Q.1 In a gene regulatory network modeled as a directed graph, what does an edge from gene A to gene B represent?
Physical binding of A's protein product to B's promoter
Co‑expression of A and B under the same conditions
Similarity in the DNA sequence of A and B
Parallel transcription of A and B
Explanation - In directed graphs for gene regulatory networks, an edge points from a regulator to its target, indicating that the regulator’s product influences the transcription of the target gene.
Correct answer is: Physical binding of A's protein product to B's promoter
Q.2 Which mathematical representation is most commonly used to describe the dynamics of a biochemical reaction network?
Laplace transforms
Ordinary differential equations (ODEs)
Fourier series
Discrete Fourier transform
Explanation - ODEs capture the continuous change of species concentrations over time based on reaction rates, making them the standard tool for modeling biochemical networks.
Correct answer is: Ordinary differential equations (ODEs)
Q.3 In Boolean network models of gene regulation, what does the logical AND operator (∧) signify?
Either of the two regulators can activate the target gene
Both regulators must be active for the target gene to be expressed
The regulators inhibit each other
The regulators are mutually exclusive
Explanation - The AND operator returns true only when all its inputs are true, mirroring the requirement that all upstream regulators be present for activation.
Correct answer is: Both regulators must be active for the target gene to be expressed
Q.4 Which network motif is characterized by a feed‑forward loop (FFL) where gene X activates gene Y and both X and Y activate gene Z?
Negative feedback loop
Coherent type‑1 feed‑forward loop
Incoherent type‑2 feed‑forward loop
Bistable switch
Explanation - In a coherent type‑1 FFL, all interactions are activating, leading to a delayed but robust response of Z to X.
Correct answer is: Coherent type‑1 feed‑forward loop
Q.5 When constructing a weighted adjacency matrix for a metabolic network, what does a non‑zero entry a_ij typically represent?
The presence of gene i in chromosome j
The flux magnitude of reaction i converting metabolite j
The number of proteins encoded by gene i
The distance between metabolites i and j
Explanation - Weighted adjacency matrices encode quantitative interaction strengths; in metabolic networks, entries often correspond to reaction fluxes or stoichiometric coefficients.
Correct answer is: The flux magnitude of reaction i converting metabolite j
Q.6 Which concept from control theory is used to assess the robustness of a synthetic gene circuit to parameter variations?
Bode plot
Lyapunov stability
Nyquist criterion
Gain margin
Explanation - Lyapunov methods provide a systematic way to prove that a system returns to an equilibrium despite disturbances, a key requirement for robust synthetic circuits.
Correct answer is: Lyapunov stability
Q.7 In a bipartite graph representation of a protein–protein interaction network, which two node types are present?
Proteins and metabolites
Proteins and DNA sequences
Proteins and interaction domains
Proteins and functional annotations
Explanation - A bipartite graph separates two distinct sets of nodes; for PPIs, one set can be proteins, the other the domains that mediate binding.
Correct answer is: Proteins and interaction domains
Q.8 What does the eigenvalue with the largest real part of the Jacobian matrix indicate in a biochemical network model?
The fastest reaction rate
The stability of the steady state
The number of genes in the network
The total concentration of metabolites
Explanation - If the dominant eigenvalue has a positive real part, the steady state is unstable; a negative real part indicates local stability.
Correct answer is: The stability of the steady state
Q.9 Which algorithm is commonly used for community detection in large-scale biological networks?
Dijkstra's algorithm
Girvan‑Newman algorithm
Fast Fourier Transform
Bellman‑Ford algorithm
Explanation - Girvan‑Newman iteratively removes edges with high betweenness, revealing community structure typical of modular biological networks.
Correct answer is: Girvan‑Newman algorithm
Q.10 In the context of electrical analogues of biological circuits, what does a capacitor model?
Enzyme concentration
Membrane capacitance
Gene transcription rate
Protein degradation
Explanation - Capacitors store charge, analogous to the ability of a cell membrane to hold an electric potential across its lipid bilayer.
Correct answer is: Membrane capacitance
Q.11 What is the primary purpose of a sensitivity analysis in a kinetic model of a signaling pathway?
To identify which parameters most influence model output
To compute the steady‑state concentrations directly
To determine the network's topology
To convert the model to a Boolean framework
Explanation - Sensitivity analysis quantifies how variations in parameters affect predictions, highlighting critical reactions or regulators.
Correct answer is: To identify which parameters most influence model output
Q.12 Which of the following best describes a scale‑free network?
All nodes have the same degree
The degree distribution follows a power‑law
The network contains many short cycles
It has a regular lattice structure
Explanation - Scale‑free networks are characterized by a few highly connected hubs and many nodes with low degree, leading to a power‑law degree distribution.
Correct answer is: The degree distribution follows a power‑law
Q.13 When modeling a gene circuit with ordinary differential equations, the term "Hill coefficient" typically reflects:
The degradation rate of mRNA
The cooperativity of transcription factor binding
The diffusion constant of the protein
The basal transcription level
Explanation - The Hill coefficient (n) captures how many molecules of a regulator must bind to affect transcription, influencing the steepness of the response curve.
Correct answer is: The cooperativity of transcription factor binding
Q.14 Which of the following is a key advantage of using Petri nets for modeling metabolic pathways?
They inherently incorporate stochasticity
They provide a visual representation of concurrent events
They require fewer parameters than ODEs
They are always solvable analytically
Explanation - Petri nets capture the parallelism and synchronization of biochemical reactions, making them intuitive for pathway analysis.
Correct answer is: They provide a visual representation of concurrent events
Q.15 In a synthetic gene oscillator (e.g., the repressilator), what role does negative feedback play?
It amplifies the signal
It stabilizes the system at a fixed point
It creates sustained oscillations
It reduces noise in gene expression
Explanation - Negative feedback with appropriate time delays can generate limit‑cycle behavior, leading to rhythmic gene expression.
Correct answer is: It creates sustained oscillations
Q.16 Which metric measures the importance of a node based on the number of shortest paths that pass through it?
Clustering coefficient
Degree centrality
Betweenness centrality
Eigenvector centrality
Explanation - Betweenness centrality quantifies how often a node lies on the shortest paths between other node pairs, indicating its control over information flow.
Correct answer is: Betweenness centrality
Q.17 When converting a continuous ODE model of a signaling cascade into a discrete-time model for simulation, which method is most commonly used?
Runge‑Kutta 4th order
Euler forward integration
Laplace transformation
Z‑transform
Explanation - Euler's method approximates derivatives by finite differences, allowing ODEs to be simulated with discrete time steps.
Correct answer is: Euler forward integration
Q.18 In graph theory, what does a "clique" refer to?
A set of nodes with no connections between them
A subgraph where every node is connected to every other node
A node with the highest degree
A cycle of length three
Explanation - A clique is a completely connected subset of vertices, often used to identify tightly interacting groups in biological networks.
Correct answer is: A subgraph where every node is connected to every other node
Q.19 Which of the following best describes "parameter identifiability" in a systems biology model?
The ability to measure all species concentrations experimentally
The uniqueness of parameter values that reproduce observed data
The speed at which a simulation runs
The number of nodes in the network
Explanation - Identifiability determines whether distinct parameter sets can be distinguished based on the data, crucial for reliable model inference.
Correct answer is: The uniqueness of parameter values that reproduce observed data
Q.20 In a gene regulatory network, a "negative autoregulation" loop typically:
Increases response time
Creates bistability
Speeds up the system’s response and reduces noise
Blocks transcription entirely
Explanation - Negative autoregulation provides rapid feedback, leading to faster settling times and dampening of stochastic fluctuations.
Correct answer is: Speeds up the system’s response and reduces noise
Q.21 Which of the following is a common method to infer network structure from time‑series gene expression data?
Principal Component Analysis (PCA)
Dynamic Bayesian Networks (DBN)
Linear regression without regularization
K‑means clustering
Explanation - DBNs capture probabilistic dependencies over time, allowing inference of directed interactions in dynamic biological systems.
Correct answer is: Dynamic Bayesian Networks (DBN)
Q.22 When modeling ion channels in neuronal membranes, which electrical component best captures the voltage‑dependent opening probability?
Inductor
Resistor
Voltage‑controlled current source
Capacitor
Explanation - A voltage‑controlled current source can emulate the conductance change of an ion channel that depends on membrane potential.
Correct answer is: Voltage‑controlled current source
Q.23 What is the main difference between a deterministic and a stochastic model of a biochemical network?
Deterministic models use ODEs, stochastic models use partial differential equations
Deterministic models predict a single trajectory, stochastic models produce a distribution of possible trajectories
Deterministic models are always linear, stochastic models are always nonlinear
Deterministic models require fewer parameters
Explanation - Deterministic approaches yield fixed outcomes given initial conditions, whereas stochastic approaches incorporate randomness, reflecting molecular noise.
Correct answer is: Deterministic models predict a single trajectory, stochastic models produce a distribution of possible trajectories
Q.24 In a metabolic network, the term "essential reaction" refers to:
A reaction that consumes the most ATP
A reaction whose removal prevents the organism from growing under defined conditions
A reaction that occurs only in eukaryotes
A reaction with the highest flux in all simulations
Explanation - Essential reactions are critical for viability; their knockout leads to lethality or severe growth defects.
Correct answer is: A reaction whose removal prevents the organism from growing under defined conditions
Q.25 Which of the following is a property of a stable limit cycle in a nonlinear ODE model of a biological oscillator?
All trajectories converge to a fixed point
Trajectories approach a closed orbit regardless of initial conditions
The system exhibits chaotic behavior
The amplitude of oscillations grows without bound
Explanation - A stable limit cycle attracts nearby trajectories, resulting in sustained periodic oscillations.
Correct answer is: Trajectories approach a closed orbit regardless of initial conditions
Q.26 In the context of synthetic biology, a "toggle switch" is best described as:
A circuit that continuously oscillates
A bistable system with two stable steady states
A linear amplifier of gene expression
A feed‑forward motif that filters noise
Explanation - Toggle switches consist of mutually repressing genes, enabling the system to stably reside in one of two states.
Correct answer is: A bistable system with two stable steady states
Q.27 What does the term "degree distribution" refer to in the analysis of a biological network?
The distribution of gene expression levels
The histogram of the number of connections per node
The variation of kinetic parameters across reactions
The spread of metabolite concentrations
Explanation - Degree distribution captures how many nodes have a given number of edges, revealing network topology such as scale‑free or random characteristics.
Correct answer is: The histogram of the number of connections per node
Q.28 Which computational tool is specifically designed for simulating stochastic biochemical reaction networks?
COPASI
MATLAB Simulink
Gillespie algorithm (SSA)
SPICE
Explanation - The stochastic simulation algorithm (SSA) by Gillespie generates exact trajectories for chemically reacting systems at the molecular level.
Correct answer is: Gillespie algorithm (SSA)
Q.29 In a directed acyclic graph (DAG) representing a signaling cascade, what property does the graph guarantee?
Presence of cycles
Unique paths from source to sink
No feedback loops
Equal indegree for all nodes
Explanation - A DAG has no directed cycles, meaning signals propagate only forward without returning to upstream components.
Correct answer is: No feedback loops
Q.30 When applying the Laplacian matrix of a network for community detection, which eigenvector is commonly examined?
Eigenvector associated with the largest eigenvalue
Eigenvector associated with the smallest non‑zero eigenvalue (Fiedler vector)
Eigenvector of the zero eigenvalue
Eigenvector of the median eigenvalue
Explanation - The Fiedler vector captures the optimal bipartition of the graph and is used in spectral clustering methods.
Correct answer is: Eigenvector associated with the smallest non‑zero eigenvalue (Fiedler vector)
Q.31 What does a "positive feedback loop" typically do to a biological system's response?
Attenuates the response and speeds up return to baseline
Creates amplification and can lead to bistability
Eliminates noise completely
Prevents any change in the system
Explanation - Positive feedback reinforces a signal, potentially resulting in switch‑like behavior and multiple stable states.
Correct answer is: Creates amplification and can lead to bistability
Q.32 In a kinetic model of enzyme catalysis, the Michaelis‑Menten constant (K_m) is defined as:
The substrate concentration at which the reaction rate is half its maximum
The maximal reaction velocity
The enzyme concentration required for activity
The equilibrium constant of the reaction
Explanation - K_m reflects enzyme affinity; low K_m indicates high affinity for the substrate.
Correct answer is: The substrate concentration at which the reaction rate is half its maximum
Q.33 Which type of graph is most suitable for representing a metabolic network where reactions are nodes and metabolites are edges?
Undirected graph
Bipartite graph
Weighted directed graph
Tree
Explanation - In a bipartite representation, one node set corresponds to metabolites, the other to reactions, with edges indicating participation.
Correct answer is: Bipartite graph
Q.34 What is the main advantage of using a "modular" approach in designing synthetic gene circuits?
It reduces the number of required DNA bases
Modules can be independently characterized and recombined
It eliminates the need for promoters
Modules guarantee zero metabolic burden
Explanation - Modularity enables reuse of well‑characterized parts, facilitating rapid assembly of complex circuits.
Correct answer is: Modules can be independently characterized and recombined
Q.35 In the context of network robustness, the term "percolation threshold" refers to:
The minimum number of nodes required for a network to exist
The fraction of nodes that must be removed before the network fragments
The maximum degree a node can have
The time it takes for a signal to traverse the network
Explanation - Percolation theory quantifies the critical point at which a network loses its giant connected component under random failures.
Correct answer is: The fraction of nodes that must be removed before the network fragments
Q.36 Which of the following statements about the Hill equation is true?
It is only applicable to linear systems
A higher Hill coefficient produces a more switch‑like response
It describes the diffusion of metabolites
It cannot model cooperative binding
Explanation - Increasing the Hill coefficient steepens the sigmoidal curve, reflecting stronger cooperativity.
Correct answer is: A higher Hill coefficient produces a more switch‑like response
Q.37 In a Boolean model, what does the update rule "NOT A" represent?
A is always active
A's activity is inverted each time step
A activates itself
A is ignored in the model
Explanation - The NOT operator flips the truth value of A, turning true to false and vice versa at each update.
Correct answer is: A's activity is inverted each time step
Q.38 Which method is used to reduce the dimensionality of high‑throughput gene expression data before network inference?
Hierarchical clustering
Principal Component Analysis (PCA)
Monte Carlo simulation
Finite element analysis
Explanation - PCA transforms correlated variables into a smaller set of orthogonal components, simplifying downstream analysis.
Correct answer is: Principal Component Analysis (PCA)
Q.39 What is the purpose of using a "sink node" in a metabolic network model?
To represent the cell membrane
To balance mass by consuming metabolites that leave the system
To store energy in the form of ATP
To indicate gene repression
Explanation - Sink nodes act as drains for metabolites, ensuring mass balance when modeling open systems.
Correct answer is: To balance mass by consuming metabolites that leave the system
Q.40 Which of the following best describes the concept of "flux balance analysis" (FBA)?
A stochastic simulation of reaction kinetics
A linear programming approach to predict steady‑state reaction rates
A method for measuring protein–protein binding affinities
A technique for visualizing gene expression heatmaps
Explanation - FBA optimizes an objective function (e.g., biomass) subject to stoichiometric constraints, yielding feasible flux distributions.
Correct answer is: A linear programming approach to predict steady‑state reaction rates
Q.41 When a biological network exhibits "small‑world" properties, which two characteristics are typically observed?
High clustering coefficient and short average path length
Low degree variance and tree‑like structure
Uniform degree distribution and high diameter
Absence of hubs and long cycles
Explanation - Small‑world networks combine local clustering with global efficiency, a hallmark of many cellular interaction maps.
Correct answer is: High clustering coefficient and short average path length
Q.42 In an electrical circuit analog of a signaling pathway, a resistor typically models:
Enzymatic catalysis rate
Diffusive resistance of a molecule
Gene transcription repression
Membrane potential
Explanation - Resistors impede current flow, analogous to diffusion barriers that limit molecular transport.
Correct answer is: Diffusive resistance of a molecule
Q.43 Which statistical test is most appropriate for determining whether two gene expression profiles are significantly correlated?
Chi‑square test
Pearson correlation coefficient significance test
Student's t‑test for means
Mann‑Whitney U test
Explanation - Pearson's test evaluates the linear relationship between two continuous variables and provides a p‑value for significance.
Correct answer is: Pearson correlation coefficient significance test
Q.44 In a kinetic model, the term "stiff system" refers to:
A system with many parallel pathways
A set of ODEs with widely varying time scales requiring specialized solvers
A network that cannot be reduced
A model with no steady state
Explanation - Stiffness arises when some reactions occur much faster than others, making explicit integration unstable unless very small steps are used.
Correct answer is: A set of ODEs with widely varying time scales requiring specialized solvers
Q.45 Which type of experimental data is most directly used to construct a protein interaction network?
RNA‑seq expression levels
Yeast two‑hybrid assay results
Chromatin immunoprecipitation (ChIP) data
Metabolite concentration measurements
Explanation - Yeast two‑hybrid screens identify physical interactions between proteins, providing edges for interaction networks.
Correct answer is: Yeast two‑hybrid assay results
Q.46 What is the main purpose of adding a "delay" term in a differential equation model of transcription?
To account for the time needed for transcription and translation processes
To speed up numerical simulation
To model protein degradation
To enforce mass conservation
Explanation - Delays capture the finite time between gene activation and functional protein appearance, affecting dynamics such as oscillations.
Correct answer is: To account for the time needed for transcription and translation processes
Q.47 Which metric quantifies how evenly the connections are distributed among nodes in a network?
Assortativity coefficient
Degree heterogeneity
Clustering coefficient
Network density
Explanation - Degree heterogeneity measures variance in node degrees; low heterogeneity indicates even distribution.
Correct answer is: Degree heterogeneity
Q.48 In a stochastic simulation, the "propensity function" for a reaction defines:
The deterministic rate constant
The probability per unit time that the reaction occurs given the current state
The final concentration of products
The spatial location of reactants
Explanation - Propensities translate molecular counts into reaction probabilities used by algorithms like Gillespie's SSA.
Correct answer is: The probability per unit time that the reaction occurs given the current state
Q.49 What does the term "bifurcation" mean in the analysis of a biological system's ODE model?
A point where the system splits into two separate networks
A parameter value at which the qualitative behavior of the system changes
A method for solving linear equations
A type of noise in gene expression
Explanation - Bifurcations indicate transitions such as from a stable steady state to oscillations or bistability.
Correct answer is: A parameter value at which the qualitative behavior of the system changes
Q.50 Which of the following best describes a "feed‑back inhibition" mechanism in metabolic pathways?
An end product activates the first enzyme
An end product inhibits an upstream enzyme
All enzymes are expressed constitutively
Substrates are transported out of the cell
Explanation - Feedback inhibition regulates flux by having the pathway’s product bind to and inhibit an earlier enzyme.
Correct answer is: An end product inhibits an upstream enzyme
Q.51 When performing network motif analysis, the null model is used to:
Generate random networks with the same degree sequence for statistical comparison
Remove all edges from the original network
Identify the longest path in the network
Calculate the exact number of triangles
Explanation - The null model preserves certain properties (e.g., degree distribution) while randomizing others, allowing assessment of motif enrichment.
Correct answer is: Generate random networks with the same degree sequence for statistical comparison
Q.52 In a synthetic biology context, the term "orthogonal" refers to:
Components that function independently of host cellular processes
Genes that are located on different chromosomes
Interactions that are mutually exclusive
A network with zero feedback
Explanation - Orthogonal parts minimize cross‑talk, ensuring predictable behavior when introduced into a new host.
Correct answer is: Components that function independently of host cellular processes
Q.53 Which of the following is a common method for visualizing large‑scale interaction networks?
Scatter plot
Force‑directed layout
Histogram
Bar chart
Explanation - Force‑directed algorithms position nodes using simulated physical forces, revealing clusters and hubs in complex networks.
Correct answer is: Force‑directed layout
Q.54 In a gene circuit modeled with ODEs, the term "leakiness" of a promoter refers to:
The maximum transcription rate
Basal transcription occurring even when the promoter is repressed
The speed at which mRNA degrades
The probability of promoter mutation
Explanation - Leakiness quantifies unintended low‑level expression, which can affect circuit performance.
Correct answer is: Basal transcription occurring even when the promoter is repressed
Q.55 Which mathematical concept is used to quantify the similarity between two probability distributions of gene expression levels?
Euclidean distance
Kullback‑Leibler (KL) divergence
Pearson correlation
Jaccard index
Explanation - KL divergence measures how one probability distribution diverges from a reference distribution, useful for comparing expression profiles.
Correct answer is: Kullback‑Leibler (KL) divergence
Q.56 When analyzing a signaling network, a node with a high "betweenness centrality" is likely to be:
A peripheral protein with few interactions
A critical hub that connects different pathways
A membrane lipid
A gene with low expression
Explanation - High betweenness indicates the node lies on many shortest paths, acting as a bridge between modules.
Correct answer is: A critical hub that connects different pathways
Q.57 In a Boolean network, the "synchronous update" scheme updates:
Only one randomly chosen node per time step
All nodes simultaneously at each discrete time step
Nodes in a random order
Only the nodes with the highest degree
Explanation - Synchronous update applies the Boolean rule to every node at the same time, simplifying analysis but sometimes producing unrealistic dynamics.
Correct answer is: All nodes simultaneously at each discrete time step
Q.58 Which parameter in a Hill function determines the steepness of the response curve?
K_d (dissociation constant)
Maximum velocity (V_max)
Hill coefficient (n)
Baseline activity (b)
Explanation - The Hill coefficient controls cooperativity; larger n yields a more switch‑like transition.
Correct answer is: Hill coefficient (n)
Q.59 In a reaction network, the "stoichiometric matrix" (S) has dimensions:
Number of species × number of reactions
Number of reactions × number of species
Number of species × number of species
Number of reactions × number of reactions
Explanation - Each column corresponds to a reaction, each row to a species, with entries indicating consumption (negative) or production (positive).
Correct answer is: Number of species × number of reactions
Q.60 What is the main purpose of "parameter sweeps" in computational modeling?
To find the single best set of parameters
To explore how model behavior changes across a range of parameter values
To reduce the dimensionality of the model
To eliminate the need for experimental data
Explanation - Parameter sweeps systematically vary parameters, revealing sensitivity, robustness, and possible regimes of behavior.
Correct answer is: To explore how model behavior changes across a range of parameter values
Q.61 In a gene regulatory network, a "source node" is defined as:
A node with only outgoing edges
A node with only incoming edges
A node with equal in‑ and out‑degree
A node that participates in a feedback loop
Explanation - Source nodes have no regulators (zero indegree) but may regulate many downstream genes.
Correct answer is: A node with only outgoing edges
Q.62 Which technique is commonly used to measure real‑time changes in intracellular calcium concentration, a common second messenger in signaling networks?
Western blotting
Fluorescent calcium indicator dyes (e.g., Fura‑2)
PCR amplification
Chromatography
Explanation - These dyes change fluorescence upon binding calcium, allowing dynamic monitoring of signaling events.
Correct answer is: Fluorescent calcium indicator dyes (e.g., Fura‑2)
Q.63 When using the Gillespie algorithm, the "next reaction method" improves efficiency by:
Parallelizing the simulation on GPUs
Updating only the propensities of reactions affected by the previous event
Converting the stochastic model to deterministic ODEs
Using larger time steps
Explanation - The next‑reaction method avoids recomputing all propensities after each event, reducing computational overhead.
Correct answer is: Updating only the propensities of reactions affected by the previous event
Q.64 Which of the following best explains why "scale‑free" networks are robust to random failures but vulnerable to targeted attacks on hubs?
They have uniform degree distribution
Most nodes are low‑degree; removing a hub eliminates many connections
All nodes are equally important
They possess many redundant pathways
Explanation - Random removal likely hits low‑degree nodes, leaving connectivity intact, whereas targeting hubs quickly fragments the network.
Correct answer is: Most nodes are low‑degree; removing a hub eliminates many connections
Q.65 In the context of network modeling, what does the term "modularity" quantify?
The total number of edges in the network
The degree to which a network can be divided into distinct communities with dense intra‑community connections
The average path length
The ratio of nodes to edges
Explanation - Higher modularity indicates clear community structure, often reflecting functional modules in biological systems.
Correct answer is: The degree to which a network can be divided into distinct communities with dense intra‑community connections
Q.66 Which of the following statements about "mass action kinetics" is correct?
Reaction rate is independent of reactant concentrations
Rate is proportional to the product of the concentrations of reactants raised to their stoichiometric coefficients
It only applies to enzymatic reactions
It assumes Michaelis‑Menten saturation
Explanation - Mass action law states that the rate law follows the stoichiometry of the elementary reaction.
Correct answer is: Rate is proportional to the product of the concentrations of reactants raised to their stoichiometric coefficients
Q.67 In a synthetic gene circuit, the use of a "ribosome binding site (RBS) library" primarily allows:
Control over transcription initiation rates
Tuning of translation initiation strength
Modification of DNA replication speed
Adjustment of protein degradation rates
Explanation - Different RBS sequences have varying affinities for ribosomes, affecting protein synthesis rates.
Correct answer is: Tuning of translation initiation strength
Q.68 Which algorithm is used to compute the shortest path lengths in a weighted directed graph representing a signaling network?
Prim's algorithm
Dijkstra's algorithm
Kruskal's algorithm
Bellman‑Ford algorithm
Explanation - Dijkstra's algorithm efficiently finds shortest paths from a source node to all other nodes in graphs with non‑negative edge weights.
Correct answer is: Dijkstra's algorithm
Q.69 When modeling gene expression noise, the "intrinsic noise" component originates from:
Variability in external environmental conditions
Random timing of transcription and translation events within a cell
Differences between individual cells in a population
Measurement errors in sequencing
Explanation - Intrinsic noise reflects stochastic fluctuations inherent to the biochemical processes of gene expression.
Correct answer is: Random timing of transcription and translation events within a cell
Q.70 In a network model, a "self‑loop" on a node indicates:
The node is isolated
The node regulates itself (auto‑regulation)
The node has no outgoing edges
The node belongs to multiple communities
Explanation - Self‑loops capture auto‑regulatory interactions, which can be positive or negative.
Correct answer is: The node regulates itself (auto‑regulation)
Q.71 Which of the following best describes the "Erdoğan–Kumar" method (hypothetical for this question) used in network modeling?
A technique for exact solution of nonlinear ODEs
A method for approximating large‑scale network dynamics using coarse‑graining
An algorithm for finding Hamiltonian cycles
A statistical test for differential expression
Explanation - Coarse‑graining reduces model complexity by aggregating groups of nodes while preserving essential dynamics.
Correct answer is: A method for approximating large‑scale network dynamics using coarse‑graining
Q.72 In a gene regulatory network, the term "motif enrichment" refers to:
An increase in gene expression levels
A statistical over‑representation of specific small sub‑graph patterns compared to random networks
A higher number of transcription factors overall
A larger genome size
Explanation - Motif enrichment suggests functional significance of recurring interaction patterns.
Correct answer is: A statistical over‑representation of specific small sub‑graph patterns compared to random networks
Q.73 When applying a "linear noise approximation" (LNA) to a stochastic biochemical system, the resulting equations describe:
Deterministic steady‑state concentrations only
The evolution of mean concentrations and covariance of fluctuations around the deterministic trajectory
Exact trajectories of each molecule
The distribution of gene lengths
Explanation - LNA linearizes the master equation to capture both average behavior and variance due to stochasticity.
Correct answer is: The evolution of mean concentrations and covariance of fluctuations around the deterministic trajectory
Q.74 Which of the following is NOT a typical assumption in Flux Balance Analysis (FBA)?
Steady‑state mass balance for internal metabolites
Linear objective function
Known kinetic rate constants for all reactions
Fixed reaction stoichiometry
Explanation - FBA does not require kinetic parameters; it relies on stoichiometry and constraints to infer fluxes.
Correct answer is: Known kinetic rate constants for all reactions
Q.75 In a synthetic biology design, a "kill switch" is intended to:
Increase production of a desired metabolite
Induce cell death under specific conditions
Amplify signal transduction
Stabilize plasmid copy number
Explanation - Kill switches provide biosafety by triggering programmed cell death when predefined triggers are detected.
Correct answer is: Induce cell death under specific conditions
Q.76 Which graph‑theoretical measure is most appropriate for detecting densely connected sub‑structures in a protein interaction network?
Degree centrality
Clustering coefficient
Betweenness centrality
Network diameter
Explanation - The clustering coefficient quantifies the likelihood that a node’s neighbors are also connected, highlighting dense clusters.
Correct answer is: Clustering coefficient
Q.77 In a deterministic ODE model, what does a "fixed point" correspond to?
A time‑varying oscillation
A state where all derivatives are zero (steady state)
A point where the system crashes
A random fluctuation
Explanation - Fixed points satisfy dX/dt = 0 for all state variables, representing equilibrium conditions.
Correct answer is: A state where all derivatives are zero (steady state)
Q.78 When constructing a gene regulatory network from ChIP‑seq data, the edges are typically derived from:
Co‑localization of genes on chromosomes
Binding peaks of transcription factors near gene promoters
Protein abundance measurements
Metabolite concentrations
Explanation - ChIP‑seq identifies DNA regions bound by specific TFs, indicating regulatory relationships.
Correct answer is: Binding peaks of transcription factors near gene promoters
Q.79 In a Boolean network model, the "attractor" of the system represents:
A transient state that the system passes through quickly
A set of states (single or cyclic) that the system eventually reaches and stays in
The node with the highest degree
The input signal with maximum amplitude
Explanation - Attractors correspond to stable patterns of gene activity, akin to cell fates.
Correct answer is: A set of states (single or cyclic) that the system eventually reaches and stays in
Q.80 Which of the following best describes "heterogeneity" in a cell population when modeling signaling networks?
All cells have identical parameters
Cells differ in parameters such as receptor levels or reaction rates
The network topology changes over time
The model uses only deterministic equations
Explanation - Heterogeneity captures variability among cells, influencing population‑level responses.
Correct answer is: Cells differ in parameters such as receptor levels or reaction rates
Q.81 In a synthetic circuit, a "CRISPRi" system functions primarily as:
A transcriptional activator
A transcriptional repressor using dead Cas9 and guide RNA
A DNA replicase
An RNA polymerase
Explanation - CRISPR interference (CRISPRi) blocks transcription by sterically hindering RNA polymerase binding.
Correct answer is: A transcriptional repressor using dead Cas9 and guide RNA
Q.82 When simulating a large biochemical network, the "stiffness" of the ODE system can be mitigated by using which numerical method?
Explicit Euler method
Runge‑Kutta 4th order (non‑stiff)
Implicit backward differentiation formula (BDF)
Monte Carlo integration
Explanation - Implicit methods like BDF are stable for stiff systems, allowing larger time steps.
Correct answer is: Implicit backward differentiation formula (BDF)
Q.83 Which of the following is a characteristic of a "feed‑forward loop" that provides a delay filter in gene regulation?
Immediate activation of the target gene
Transient activation only if the input signal persists long enough
Complete repression of the target gene
Oscillatory output regardless of input
Explanation - Certain FFL types act as persistence detectors, filtering out short, noisy inputs.
Correct answer is: Transient activation only if the input signal persists long enough
Q.84 In a directed graph, the "indegree" of a node measures:
The number of outgoing edges
The total number of edges in the graph
The number of incoming edges
The length of the longest path ending at the node
Explanation - Indegree counts how many edges point toward the node, indicating how many regulators affect it.
Correct answer is: The number of incoming edges
Q.85 When analyzing a metabolic network, the term "dead‑end metabolite" refers to:
A metabolite that participates in cycles only
A metabolite that is produced but not consumed (or vice versa) within the network
A metabolite with the highest concentration
A metabolite that is not detectable experimentally
Explanation - Dead‑ends indicate missing reactions or gaps in the reconstruction.
Correct answer is: A metabolite that is produced but not consumed (or vice versa) within the network
Q.86 Which statistical approach is commonly employed to fit parameters of an ODE model to time‑course experimental data?
Least‑squares minimization
Principal component analysis
K‑means clustering
Random forest classification
Explanation - Least‑squares finds parameter values that minimize the squared differences between model predictions and observed data.
Correct answer is: Least‑squares minimization
Q.87 In a synthetic biology context, a "riboswitch" is a:
DNA segment that binds transcription factors
RNA element that changes conformation upon ligand binding to regulate translation
Protein that degrades mRNA
Promoter that is constitutively active
Explanation - Riboswitches act post‑transcriptionally, controlling gene expression in response to small molecules.
Correct answer is: RNA element that changes conformation upon ligand binding to regulate translation
Q.88 When constructing a Boolean model, the "asynchronous update" scheme differs from the synchronous one by:
Updating all nodes at the same time
Updating nodes in a random order, one at a time
Updating only nodes with zero indegree
Updating nodes based on their degree
Explanation - Asynchronous updates can capture more realistic timing and avoid artifacts caused by simultaneous updates.
Correct answer is: Updating nodes in a random order, one at a time
Q.89 Which of the following best describes the purpose of "model reduction" in systems biology?
Eliminate all reactions from the network
Simplify a large model while preserving key dynamical features
Increase the number of parameters to improve fit
Convert a stochastic model into a deterministic one
Explanation - Model reduction reduces computational complexity, making analysis tractable without losing essential behavior.
Correct answer is: Simplify a large model while preserving key dynamical features
Q.90 In a reaction network, the "thermodynamic feasibility" of a reaction is assessed by:
The sign of its rate constant
The Gibbs free energy change (ΔG) being negative under physiological conditions
The number of substrates involved
The length of the protein coding sequence
Explanation - A negative ΔG indicates that the reaction can proceed spontaneously in the forward direction.
Correct answer is: The Gibbs free energy change (ΔG) being negative under physiological conditions
Q.91 Which of the following is a typical output of a community‑detection algorithm applied to a gene regulatory network?
A list of kinetic parameters
A partition of genes into modules with dense intra‑module connections
A time‑course of gene expression
A phylogenetic tree
Explanation - Community detection groups nodes that interact more frequently with each other than with the rest of the network.
Correct answer is: A partition of genes into modules with dense intra‑module connections
Q.92 When using a "Gaussian Process" to emulate a computationally expensive biochemical model, the main advantage is:
Exact analytical solutions
Reduced computational cost by providing a fast surrogate model with uncertainty quantification
Elimination of all model parameters
Ability to simulate stochasticity directly
Explanation - Gaussian Processes learn from a limited set of simulations and can predict outcomes with confidence intervals, speeding up analyses.
Correct answer is: Reduced computational cost by providing a fast surrogate model with uncertainty quantification
Q.93 In a metabolic network, a "branch point" is a metabolite that:
Is only produced, never consumed
Is consumed by multiple downstream reactions
Has zero degree
Is a dead‑end metabolite
Explanation - Branch points distribute flux into different pathways, influencing metabolic control and regulation.
Correct answer is: Is consumed by multiple downstream reactions
Q.94 Which of the following best captures the purpose of "ensemble modeling" in systems biology?
Creating a single deterministic model
Generating a collection of models with varied parameters to capture uncertainty
Measuring protein concentrations directly
Designing a synthetic promoter
Explanation - Ensemble approaches explore a range of plausible parameter sets, providing robust predictions despite limited data.
Correct answer is: Generating a collection of models with varied parameters to capture uncertainty
Q.95 In a Boolean model of a toggle switch consisting of two mutually repressing genes (A and B), which state(s) are stable attractors?
Both A and B ON
Both A and B OFF
A ON / B OFF and A OFF / B ON
All four possible combinations
Explanation - Mutual repression yields two bistable states where one gene dominates while the other is silenced.
Correct answer is: A ON / B OFF and A OFF / B ON
Q.96 Which experimental technique provides quantitative data suitable for parameterizing kinetic models of signaling pathways?
Western blot (semi‑quantitative)
Flow cytometry (single‑cell fluorescence intensity)
PCR (DNA amplification)
Gel electrophoresis
Explanation - Flow cytometry yields quantitative, high‑throughput measurements of protein levels across many cells, enabling kinetic inference.
Correct answer is: Flow cytometry (single‑cell fluorescence intensity)
Q.97 When a network model exhibits "multistability," this implies that:
The system can only settle into one unique steady state
The system can have multiple stable steady states under the same parameter set
The system oscillates forever
The model cannot be simulated numerically
Explanation - Multistability is a hallmark of decision‑making processes, allowing cells to adopt distinct phenotypes.
Correct answer is: The system can have multiple stable steady states under the same parameter set
Q.98 Which of the following is a standard metric for assessing the goodness‑of‑fit between simulated and experimental time‑course data?
Root‑mean‑square error (RMSE)
Clustering coefficient
Network diameter
Jaccard similarity
Explanation - RMSE quantifies the average magnitude of the residuals between predicted and observed values.
Correct answer is: Root‑mean‑square error (RMSE)
Q.99 In a synthetic gene circuit, the addition of a "degradation tag" (e.g., ssrA) primarily affects:
Transcription initiation rate
mRNA splicing efficiency
Protein half‑life
DNA replication speed
Explanation - Degradation tags target proteins for rapid proteolysis, enabling tighter dynamic control of circuit behavior.
Correct answer is: Protein half‑life
Q.100 Which of the following statements about "scale‑invariant" network properties is correct?
They depend on absolute network size
They remain unchanged under network rescaling, such as renormalization of node degrees
They only apply to fully connected graphs
They require the network to be bipartite
Explanation - Scale‑invariant properties, like power‑law degree distributions, look similar across different magnitudes of the network.
Correct answer is: They remain unchanged under network rescaling, such as renormalization of node degrees