Big Data and Biological Networks · End Term · Jan 2026 · AN

In a biological network where nodes represent proteins and edges represent physical interactions, a specific node

has a very high betweenness centrality but a relatively low degree centrality. What is the most likely biological role of this protein?

You are performing motif identification in a large gene regulatory network and are looking for a specific regulatory circuit (shown in the reference image). Which of the following visual layouts of newly discovered genetic circuits is isomorphic to your target motif, i.e., it has the exact same biological connectivity regardless of how the genes are physically arranged on the page?

Which of the following statements describe synthetic lethality ?

After counting the motif

in

randomized networks, you plot a distribution of the counts. If the count in the real network (

) falls at the

percentile of this distribution, what does this indicate?

During DNA replication, what is the main role of helicase?

According to the central dogma of molecular biology, genetic information flows from:

In eukaryotic cells, which enzyme synthesizes RNA during transcription?

A researcher studies changes in RNA levels between tumor and normal cells to find dysregulated genes. Which -omics approach fits best?

Consider the following statements: Assertion (A): The Eulerian Path algorithm is preferred over the Hamiltonian Path algorithm for the genome assembly problem. Reason (R): A Hamiltonian Path passes through all the nodes of a graph. Now, which of the following options is true:

Which of the following is true about genome assembly?

What is the goal of the pooling function

in graph pooling?

What is the primary purpose of introducing a normalization step in a neural network?

The average degree (regardless of the direction) of the 4-mer overlap graph constructed from “GAATTCAGTTC” is (upto two decimal points)

The best local alignment score for the sequences "GTACTG" and "TAGTCTG" with the scoring scheme, **matches** = +2, **mismatches**= -1, and a constant gap penalty of -10, is

Given two node embeddings

and

, The

−norm

is

In the DeepWalk model using a standard Softmax function, if the graph

has 500 nodes and 1500 edges, the number of "dot products" that must be computed to evaluate the similarity

for a single node pair is

Which of the following network representations can be used to determine whether a metabolite can be converted into another metabolite through a sequence of reactions?

Which information is lost or distorted after projecting a Drug-Target bipartite network into a Drug- Drug network?

Which of the following statements about NetworkX graph objects are correct? (Select all that apply)

Gene expression regulation in eukaryotes can occur at:

Key advantages of NGS over Sanger sequencing include:

What are the limitations of microarrays compared to RNA-seq? Select all that apply.

Which enzymes are essential for completing lagging-strand synthesis?

Which statements about tRNA are correct?

Which of the following are true for graph filters:

Consider the following reaction system and answer the given sub-questions:

The number of edges present in the substrate graph, reaction graph and bipartite graph constructed from this system will be:

Consider the following reaction system and answer the given sub-questions:

Which node(s) in the substrate graph have the highest out-degree?

The number of unique 2-mers can be generated from the sequence “GTACTATGCA" is

Consider the following graph:

What will be the adjacency matrix

?

Choose the most appropriate option:

is the feature matrix and

is the identity matrix

Perform a single-step filtering using the Graph Convolutional Network filter for the following graph: The feature vectors are:

,

,

,

,

The parameter matrix (

) is:

A two-layer neural network with 2 features,

,

is defined below:

Given the following numerical values:

Compute the values of

and

You are constructing an Erdős-Rényi random network,

, to serve as a null model for a protein-protein interaction study. The network contains exactly

nodes. Based on the connectivity of your experimental data, you require the expected total number of edges (

) in this random network to be 500. Calculate the required edge probability

for this model.

Match the specific network model or concept in Column A with its corresponding definition/application in Column B. (Answer should be in this format without space: "1-E,2-F,3-A,...")

The following DNA sequences are given: Strand I: 5′ → 3′ : ATGCCGATGGCG Strand II: 3′ → 5′ : TACGGCTACCGC Based on the above data, answer the given subquestions.

Identify the template strand and briefly explain how RNA polymerase “knows” which strand to use. **NOTE:** Your answer should not exceed 50 words.

The following DNA sequences are given: Strand I: 5′ → 3′ : ATGCCGATGGCG Strand II: 3′ → 5′ : TACGGCTACCGC Based on the above data, answer the given subquestions.

Write the RNA sequence synthesised and indicate its direction (5′ → 3′). **NOTE:** Your answer should not exceed 20 words.

The following DNA sequences are given: Strand I: 5′ → 3′ : ATGCCGATGGCG Strand II: 3′ → 5′ : TACGGCTACCGC Based on the above data, answer the given subquestions.

State the first amino acid encoded by this RNA and explain why translation starts at that position. **NOTE:** Your answer should not exceed 100 words.

Based on the above data, answer the given subquestions.

Write the corresponding mRNA sequence. **NOTE:** Your answer should not exceed 20 words.

Based on the above data, answer the given subquestions.

Identify the start codon and the stop codon(s) present in the mRNA. **NOTE:** Your answer should not exceed 20 words.

Based on the above data, answer the given subquestions.

Write the amino acid sequence coded by this nucleotide sequence. **NOTE:** Your answer should not exceed 50 words.