Q.1 What does ‘omics’ refer to in biology?
A group of small proteins
All large-scale studies of a biological system
A type of microscope
A specific DNA sequencing technique
Explanation - The suffix ‘-omics’ (e.g., genomics, proteomics) denotes large-scale, comprehensive analyses of a particular set of molecules in a biological system.
Correct answer is: All large-scale studies of a biological system
Q.2 Which omics technology directly measures RNA levels?
Genomics
Proteomics
Transcriptomics
Metabolomics
Explanation - Transcriptomics analyzes the complete set of RNA transcripts in a cell, reflecting gene expression patterns.
Correct answer is: Transcriptomics
Q.3 Which of the following best describes genomics?
The study of proteins in a cell
The study of all DNA in an organism
The study of metabolic products
The study of cell membranes
Explanation - Genomics focuses on sequencing and analyzing the entire genome, i.e., all DNA sequences of an organism.
Correct answer is: The study of all DNA in an organism
Q.4 Mass spectrometry is commonly used for which omics analysis?
Genomics
Transcriptomics
Proteomics
All of the above
Explanation - Mass spectrometry is the gold standard for identifying and quantifying proteins, making it essential for proteomics.
Correct answer is: Proteomics
Q.5 Which of these is NOT a typical omics data type?
DNA methylation arrays
Protein phosphorylation profiles
Metabolite concentration levels
Microscopic images of cell structure
Explanation - Microscopic images are imaging data, not part of traditional omics categories like genomics or proteomics.
Correct answer is: Microscopic images of cell structure
Q.6 In a typical RNA‑seq workflow, what is the first step after isolating total RNA?
Library preparation
Sequencing
Data alignment
Quality control
Explanation - RNA‑seq begins with converting RNA into a sequencing‑ready library, usually by reverse transcription and adapter ligation.
Correct answer is: Library preparation
Q.7 What does the acronym ‘GWAS’ stand for?
Genetic Wide Association Study
Genome-Wide Association Study
General Whole Analysis System
Gene-Wide Anomaly Screening
Explanation - GWAS examines genetic variants across the genome to find associations with traits or diseases.
Correct answer is: Genome-Wide Association Study
Q.8 Which computational method is commonly used to cluster proteins based on sequence similarity?
Principal Component Analysis
BLAST
k‑Means Clustering
Hidden Markov Models
Explanation - BLAST (Basic Local Alignment Search Tool) quickly finds regions of local similarity between sequences.
Correct answer is: BLAST
Q.9 Metabolomics studies which of the following?
Small molecule metabolites in biological samples
Gene expression patterns
Protein structures
Microbial communities
Explanation - Metabolomics focuses on quantifying metabolites—small molecules like sugars, amino acids, lipids—within cells or tissues.
Correct answer is: Small molecule metabolites in biological samples
Q.10 Which sequencing platform is known for producing very long reads?
Illumina MiSeq
PacBio Sequel II
Ion Torrent PGM
Sanger Sequencing
Explanation - Pacific Biosciences (PacBio) platforms produce reads up to tens of kilobases, useful for structural variant detection.
Correct answer is: PacBio Sequel II
Q.11 What does an FDR value represent in a proteomics experiment?
False Discovery Rate
Fast Data Retrieval
Fold Distribution Ratio
Functional Domain Ratio
Explanation - FDR estimates the proportion of false positives among identified peptides or proteins.
Correct answer is: False Discovery Rate
Q.12 In the context of bioinformatics, what is a 'gene ontology' (GO) term used for?
Describing gene functions and relationships
Sequencing genes directly
Predicting protein folding
Measuring gene expression levels
Explanation - Gene Ontology provides a structured vocabulary to describe gene product attributes across species.
Correct answer is: Describing gene functions and relationships
Q.13 Which of the following is a key challenge in integrating multi‑omics datasets?
Lack of computational power
High cost of single‑omics experiments
Different data scales and missing values
Inability to sequence DNA
Explanation - Multi‑omics data vary in units, dynamic range, and often contain missing entries, complicating integration.
Correct answer is: Different data scales and missing values
Q.14 What is the primary purpose of a 'phylogenetic tree' in genomics?
To show metabolic pathways
To illustrate evolutionary relationships
To map protein‑protein interactions
To identify metabolites
Explanation - Phylogenetic trees depict how species or genes diverged over time based on genetic similarities.
Correct answer is: To illustrate evolutionary relationships
Q.15 Which of the following best describes 'variant calling' in genomics?
Identifying differences between DNA sequences and a reference
Sequencing the entire genome
Measuring protein abundance
Quantifying metabolite levels
Explanation - Variant calling detects SNPs, indels, and structural variants by comparing sequenced data to a reference genome.
Correct answer is: Identifying differences between DNA sequences and a reference
Q.16 Which algorithm is commonly used for aligning RNA‑seq reads to a reference genome?
BWA
STAR
ClustalW
HMMER
Explanation - STAR (Spliced Transcripts Alignment to a Reference) is optimized for fast alignment of spliced RNA‑seq reads.
Correct answer is: STAR
Q.17 In proteomics, what is a 'label‑free quantification' method?
Using isotopic labels to measure protein abundance
Using spectral counts or peak intensities without labels
Labeling proteins with fluorescent tags
Using DNA labels for proteins
Explanation - Label‑free methods rely on measuring signal intensity or spectral counts to estimate protein abundance.
Correct answer is: Using spectral counts or peak intensities without labels
Q.18 Which of the following is a commonly used database for protein structure prediction?
PDB
UniProt
NCBI Taxonomy
KEGG
Explanation - The Protein Data Bank (PDB) houses experimentally determined 3D structures of proteins.
Correct answer is: PDB
Q.19 Which type of data is most often generated by a microarray experiment?
DNA sequences
Gene expression levels
Protein structures
Metabolite concentrations
Explanation - Microarrays hybridize labeled cDNA to probes, providing relative expression levels for many genes.
Correct answer is: Gene expression levels
Q.20 In the context of metabolomics, what does 'untargeted analysis' mean?
Analyzing only known metabolites
Analyzing all possible metabolites without pre‑selection
Targeting specific pathways
Using targeted mass spectrometry only
Explanation - Untargeted metabolomics seeks to detect as many metabolites as possible, including unknowns.
Correct answer is: Analyzing all possible metabolites without pre‑selection
Q.21 Which bioinformatics tool is designed for de novo genome assembly?
BLAST
SPAdes
IGV
MAFFT
Explanation - SPAdes assembles genomes from short reads without requiring a reference sequence.
Correct answer is: SPAdes
Q.22 What is the main advantage of using long‑read sequencing for structural variant detection?
Lower error rates
Higher throughput
Ability to span large repeats
Cheaper reagent cost
Explanation - Long reads can cover repetitive or complex regions, improving detection of large insertions/deletions.
Correct answer is: Ability to span large repeats
Q.23 Which statistical method is commonly used to correct for multiple testing in GWAS?
Bonferroni correction
Chi‑square test
T‑test
Logistic regression
Explanation - Bonferroni adjusts p‑values to control the family‑wise error rate when many SNPs are tested.
Correct answer is: Bonferroni correction
Q.24 In transcriptomics, what does RPKM stand for?
Reads Per Kilobase of transcript per Million mapped reads
RNA‑Protein Kinetic Measurement
Relative Protein Quantity Metric
Randomized Protein Kinase Map
Explanation - RPKM normalizes read counts by gene length and sequencing depth to estimate expression levels.
Correct answer is: Reads Per Kilobase of transcript per Million mapped reads
Q.25 Which omics approach would you use to study post‑translational modifications such as phosphorylation?
Genomics
Transcriptomics
Proteomics
Metabolomics
Explanation - Proteomics, especially phosphoproteomics, identifies and quantifies PTMs on proteins.
Correct answer is: Proteomics
Q.26 What is the function of a 'read mapper' in sequencing data processing?
To convert reads into proteins
To align sequencing reads to a reference genome
To trim adapters from reads
To assemble genomes de novo
Explanation - Read mappers (e.g., BWA, Bowtie) place short DNA fragments onto a reference sequence.
Correct answer is: To align sequencing reads to a reference genome
Q.27 Which of the following is a commonly used tool for differential gene expression analysis?
DESeq2
BLAST
HMMER
PhyML
Explanation - DESeq2 models count data to identify genes whose expression changes between conditions.
Correct answer is: DESeq2
Q.28 What does 'coverage' refer to in genome sequencing?
Number of times each base is read
Length of the read
The size of the genome
The number of genes
Explanation - Coverage (often expressed as ×) indicates average sequencing depth across the genome.
Correct answer is: Number of times each base is read
Q.29 Which of the following best describes 'epigenomics'?
Study of the genome’s protein composition
Study of modifications on DNA and histones that affect gene expression
Study of metabolic pathways
Study of gene duplication events
Explanation - Epigenomics focuses on chemical marks like methylation that regulate chromatin structure and gene activity.
Correct answer is: Study of modifications on DNA and histones that affect gene expression
Q.30 Which software tool is used to visualize sequencing read alignments?
IGV
BLAST
SPAdes
Cytoscape
Explanation - Integrative Genomics Viewer (IGV) displays aligned reads, variant calls, and annotations.
Correct answer is: IGV
Q.31 Which method is used to identify metabolites that differ between disease states?
Differential expression analysis
Metabolite profiling with multivariate statistics
Sequence alignment
Phylogenetic tree construction
Explanation - Statistical tools like PCA and PLS‑DA help reveal metabolite signatures associated with disease.
Correct answer is: Metabolite profiling with multivariate statistics
Q.32 What does a 'false positive rate' (FPR) indicate?
Rate of correctly identified positives
Rate of incorrectly identified positives
Rate of missed true positives
Rate of correctly identified negatives
Explanation - FPR is the proportion of negative samples incorrectly labeled as positive.
Correct answer is: Rate of incorrectly identified positives
Q.33 Which technique is commonly used for large‑scale protein interaction mapping?
Yeast two‑hybrid
Sanger sequencing
qPCR
Western blot
Explanation - The yeast two‑hybrid system detects binary protein‑protein interactions on a high‑throughput scale.
Correct answer is: Yeast two‑hybrid
Q.34 What is the purpose of a 'control sample' in an omics experiment?
To calibrate instruments
To provide a baseline for comparison
To replace missing data
To increase sequencing depth
Explanation - Controls allow researchers to distinguish experimental effects from background variation.
Correct answer is: To provide a baseline for comparison
Q.35 Which of the following is a common format for storing DNA sequencing data?
FASTA
BAM
CSV
PNG
Explanation - BAM (Binary Alignment/Map) stores aligned sequencing reads efficiently.
Correct answer is: BAM
Q.36 What does the term 'heterozygous' refer to in genetics?
Having two identical alleles
Having two different alleles
Having no alleles
Having one allele only
Explanation - Heterozygous means the two copies of a gene differ in sequence.
Correct answer is: Having two different alleles
Q.37 Which of the following best describes the central dogma of molecular biology?
DNA → RNA → Protein
Protein → DNA → RNA
RNA → Protein → DNA
Protein → RNA → DNA
Explanation - The central dogma explains the flow of genetic information from DNA to RNA to protein.
Correct answer is: DNA → RNA → Protein
Q.38 Which type of RNA is typically used as a reference for normalization in microarray studies?
mRNA
rRNA
tRNA
snRNA
Explanation - mRNA levels reflect gene expression and are commonly used for normalization.
Correct answer is: mRNA
Q.39 What is a key feature of 'single‑cell RNA‑seq'?
Sequencing entire genomes
Capturing gene expression of individual cells
Measuring protein abundance
Profiling metabolites
Explanation - Single‑cell RNA‑seq allows the analysis of heterogeneity among individual cells.
Correct answer is: Capturing gene expression of individual cells
Q.40 Which of the following is NOT a common step in protein mass spectrometry sample preparation?
Protein extraction
Digestion with trypsin
Labeling with stable isotopes
DNA sequencing
Explanation - DNA sequencing is unrelated to protein mass spectrometry, which focuses on peptide analysis.
Correct answer is: DNA sequencing
Q.41 In a differential expression analysis, what does a log2 fold change of 1 indicate?
No change in expression
Two‑fold increase in expression
Half‑fold decrease in expression
Ten‑fold increase in expression
Explanation - A log2 fold change of 1 equals 2¹ = 2‑fold change.
Correct answer is: Two‑fold increase in expression
Q.42 Which database contains metabolic pathway maps?
KEGG
PubMed
GenBank
UniProt
Explanation - KEGG provides curated pathway maps integrating genomic and metabolomic data.
Correct answer is: KEGG
Q.43 Which of the following is a hallmark of a well‑controlled RNA‑seq experiment?
Duplicate reads across samples
High sequencing depth
Variable library sizes
Randomly chosen samples
Explanation - Sufficient depth ensures reliable detection of low‑abundance transcripts.
Correct answer is: High sequencing depth
Q.44 Which type of sequencing read is most suitable for detecting splice junctions?
Short paired‑end reads
Long single‑end reads
Long paired‑end reads
Both short and long reads equally
Explanation - Long reads can span splice junctions, simplifying alignment of alternative splicing events.
Correct answer is: Long paired‑end reads
Q.45 What is the primary aim of 'metatranscriptomics'?
Sequencing of microbial genomes
Profiling RNA expression in microbial communities
Measuring metabolite concentrations in microbes
Sequencing host DNA only
Explanation - Metatranscriptomics captures the active gene expression of all microbes in a sample.
Correct answer is: Profiling RNA expression in microbial communities
Q.46 Which metric is used to assess the quality of a genome assembly?
GC‑content
N50
Average read length
Number of contigs
Explanation - N50 represents the contig length where 50% of the genome is contained in contigs of that size or larger.
Correct answer is: N50
Q.47 In proteomics, what does the term 'peptide spectral match' (PSM) refer to?
Matching a peptide to a reference genome
Matching a mass spectrum to a peptide sequence
Matching a protein to its gene
Matching a metabolite to a pathway
Explanation - A PSM is the assignment of a measured MS/MS spectrum to a specific peptide.
Correct answer is: Matching a mass spectrum to a peptide sequence
Q.48 Which of the following best describes a 'copy‑number variation' (CNV)?
A single base change
A change in the number of copies of a genomic region
A gene duplication within a plasmid
A change in protein structure
Explanation - CNVs involve deletions or duplications of segments of DNA, altering copy number.
Correct answer is: A change in the number of copies of a genomic region
Q.49 What is a primary advantage of using CRISPR‑Cas9 in functional genomics?
It sequences DNA
It edits genes to study function
It measures protein levels
It analyzes metabolites
Explanation - CRISPR‑Cas9 enables targeted gene knockouts or edits to investigate gene roles.
Correct answer is: It edits genes to study function
Q.50 Which type of alignment file stores paired‑end read information?
FASTA
FASTQ
SAM/BAM
VCF
Explanation - SAM/BAM files include mapping positions and pairing information for each read.
Correct answer is: SAM/BAM
Q.51 What does the acronym 'MSI' stand for in proteomics?
Mass Spectrometry Imaging
Multiple Sample Indexing
Molecular Sequence Identification
Metabolite Spectra Interpretation
Explanation - MSI visualizes the spatial distribution of molecules in tissues using mass spectrometry.
Correct answer is: Mass Spectrometry Imaging
Q.52 Which of the following is a common method to reduce bias in RNA‑seq library prep?
Poly‑A selection
DNA fragmentation
Protein precipitation
Metabolite extraction
Explanation - Poly‑A selection enriches for messenger RNA, reducing rRNA contamination.
Correct answer is: Poly‑A selection
Q.53 Which database provides curated information on genetic diseases?
ClinVar
PDB
KEGG
NCBI Taxonomy
Explanation - ClinVar aggregates variant interpretations linked to human diseases.
Correct answer is: ClinVar
Q.54 In metabolomics, what does the term 'feature detection' refer to?
Identifying metabolites by mass/charge peaks
Sequencing genes that encode enzymes
Predicting protein structure
Analyzing transcript abundance
Explanation - Feature detection involves extracting peaks from mass spectra that correspond to metabolites.
Correct answer is: Identifying metabolites by mass/charge peaks
Q.55 Which of the following is an example of a 'short read' sequencing technology?
Nanopore sequencing
PacBio HiFi
Illumina NovaSeq
Sanger sequencing
Explanation - Illumina platforms produce short reads (~100–300 bp) suitable for high‑throughput projects.
Correct answer is: Illumina NovaSeq
Q.56 Which type of data is typically visualized using a volcano plot?
Gene expression fold changes vs. significance
Phylogenetic distances
Metabolite concentrations
Protein structures
Explanation - Volcano plots display log2 fold change on the x‑axis and –log10 p‑value on the y‑axis.
Correct answer is: Gene expression fold changes vs. significance
Q.57 What is a key feature of a 'paired‑end library' in sequencing?
Both ends of each DNA fragment are sequenced
Only one end is sequenced
Fragments are sequenced twice for redundancy
It uses RNA templates
Explanation - Paired‑end sequencing reads both termini of a DNA fragment, improving mapping accuracy.
Correct answer is: Both ends of each DNA fragment are sequenced
Q.58 Which statistical test is most appropriate for comparing two independent groups in metabolomics?
ANOVA
Student's t‑test
Chi‑square test
Mann‑Whitney U test
Explanation - A t‑test compares the means of two independent samples when data are normally distributed.
Correct answer is: Student's t‑test
Q.59 In the context of CRISPR, what does 'sgRNA' stand for?
Single guide RNA
Small guide RNA
Sequence‑genome RNA
Standard gene RNA
Explanation - sgRNA directs Cas9 nuclease to a specific genomic locus for editing.
Correct answer is: Single guide RNA
Q.60 Which of the following best describes an 'operon'?
A cluster of genes regulated together
A single‑strand RNA transcript
A protein complex
A type of metabolite
Explanation - An operon is a unit of transcription in prokaryotes where multiple genes share a promoter.
Correct answer is: A cluster of genes regulated together
Q.61 What is the purpose of 'trimGalore' in RNA‑seq preprocessing?
To trim adapter sequences and low‑quality bases
To align reads to a reference genome
To assemble a transcriptome
To quantify gene expression
Explanation - TrimGalore combines Cutadapt and FastQC to clean reads before alignment.
Correct answer is: To trim adapter sequences and low‑quality bases
Q.62 Which of the following is a hallmark of a 'biologically relevant' differential gene expression result?
Large fold change and low p‑value
High fold change but high p‑value
Low fold change but low p‑value
High fold change and high p‑value
Explanation - Statistically significant, large‑magnitude changes are more likely to be biologically meaningful.
Correct answer is: Large fold change and low p‑value
Q.63 Which omics approach would best help identify potential drug targets for a disease?
Genomics
Transcriptomics
Proteomics
All of the above
Explanation - Integrating data from genomics, transcriptomics, and proteomics provides comprehensive insight into disease mechanisms.
Correct answer is: All of the above
Q.64 In a phylogenetic tree, what does a short branch length indicate?
Recent divergence
Large number of mutations
High evolutionary rate
Low confidence
Explanation - Short branches denote fewer genetic changes and a more recent common ancestor.
Correct answer is: Recent divergence
Q.65 Which of the following is NOT a typical output of a genome assembly?
Contig sequences
Assembly statistics (N50)
Gene annotations
Mass spectrometry spectra
Explanation - MS spectra are generated in proteomics, not genome assembly.
Correct answer is: Mass spectrometry spectra
Q.66 What does 'coverage depth' of 30× imply?
Each base is read 30 times on average
The genome is 30 megabases long
30 samples were sequenced
30% of the genome is covered
Explanation - 30× coverage means each base position is covered by 30 reads, on average.
Correct answer is: Each base is read 30 times on average
Q.67 Which of the following is a common approach to handle batch effects in omics datasets?
Randomized block design
Normalization and correction algorithms (e.g., ComBat)
Increasing sequencing depth
Discarding all data
Explanation - ComBat adjusts for systematic technical differences across batches.
Correct answer is: Normalization and correction algorithms (e.g., ComBat)
Q.68 Which software package is widely used for analyzing single‑cell RNA‑seq data?
Seurat
BLAST
MAFFT
Cytoscape
Explanation - Seurat provides tools for quality control, clustering, and differential expression in single‑cell data.
Correct answer is: Seurat
Q.69 What is the main purpose of a 'variant call set' in a genome analysis pipeline?
List of identified genetic variants
Sequence of the entire genome
Alignment file
Protein structure models
Explanation - A variant call set records SNPs, indels, and other mutations relative to a reference.
Correct answer is: List of identified genetic variants
Q.70 Which of the following best defines 'annotation' in the context of a genome?
Adding functional information to genes and other genomic features
Sequencing the genome again for accuracy
Aligning reads to the genome
Compressing the genome file
Explanation - Annotation maps genes, exons, regulatory elements, and other features onto the sequence.
Correct answer is: Adding functional information to genes and other genomic features
Q.71 Which metric is most commonly used to assess differential expression significance after multiple testing correction?
p‑value
q‑value
Fold change
RPKM
Explanation - The q‑value is the false discovery rate–adjusted p‑value.
Correct answer is: q‑value
Q.72 What does the term 'co‑expression network' refer to?
Network of interacting proteins
Network of genes with correlated expression patterns
Network of metabolites
Network of DNA methylation sites
Explanation - Co‑expression networks cluster genes that show similar expression across samples.
Correct answer is: Network of genes with correlated expression patterns
Q.73 Which of the following best describes a 'long‑read error profile'?
High accuracy, low error rate
High error rate but able to resolve complex regions
Zero error rate
Consistent error at start and end of reads
Explanation - Long‑read platforms like PacBio and Nanopore have higher per‑base error rates but can span repeats.
Correct answer is: High error rate but able to resolve complex regions
Q.74 Which type of analysis is performed by the software 'Cytoscape'?
Visualization and analysis of molecular interaction networks
Alignment of DNA sequences
Quantification of gene expression
Mass spectrometry data preprocessing
Explanation - Cytoscape specializes in network visualization and analysis.
Correct answer is: Visualization and analysis of molecular interaction networks
Q.75 In a genome‑wide association study, why is the 'genotype imputation' step used?
To fill in missing genotype data using reference panels
To sequence the entire genome again
To measure gene expression
To identify metabolites
Explanation - Imputation increases marker density and statistical power.
Correct answer is: To fill in missing genotype data using reference panels
Q.76 Which of the following best describes a 'metabolite fingerprint'?
Complete genome sequence
Distinct pattern of metabolites in a sample
Protein structure map
Gene expression profile
Explanation - A metabolite fingerprint captures the unique metabolic composition of a biological sample.
Correct answer is: Distinct pattern of metabolites in a sample
Q.77 What is the primary output of a 'variant effect predictor' tool like SnpEff?
Predicted protein structures
Functional annotation of genetic variants
RNA‑seq read counts
Metabolite concentration data
Explanation - SnpEff predicts the effect of variants (e.g., missense, nonsense) on genes and proteins.
Correct answer is: Functional annotation of genetic variants
Q.78 Which of the following is a common challenge when working with RNA‑seq data from low‑input samples?
Over‑representation of ribosomal RNA
Excess of long reads
High sequencing depth
Low error rates
Explanation - Low‑input RNA‑seq often suffers from contamination with abundant rRNA.
Correct answer is: Over‑representation of ribosomal RNA
Q.79 In metabolomics, what is a 'standard curve' used for?
To determine metabolite identity
To quantify metabolite concentration
To sequence DNA
To normalize protein expression
Explanation - A standard curve of known concentrations allows absolute quantification.
Correct answer is: To quantify metabolite concentration
Q.80 Which of the following best describes a 'gene regulatory network'?
Network of genes regulated by transcription factors
Network of metabolic pathways
Network of protein–protein interactions
Network of DNA methylation sites
Explanation - Gene regulatory networks map transcription factor interactions controlling gene expression.
Correct answer is: Network of genes regulated by transcription factors
Q.81 In the context of proteomics, what is a 'spectral library'?
A database of protein sequences
A repository of experimentally observed MS/MS spectra for peptides
A list of metabolite standards
A collection of genomic variants
Explanation - Spectral libraries enable faster and more accurate peptide identification.
Correct answer is: A repository of experimentally observed MS/MS spectra for peptides
Q.82 Which type of sequencing data is best suited for detecting structural variants larger than 1 kb?
Short‑read Illumina sequencing
Long‑read PacBio sequencing
Microarray expression data
RNA‑seq data
Explanation - Long reads can span large structural variants, enabling their detection.
Correct answer is: Long‑read PacBio sequencing
Q.83 Which of the following is a typical feature of a 'de novo transcriptome assembly'?
Requires a reference genome
Reconstructs transcripts from short reads without a reference
Aligns reads to a known transcriptome
Sequences only coding DNA
Explanation - De novo assembly builds transcript sequences solely from read data.
Correct answer is: Reconstructs transcripts from short reads without a reference
Q.84 What is the purpose of 'peptide‑level quantification' in label‑free proteomics?
To count the number of proteins
To estimate protein abundance using individual peptide intensities
To identify DNA variants
To measure metabolite levels
Explanation - Peptide intensities are summed or averaged to infer protein abundance.
Correct answer is: To estimate protein abundance using individual peptide intensities
Q.85 Which of the following best describes a 'false discovery rate' (FDR) in high‑throughput experiments?
Proportion of true positives among all findings
Proportion of false positives among all discoveries
Proportion of missing data points
Proportion of reads that failed alignment
Explanation - FDR controls the expected proportion of false discoveries among declared significant results.
Correct answer is: Proportion of false positives among all discoveries
Q.86 Which of the following is a key advantage of using RNA‑seq over microarrays?
Lower cost
Higher dynamic range and ability to detect novel transcripts
Requires no library preparation
Cannot detect splice variants
Explanation - RNA‑seq captures a broader spectrum of transcripts, including novel isoforms.
Correct answer is: Higher dynamic range and ability to detect novel transcripts
Q.87 In a proteomics study, what does the term 'label‑based quantification' refer to?
Using isotopic tags to distinguish samples
Counting the number of peptides directly
Using fluorescent dyes to stain proteins
Sequencing DNA fragments
Explanation - Isotopic labeling (e.g., SILAC) allows accurate relative quantification across samples.
Correct answer is: Using isotopic tags to distinguish samples
Q.88 What is the role of 'Gene Ontology (GO)' in omics data analysis?
To store protein sequences
To classify genes and gene products into standardized terms
To sequence genomes
To measure metabolite concentrations
Explanation - GO provides structured vocabularies for biological processes, cellular components, and molecular functions.
Correct answer is: To classify genes and gene products into standardized terms
Q.89 Which of the following is a typical output of a 'variant annotation pipeline' like VEP?
Annotated list of genetic variants with predicted impacts
Protein crystal structures
Metabolite concentration tables
Sequencing quality scores
Explanation - Variant effect predictor (VEP) annotates variants with functional consequences.
Correct answer is: Annotated list of genetic variants with predicted impacts
Q.90 Which technique is commonly used to isolate DNA from cells?
Protein precipitation
Phenol‑chloroform extraction
Metabolite extraction
RNA‑seq library prep
Explanation - Phenol‑chloroform is a classic method for extracting DNA from biological samples.
Correct answer is: Phenol‑chloroform extraction
Q.91 In a 'mass spectrometry‑based proteomics' experiment, what does the 'm/z' value represent?
Mass to charge ratio of a peptide ion
Mass of the protein
Molarity of the sample
Metabolite concentration
Explanation - Mass spectrometers measure the mass/charge ratio (m/z) of ionized molecules.
Correct answer is: Mass to charge ratio of a peptide ion
Q.92 Which of the following best defines 'single‑cell proteomics'?
Analyzing proteins from a whole tissue sample
Measuring protein levels in individual cells
Sequencing proteins from a population
Quantifying metabolites in a single cell
Explanation - Single‑cell proteomics captures protein expression heterogeneity at the cellular level.
Correct answer is: Measuring protein levels in individual cells
Q.93 What is the main purpose of 'quality control (QC)' in sequencing experiments?
To align reads to a reference genome
To evaluate and ensure data quality before downstream analysis
To sequence the entire genome again
To annotate genes
Explanation - QC checks for issues like adapter contamination, low‑quality bases, and GC bias.
Correct answer is: To evaluate and ensure data quality before downstream analysis
Q.94 Which of the following best describes a 'feature table' in metabolomics?
A list of protein sequences
A matrix of metabolite features (m/z, retention time) by sample
A table of genomic variants
A list of gene expression levels
Explanation - The feature table records detected peaks and their intensities across samples.
Correct answer is: A matrix of metabolite features (m/z, retention time) by sample
Q.95 Which of the following tools is commonly used for variant filtering in GWAS?
PLINK
BLAST
MAFFT
Cytoscape
Explanation - PLINK filters and processes genotype data for association studies.
Correct answer is: PLINK
Q.96 Which of the following best explains the term 'coverage breadth' in genome sequencing?
The number of times each base is read
The proportion of the genome that is covered by at least one read
The depth of sequencing at each position
The total number of reads
Explanation - Coverage breadth indicates how much of the genome is represented in the sequencing data.
Correct answer is: The proportion of the genome that is covered by at least one read
Q.97 In proteomics, what does 'label‑free spectral count' measure?
Number of times a peptide appears in the dataset
Mass of a protein
Gene expression level
Metabolite abundance
Explanation - Spectral count is a crude but useful proxy for protein abundance based on how many MS/MS spectra were matched.
Correct answer is: Number of times a peptide appears in the dataset
Q.98 Which of the following is a key advantage of 'epigenome editing' using CRISPR‑dCas9 fused to epigenetic modifiers?
Permanent genome sequence alteration
Targeted, reversible changes in gene expression without DNA mutation
Mass production of proteins
Sequencing of RNA
Explanation - dCas9 fused to modifiers can add/remove epigenetic marks to modulate transcription.
Correct answer is: Targeted, reversible changes in gene expression without DNA mutation
Q.99 Which of the following best describes a 'single‑cell ATAC‑seq' experiment?
Measuring DNA methylation levels
Assessing chromatin accessibility at single‑cell resolution
Sequencing whole genomes of individual cells
Quantifying RNA transcripts in single cells
Explanation - ATAC‑seq uses transposase to probe open chromatin; the single‑cell version does this per cell.
Correct answer is: Assessing chromatin accessibility at single‑cell resolution
Q.100 What does the 'RSEM' tool calculate in RNA‑seq data analysis?
Read error metrics
Estimated transcript abundances
Variant calling probabilities
Protein structures
Explanation - RSEM models read mapping uncertainty to estimate transcript‑level expression.
Correct answer is: Estimated transcript abundances
Q.101 Which of the following is a common challenge when integrating proteomics and metabolomics data?
Both datasets use the same units
Metabolite IDs are not standardized
Protein data is always more complete
Data are identical across omics
Explanation - Different naming conventions and databases make cross‑omics mapping difficult.
Correct answer is: Metabolite IDs are not standardized
Q.102 Which of the following best defines a 'gene set enrichment analysis (GSEA)'?
Identifying individual gene mutations
Testing whether predefined gene sets are over‑represented among differential expression results
Aligning DNA reads to a reference
Quantifying metabolite concentrations
Explanation - GSEA evaluates if a set of related genes (e.g., a pathway) shows coordinated up‑ or down‑regulation.
Correct answer is: Testing whether predefined gene sets are over‑represented among differential expression results
Q.103 In a mass spectrometry‑based metabolomics workflow, what is the purpose of the 'internal standard'?
To identify metabolites
To correct for variations in instrument response
To sequence the genome
To label proteins
Explanation - An internal standard of known concentration compensates for technical variability.
Correct answer is: To correct for variations in instrument response
Q.104 Which of the following is NOT a typical component of a 'variant call format (VCF)' file?
Chromosome and position
Reference and alternate allele
Read depth
Protein sequence
Explanation - VCF files describe genomic variants, not protein sequences.
Correct answer is: Protein sequence
Q.105 Which of the following best explains 'phasing' in genomics?
Aligning reads to a reference genome
Determining which alleles are inherited together on the same chromosome
Sequencing DNA fragments
Measuring gene expression
Explanation - Phasing assigns variants to maternal or paternal haplotypes.
Correct answer is: Determining which alleles are inherited together on the same chromosome
Q.106 Which of the following best describes a 'single‑cell RNA‑seq droplet platform'?
Separates cells by magnetic beads
Encapsulates single cells in droplets with barcoded primers
Sequences entire genomes of cells
Measures protein levels in single cells
Explanation - Droplet‑based scRNA‑seq (e.g., 10x Genomics) captures thousands of cells in individual droplets.
Correct answer is: Encapsulates single cells in droplets with barcoded primers
Q.107 In proteomics, what does a 'z‑score' indicate when analyzing peptide intensities?
The mass/charge ratio
The deviation of a peptide's intensity from the mean, in standard deviations
The number of peptides per protein
The p‑value of differential expression
Explanation - Z‑scores standardize data, making it easier to compare across peptides.
Correct answer is: The deviation of a peptide's intensity from the mean, in standard deviations
Q.108 Which of the following best describes a 'transcript isoform'?
A variant of a protein
A different mRNA transcript produced from the same gene due to alternative splicing
A type of metabolite
A DNA replication fork
Explanation - Alternative splicing generates multiple isoforms from a single gene locus.
Correct answer is: A different mRNA transcript produced from the same gene due to alternative splicing
Q.109 What is the primary advantage of 'shotgun proteomics'?
Targeted measurement of specific proteins
High‑throughput, untargeted identification of many proteins in a sample
Sequencing the genome
Measuring metabolite concentrations
Explanation - Shotgun proteomics digests proteins into peptides and identifies them en masse.
Correct answer is: High‑throughput, untargeted identification of many proteins in a sample
Q.110 Which of the following best describes a 'meta‑omics' study?
Integrating multiple omics datasets (e.g., genomics + proteomics) to gain holistic insight
Sequencing only the genome
Focusing solely on metabolite analysis
Studying a single type of molecules
Explanation - Meta‑omics combines several omics layers for comprehensive system analysis.
Correct answer is: Integrating multiple omics datasets (e.g., genomics + proteomics) to gain holistic insight
Q.111 Which of the following is a commonly used database for protein post‑translational modifications?
PhosphoSitePlus
GenBank
KEGG
RefSeq
Explanation - PhosphoSitePlus curates known PTMs such as phosphorylation sites.
Correct answer is: PhosphoSitePlus
Q.112 Which of the following best explains 'allele‑specific expression'?
Both alleles are expressed equally
Only one allele is transcribed more than the other
Alleles are not expressed
Alleles are deleted
Explanation - Allele‑specific expression occurs when one allele contributes more transcripts than the other.
Correct answer is: Only one allele is transcribed more than the other
Q.113 In metabolomics, what does the term 'feature clustering' refer to?
Grouping genes based on expression
Clustering similar mass‑spectral features to identify related metabolites
Merging protein sequences
Combining RNA‑seq reads
Explanation - Feature clustering groups peaks with similar retention time and mass/charge ratios.
Correct answer is: Clustering similar mass‑spectral features to identify related metabolites
Q.114 Which of the following best describes a 'phylogenetic tree with bootstrap values'?
A tree showing evolutionary relationships with confidence estimates for each branch
A list of gene sequences
A diagram of metabolic pathways
A map of protein interactions
Explanation - Bootstrap values quantify support for each branch in a phylogenetic tree.
Correct answer is: A tree showing evolutionary relationships with confidence estimates for each branch
Q.115 Which of the following best describes 'RNA‑seq alignment bias' caused by GC content?
GC‑rich regions are over‑represented in the data
GC‑poor regions are over‑represented in the data
GC content does not affect alignment
GC content only matters in proteomics
Explanation - High GC content can lead to preferential sequencing or alignment artifacts.
Correct answer is: GC‑rich regions are over‑represented in the data
Q.116 Which of the following is a key benefit of using a 'reference genome' in variant calling?
Reduces computational time
Allows alignment of reads to a known sequence to identify differences
Generates more reads
Prevents errors in mass spectrometry
Explanation - A reference provides a baseline for detecting variants in sequencing data.
Correct answer is: Allows alignment of reads to a known sequence to identify differences
Q.117 What does 'MIR' stand for in the context of miRNA studies?
MicroRNA
Metabolic Intermediary Reagent
Molecular Interaction Reporter
Massive Ion Resonance
Explanation - MIR refers to microRNA, small non‑coding RNAs involved in gene regulation.
Correct answer is: MicroRNA
Q.118 Which of the following best explains the concept of 'data normalization' in omics?
Removing sequencing adapters
Adjusting data to account for technical variation
Sequencing the genome again
Annotating genes
Explanation - Normalization corrects for biases such as library size and GC content.
Correct answer is: Adjusting data to account for technical variation
Q.119 Which of the following is a commonly used statistical test for detecting differential methylation?
Student's t‑test
Wilcoxon rank‑sum test
Chi‑square test
All of the above
Explanation - Many tests can be applied; choice depends on data distribution and study design.
Correct answer is: All of the above
Q.120 In proteomics, what does the 'label‑free label' refer to?
An isotope label added to peptides
No exogenous label, relying on spectral intensity
A fluorescent dye
A DNA barcode
Explanation - Label‑free methods quantify peptides without labeling, using MS signal directly.
Correct answer is: No exogenous label, relying on spectral intensity
Q.121 Which of the following best describes a 'metabolic flux analysis'?
Measuring steady‑state concentrations of metabolites
Tracing the flow of metabolites through pathways using labeled substrates
Sequencing DNA
Quantifying protein expression
Explanation - Flux analysis tracks how labeled atoms move through metabolic networks.
Correct answer is: Tracing the flow of metabolites through pathways using labeled substrates
Q.122 Which of the following is NOT a common quality metric for RNA‑seq data?
Mapping rate
Read duplication rate
Protein secondary structure
Insert size distribution
Explanation - Protein structure is irrelevant to RNA‑seq quality assessment.
Correct answer is: Protein secondary structure
Q.123 Which of the following best defines 'isoform‑specific quantification' in transcriptomics?
Quantifying total gene expression only
Separately measuring each splice variant of a gene
Measuring DNA methylation
Counting total protein abundance
Explanation - Isoform‑specific methods assign reads to distinct transcript variants.
Correct answer is: Separately measuring each splice variant of a gene
Q.124 In mass spectrometry‑based proteomics, which of the following best describes 'data‑dependent acquisition' (DDA)?
Pre‑selecting ions for fragmentation based on intensity thresholds
Fragmenting all ions in a non‑selective manner
Sequencing DNA
Measuring metabolite concentrations
Explanation - DDA selects the most intense precursor ions for MS/MS fragmentation during a run.
Correct answer is: Pre‑selecting ions for fragmentation based on intensity thresholds
Q.125 Which of the following best describes a 'gene set enrichment analysis (GSEA)' p‑value?
Probability of observing the enrichment by chance
Fold change of the gene set
Number of genes in the set
Sequencing depth
Explanation - GSEA p‑values indicate whether the enrichment of a gene set is statistically significant.
Correct answer is: Probability of observing the enrichment by chance