aim: propose an approach combining sequencing and network analyses to detect HGT events among bacteria in a polluted site. Approach: marker selection, assembly vs read-based strategies and criteria for HGT inference. Validation: controls for assembly artifacts and corroborating functional evidence. Relevance: environmental biosafety and AMR studies in India. Output: study design and caveats.

·  Conceptual Validation Plan for a New Molecular Assay Using External Reference Materials
Aim: outline how to select and use reference materials and proficiency panels to validate a new assay before routine use. Approach: sample panel composition, acceptance criteria and inter-lab comparison plans. Validation: staged verification with blinded panels and QC metrics. Relevance: aligns student projects with quality expectations for translational studies in India. Deliverable: validation checklist.

·  Design a Study to Evaluate RNA Stability Across Common Field Preservation Methods
Aim: compare conceptual preservation methods (dry, preservative buffers) for field-collected RNA samples and their impact on downstream assays. Approach: propose sampling scheme, expected degradation metrics and normalization strategies. Validation: pilot comparisons and recommended SOPs for fieldwork. Relevance: practical for molecular ecology and epidemiology studies in India. Output: preservation guidance and pilot plan.

·  Molecular-Assay Reporting Template for Clinically Relevant Tests (Educational)
Aim: produce a standardized result-report template emphasizing clear interpretation, limitations and QC flags. Approach: define essential sections, caveats and recommended clinician communication phrases. Validation: test template with mock cases and get clinician feedback. Relevance: improves translational clarity in Indian clinical labs. Deliverable: reporting template and usage guide.

·  Designing a Cross-Platform Sequencing Comparison Study (Short-Read vs Long-Read)
Aim: plan a comparative analysis showing strengths and weaknesses of short- and long-read technologies for a specific question (e.g., structural variants). Approach: sample selection, coverage targets and analysis pipeline conceptualization. Validation: benchmark metrics (completeness, accuracy) and hybrid-assembly recommendations. Relevance: informs technology choices for Indian genomics projects. Output: comparison plan.

·  Project Plan: Using Public Variant Databases to Annotate Candidate Mutations
Aim: design a pipeline for variant annotation combining population frequency, predicted consequence and literature evidence. Approach: prioritize variants for functional follow-up and curate evidence levels. Validation: sample annotation exercise and reporting rules. Relevance: supports student projects in human genetics and pathogen genomics in India. Deliverable: annotation pipeline and decision-tree.

·  Designing a Safe, Ethical Molecular Field Study Protocol with Community Engagement
Aim: prepare a project plan that includes consent, benefit-sharing and sample-use transparency for community-based molecular studies. Approach: consent templates, data-use statements and return-of-results policy (conceptual). Validation: stakeholder consultation and institutional ethics alignment. Relevance: crucial for ethical research practices in India. Output: protocol skeleton and engagement plan.

·  Comparative Methodology Review: Shotgun Metagenomics vs Amplicon Sequencing for Microbiome Studies
Aim: provide a balanced guide to choosing between approaches based on research questions, budgets and resolution needs. Approach: discuss taxonomic resolution, functional inference and contamination risks conceptually. Validation: decision matrix and sample-size guidance for student projects. Relevance: optimizes microbiome studies in Indian contexts. Deliverable: method-choice tool and sample plan.

·  Designing a Molecular Biology Capstone: From Hypothesis to Data-Driven Conclusions
Aim: outline a capstone project template that walks students through hypothesis formulation, experimental design (non-actionable), data analysis and interpretation. Approach: include milestones, deliverables (protocol abstract, data report, poster) and assessment rubrics. Validation: pilot with a cohort and iterate on clarity and scope. Relevance: standardizes final-year projects across Indian programs. Output: capstone blueprint and assessment rubric.

​​

Post-Graduation Level Topics

·  Single-Cell RNA-seq to Resolve Cellular Heterogeneity in a Disease Tissue
Aim: map cell populations and transcriptional states in diseased vs normal tissue using scRNA-seq. Approach: experimental design considerations, cell-capture methods selection rationale, and data-integration plans. Validation: clustering robustness, marker validation via orthogonal assays and trajectory analysis. Relevance: identifies cellular targets for therapeutics and biomarkers in Indian clinical research. Deliverable: full study abstract with analysis pipelines.

·  CRISPR Prime Editing for Precise Correction of a Point Mutation — Feasibility Study
Aim: evaluate prime-editing strategies to correct a pathogenic SNV in a model system. Approach: guide/pegRNA design rationale, prediction of byproducts and off-target assessment strategy. Validation: sequencing-based edit quantification, functional rescue assays and long-term stability checks. Relevance: preclinical gene-therapy research applicable to genetic disorders in India. Output: non-operational development plan and risk assessment.

·  Genome-Wide Association Study (GWAS) for a Complex Trait in a Regional Cohort
Aim: identify loci associated with a quantitative trait using a well-phenotyped cohort. Approach: sample-size calculation, genotyping array vs sequencing trade-offs and population-structure control. Validation: replication in independent cohorts, fine-mapping and functional follow-up prioritization. Relevance: uncovers genetic determinants relevant to Indian populations. Deliverable: GWAS protocol and downstream validation plan.

·  Long-Read Sequencing to Resolve Complex Structural Variants in Clinical Genomes
Aim: employ long-read platforms conceptually to detect SVs missed by short reads in diagnostic cases. Approach: library-choice rationale, assembly vs mapping strategies and annotation pipelines. Validation: orthogonal confirmation (PCR, optical mapping) proposals and clinical interpretation guidelines. Relevance: improves diagnostic yield in genetic disease studies in India. Output: sequencing and analysis plan.

·  Integrative Multi-Omics to Discover Mechanisms of Drug Resistance in Cancer
Aim: combine genomics, transcriptomics and proteomics to uncover pathways driving therapeutic resistance. Approach: cohort design, sampling timepoints (pre/post therapy) and integrative analysis strategies. Validation: nominate actionable targets and propose in-vitro models for mechanistic validation. Relevance: informs treatment strategies in Indian oncology. Deliverable: integrated omics study plan.

·  High-Throughput CRISPR Screening to Identify Host Factors Required for Pathogen Entry
Aim: perform genome-wide CRISPR knockout/activation screens to discover host dependency factors. Approach: library selection, infection assay design and hit-calling strategies conceptually. Validation: orthogonal genetic/chemical validation and pathway analysis. Relevance: identifies therapeutic host-targets relevant to regional pathogens in India. Output: screening and validation roadmap.

·  Epigenome Editing to Modulate Gene Expression in Disease Models
Aim: use dCas-fused epigenetic effectors to activate or repress disease-relevant loci and study phenotypic consequences. Approach: target selection, on-target effect monitoring and potential heritability assessment. Validation: multi-layered readouts (expression, chromatin marks, phenotype) and off-target surveillance. Relevance: experimental therapeutics research with translational potential for India. Deliverable: experimental design and safety considerations.

·  Population Genomics of a Threatened Species to Guide Conservation Genomics
Aim: characterize population connectivity, inbreeding and adaptive variation using whole-genome SNP data. Approach: sampling across geographic range, demographic modelling and landscape-genomic association analysis. Validation: propose management units and assisted-gene-flow strategies based on genomic evidence. Relevance: supports biodiversity conservation policy in India. Output: genomics-driven conservation plan.

·  Designing an NGS-Based Clinical Diagnostic Pipeline for Rare Disease Gene Panels
Aim: create an end-to-end plan for panel design, data processing, variant interpretation and reporting for rare Mendelian diseases. Approach: capture design rationale, QC thresholds, annotation and ACMG-like classification frameworks. Validation: clinical utility metrics, validation cohorts and accreditation considerations. Relevance: builds capacity for genetic diagnostics in Indian tertiary centers. Deliverable: pipeline SOP and validation strategy.

·  RNA Therapeutics: Aptamer Discovery and In-Vitro Validation Pipeline
Aim: discover nucleic-acid aptamers against a protein target with therapeutic potential and plan proof-of-concept assays. Approach: SELEX-design rationale, candidate ranking and binding/functional assay proposal. Validation: affinity/ specificity metrics, stability profiling and cell-based validation plans. Relevance: novel therapeutic modalities for Indian disease targets. Output: discovery and validation plan.

·  Spatial Multi-Omics to Map Tumor Microenvironment Heterogeneity
Aim: integrate spatial transcriptomics and proteomics to define spatial niches and immune interactions in tumors. Approach: sampling strategy, panel design and computational integration frameworks. Validation: correlate spatial features with clinical outcomes and validate markers in independent cohorts. Relevance: supports biomarker discovery and targeted therapy approaches in Indian oncology. Deliverable: experimental/analysis protocol.

·  Designing Gene-Drive Containment and Ecological Risk Assessment Frameworks
Aim: develop responsible research frameworks for gene-drive experiments including confinement, modeling and monitoring plans. Approach: population-dynamics modeling, staged testing and stakeholder engagement strategies. Validation: simulation-based risk assessments and contingency planning for Indian ecosystems. Relevance: essential governance groundwork for any environmental genetic control trials. Output: containment and risk-assessment blueprint.

·  Single-Cell ATAC-seq to Map Regulatory Landscapes in Development or Disease
Aim: characterize chromatin accessibility at single-cell resolution to infer regulatory programs in a tissue. Approach: cell-capture justification, peak-calling and motif-enrichment strategies conceptually. Validation: link accessibility to expression via joint assays and perform perturbation validation. Relevance: uncovers regulatory mechanisms for developmental or disease biology in Indian research contexts. Deliverable: study outline and analysis plan.

·  Molecular Mechanisms of Non-Coding Variants: Prioritization and Functional Testing Plan
Aim: prioritize regulatory variants from GWAS and design assays to test impact on gene regulation. Approach: in-silico annotation, reporter constructs, and CRISPR perturbation conceptualization. Validation: allele-specific expression and chromatin assays to establish causality. Relevance: bridges association to mechanism for traits relevant to Indian populations. Output: variant-to-function roadmap.

·  High-Resolution HLA Typing Using NGS for Transplant and Immunogenetics
Aim: implement high-resolution HLA-typing workflows for compatibility testing and population studies. Approach: locus-selection, phasing strategies and reporting resolution considerations. Validation: concordance with gold-standard typing and quality metrics for clinical use. Relevance: enhances transplant success and immunogenetic research in India. Deliverable: typing pipeline and validation plan.

·  Designing a Molecular Surveillance Network for Antimicrobial Resistance Using Genomics
Aim: propose an integrated network linking sentinel labs to sequence-based AMR surveillance and data-sharing. Approach: sampling strategies, sequencing cadence, resistance-gene reporting standards and analytics. Validation: outbreak detection performance and policy-informing dashboards. Relevance: national AMR monitoring capacity enhancement for India. Output: surveillance architecture and SOPs.

·  Proteogenomics to Improve Cancer Variant Interpretation and Neoantigen Discovery
Aim: integrate proteomics and genomics to validate expressed mutations and prioritize neoantigens for immunotherapy. Approach: sample processing, MS data integration and neoantigen-prediction pipeline conceptualization. Validation: confirm peptide presentation and immunogenicity testing plans. Relevance: personalized cancer immunotherapy research applicable to Indian cohorts. Deliverable: integrated pipeline plan.

·  Engineering Programmable RNA Switches for Conditional Gene Expression
Aim: design synthetic RNA-based regulatory devices that respond to small molecules or RNAs to control gene expression. Approach: design principles, in-silico modeling and readout strategies. Validation: dose–response characterization and orthogonality tests. Relevance: tools for synthetic biology and therapeutic regulation in Indian research. Output: device design and validation roadmap.

·  Longitudinal Multi-Omics to Characterize Host Response Trajectories in Infectious Disease
Aim: map dynamic host responses across time to identify prognostic biomarkers and therapeutic windows. Approach: cohort design, sampling frequency and integrative analytics for trajectory inference. Validation: predictive model testing and clinical utility assessment. Relevance: informs treatment timing and triage strategies for Indian healthcare. Deliverable: cohort and analysis blueprint.

·  Design and Validation of Multiplexed CRISPR Diagnostic for Pathogen Panels
Aim: conceptualize multiplex CRISPR-based detection for simultaneous identification of several pathogens relevant to regional outbreaks. Approach: guide multiplexing strategy, assay readout design and cross-reactivity controls. Validation: LOD, clinical concordance and stability testing for deployment in Indian settings. Relevance: rapid multiplexed diagnostics for public health response. Output: assay validation plan.

·  Genome-Wide DNA Methylation Profiling to Identify Epigenetic Biomarkers
Aim: discover methylation signatures associated with exposure or disease for biomarker development. Approach: cohort definition, bisulfite/array choices and statistical modeling for DMR discovery. Validation: independent cohort replication and targeted assays for clinical translation. Relevance: biomarkers for exposure, disease or prognostic use in India. Deliverable: methylome study plan.

·  Designing a Clinical-Grade Pipeline for Circulating Tumor DNA (ctDNA) Analysis
Aim: develop an end-to-end ctDNA workflow for MRD detection or therapy monitoring. Approach: panel design, error-suppression strategies and reporting thresholds for low-frequency variants. Validation: analytical LOD, clinical concordance and standard operating procedures for clinical labs. Relevance: non-invasive oncology monitoring for Indian patients. Output: pipeline SOP and validation metrics.

·  Molecular Dissection of Host–Microbiome Interactions Using Gnotobiotic Models
Aim: use defined microbiota in germ-free models to identify causal microbial effects on host phenotypes. Approach: select community members, experimental readouts and multi-omics integration strategies. Validation: transferability of phenotypes and mechanistic assays. Relevance: translational microbiome interventions for Indian health challenges. Deliverable: experimental and analysis plan.

·  Designing a CRISPR-Based Functional Screen for Non-Coding Regulatory Elements
Aim: perform tiled perturbation screens to identify cis-regulatory elements controlling a gene of interest. Approach: sgRNA library design, screening readouts and hit-prioritization criteria. Validation: orthogonal perturbations and reporter assays to confirm element function. Relevance: advances regulatory genomics in Indian research contexts. Output: screen design and validation roadmap.

·  Single-Cell Multi-Modal Profiling (RNA + Protein) to Map Immune Cell States in Disease
Aim: combine transcript and surface-protein profiling at single-cell resolution to define immune phenotypes linked to outcomes. Approach: panel design, integration methods and batch-effect controls. Validation: correlation with functional assays and clinical phenotypes. Relevance: translational immune monitoring for Indian patient cohorts. Deliverable: profiling plan and downstream analyses.

·  Designing an Ethical Framework for Clinical Genomics with Return-of-Results Policies
Aim: create practical policies for returning actionable and incidental genomic findings in clinical studies. Approach: consent content, variant-tiering and counseling pathways conceptually defined. Validation: stakeholder consultations and pilot implementation metrics. Relevance: responsible genomic medicine practice in India. Output: governance template and counseling workflow.

·  High-Throughput Structural Variant Discovery in Neurodevelopmental Disorders
Aim: develop protocols to detect and interpret SVs from WGS data associated with NDDs. Approach: callset generation, annotation pipelines and phenotype-correlation strategies. Validation: orthogonal confirmation and functional follow-up of candidate SVs. Relevance: improve diagnostic yield for complex genetic disorders in India. Deliverable: analysis pipeline and validation plan.

·  Design a Translational Pipeline for RNA-seq Biomarkers to Clinical Assays
Aim: move discovery-expression signatures into clinically-useable assays (qPCR/ targeted panels). Approach: signature reduction, assay design, analytical validation and clinical performance assessment. Validation: prospective cohort testing and regulatory dossier outline. Relevance: accelerates biomarker application for Indian healthcare. Output: translational workflow.

·  Advanced Molecular Tools to Study Chromatin Spatial Organization (Hi-C/ Capture-C Design)
Aim: map 3D chromatin contacts at loci of interest to understand regulatory interactions. Approach: capture design, depth considerations and computational contact-calling strategies. Validation: replicate reproducibility, orthogonal FISH confirmation and perturbation effects. Relevance: mechanistic genomics for disease and development research in India. Deliverable: experiment and analysis plan.

·  Designing a Multiplex Host-Pathogen Transcriptomics Study for Coinfection Dynamics
Aim: simultaneously profile host and multiple pathogens to understand interactions in coinfections. Approach: library preparation choices, read-depth balancing and bioinformatic separation strategies. Validation: co-expression network analyses and targeted validation. Relevance: informs treatment strategies for co-endemic infections in India. Output: study design and interpretation guide.

·  Molecular Strategy for Rapid Vaccine Antigen Update Using Sequencing Surveillance
Aim: propose an agile pipeline linking pathogen sequence surveillance to antigen redesign for vaccine updates. Approach: variant monitoring thresholds, antigen prioritization and in-silico immunogenicity assessment. Validation: proposed preclinical immunogenicity screens and manufacturing considerations. Relevance: rapid response framework for vaccine-relevant pathogens in India. Deliverable: surveillance-to-design pipeline.

·  Application of Base Editing for Allele-Specific Modulation of Disease Genes
Aim: explore base editing to specifically correct pathogenic alleles without double-strand breaks. Approach: targetability assessment, bystander-edit risks and delivery considerations conceptualized. Validation: deep sequencing to quantify precision and functional rescue assays. Relevance: pathway to therapeutic editing research in India. Output: planning and safety checks.

·  Molecular Methods to Quantify RNA Modifications and Their Functional Impact
Aim: map and interpret epitranscriptomic marks (m6A, Ψ) associated with biological states. Approach: sequencing-method selection, enrichment vs direct detection trade-offs and analysis pipelines. Validation: perturbation experiments and correlation with RNA stability/translation metrics. Relevance: advanced regulatory layer exploration in Indian molecular biology. Deliverable: study roadmap and validation steps.

·  Design of a Precision-Medicine Trial Using Molecular Stratification Biomarkers
Aim: conceptualize an adaptive trial design where molecular markers define treatment arms. Approach: biomarker assay standardization, statistical adaptive rules and interim analyses. Validation: simulation studies for power and operational feasibility. Relevance: brings personalized therapeutics trials to Indian clinical research. Output: trial skeleton and biomarker integration plan.

·  De Novo Genome Assembly and Annotation of a Non-Model Organism for Trait Discovery
Aim: produce high-quality assembly and annotation to enable molecular breeding or ecological studies. Approach: sequencing strategy (long/short), scaffolding and evidence-based annotation plans. Validation: BUSCO/contiguity metrics and gene-model curation pipelines. Relevance: foundational resource generation for biodiversity and applied research in India. Deliverable: assembly/annotation workflow.

·  Molecular Dissection of RNA-Protein Interactomes Using CLIP-Seq Approaches
Aim: identify RNA targets of an RNA-binding protein to map post-transcriptional regulatory networks. Approach: CLIP variant selection, library complexity considerations and peak-calling strategies. Validation: motif enrichment, orthogonal RIP-qPCR and functional assays. Relevance: important for regulatory biology studies in India. Output: experimental and analysis plan.

·  Designing a National Genomic Biobank Strategy: Standards and Consent Models
Aim: propose operational standards, consent modalities and data-governance policies for a national biobank initiative. Approach: sample types, metadata standards, access models and privacy safeguards conceptualized. Validation: pilot implementation with stakeholder evaluation and ethical review. Relevance: builds infrastructure for genomic research in India. Deliverable: policy and operational blueprint.

·  Molecular Approaches to Study Alternative Splicing Dynamics in Development or Disease
Aim: profile isoform-level changes and infer splicing regulators affecting phenotype. Approach: long-read RNA sequencing vs computational isoform inference, and regulatory motif analysis. Validation: minigene reporters and knockdown/overexpression follow-ups. Relevance: uncovers transcript diversity with clinical implications in India. Output: study design and validation roadmap.

·  Designing a High-Throughput Functional Assay for Non-Coding Variant Effects Using MPRA
Aim: prioritize regulatory variants using massively parallel reporter assays for functional impact. Approach: library design, barcode strategies and statistical models for activity calling. Validation: cross-layer corroboration with chromatin and expression data. Relevance: scales variant-to-function studies for Indian genomics. Deliverable: MPRA planning and analysis steps.

·  Optimization of Viral Vector Design and Tropism for Gene-Delivery in Specific Tissues
Aim: design conceptual improvements in vector capsid and promoter choices to target tissues with translational relevance. Approach: tropism-determination strategies, payload constraints and immune-evasion considerations. Validation: biodistribution assays, expression profiling and safety assessment plans. Relevance: enables gene-therapy pathways for Indian clinical targets. Output: vector development roadmap.

·  Advanced Molecular Forensics: Low-Template DNA Analysis and Interpretation Framework
Aim: develop interpretation models and reporting guidance for low-copy-number forensic samples using probabilistic approaches. Approach: consider stochastic effects, contamination controls and statistical reporting conventions. Validation: simulation studies and proficiency testing plans tailored to forensic labs. Relevance: improves forensic genetics practice in India. Deliverable: interpretation and QC framework.

·  Designing an Integrated Pipeline for Microbial Genome Engineering Using CRISPR and Recombineering
Aim: plan a scalable pipeline for rapid microbial chassis engineering combining CRISPR edits with recombineering templates. Approach: multiplex-edit strategies, screening and sequencing validation concepts. Validation: benchmark engineering efficiency and stability across targets. Relevance: accelerates strain development for industrial biotech in India. Output: pipeline spec and validation plan.

·  Molecular Strategy for Early Detection of Transplant Rejection Using Cell-Free DNA
Aim: develop cfDNA-based markers of graft injury and implement monitoring strategies. Approach: marker discovery, assay sensitivity needs and longitudinal sampling schema. Validation: correlate cfDNA dynamics with clinical endpoints and histology. Relevance: improves transplant outcomes in Indian transplant centers. Deliverable: study and assay plan.

·  Functional Genomics of Long Non-Coding RNAs in Development or Disease
Aim: prioritize lncRNAs with potential regulatory roles and design perturbation strategies to test function. Approach: integrative expression, conservation and interaction data to select candidates. Validation: CRISPR-interference/activation and rescue experiments to establish roles. Relevance: uncovers novel regulatory elements with translational potential in India. Output: candidate-selection and validation plan.

·  Designing a Molecular Toolkit for Synthetic Biology Education and Safe Practice
Aim: create a curriculum and modular toolkit enabling advanced synthetic biology training with safety and ethics integrated. Approach: include non-pathogenic chassis, characterized parts, simulation exercises and assessment rubrics. Validation: pilot in university programs and measure competency gains. Relevance: builds workforce for India’s synthetic biology ambitions. Deliverable: toolkit and course syllabus.

·  Molecular Approaches to Study Retrotransposon Activity and Impact on the Host Genome
Aim: investigate activity patterns of mobile elements and their regulatory consequences using sequencing assays. Approach: capture-based detection, expression profiling and insertion-site mapping strategies. Validation: correlate activity with epigenetic state and phenotypic effects. Relevance: fundamental genome biology with implications for human and crop genomics in India. Output: study design and validation steps.

·  Design of an Ethical, Rapid-Response Genomics Consortium for Emerging Pathogen Outbreaks
Aim: plan a consortium model that enables rapid, ethical genomic data generation and sharing during outbreaks. Approach: pre-negotiated data-use terms, sequencing pipelines and stakeholder engagement frameworks. Validation: tabletop exercises and pilot activations. Relevance: preparedness infrastructure for India’s public-health emergencies. Deliverable: consortium charter and operational SOPs.

·  Molecular Dissection of RNA Splicing Machinery Alterations in Cancer
Aim: identify spliceosome component dysregulation and resultant aberrant isoforms driving oncogenesis. Approach: integrative transcriptomics, splice-junction quantification and candidate splicing-factor perturbation plans. Validation: functional assays linking isoforms to oncogenic phenotypes. Relevance: therapeutic target identification for Indian cancer research. Output: study and validation roadmap.

·  Designing a Comprehensive Variant Curation and Clinical Interpretation Pipeline for Indian Populations
Aim: build an evidence-based curation process that integrates local allele frequencies, functional data and phenotype correlations. Approach: variant-tiering, evidence aggregation tools and clinician-friendly reporting templates. Validation: retrospective concordance tests and clinician usability studies. Relevance: improves variant interpretation accuracy in Indian genomic medicine. Deliverable: curation pipeline spec.

·  Roadmap for Translating Molecular Research into Clinical/Industrial Applications in India
Aim: develop a pragmatic translational roadmap covering regulatory, manufacturing and IP steps for molecular discoveries. Approach: milestone-based development plan, stakeholder mapping (academia, industry, regulators) and funding/partnership models. Validation: pilot case studies and metrics for time-to-translation improvement. Relevance: accelerates impact of molecular biology research for societal benefit in India. Output: translational roadmap and checklist.

xt.