Malay Bhattacharyya

Indian Institute of Engineering Science and Technology, Shibpur | IIEST · Department of Information Technology

Background Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. Result We have studied gene co-expression network obtained f...

MicroRNAs (miRNAs) are small non-coding RNAs that help in post-transcriptional gene silencing. These endogenous RNAs develop a post-transcriptional gene-regulatory network by binding to complementary sequences of target mRNAs and essentially degrade them. Cancer is a class of diseases that is caused by the uncontrolled cell growth, thereby resultin...

Studying networks is promising for diverse applications. We are often interested in exploring significant substructures in different types of real-life networks. Finding cliques, which denote a complete subgraph of a graph, is one such important problem in network analysis. Interestingly, many real-life networks often contain a significant number o...

MicroRNAs (miRNAs) are a kind of short non-coding RNAs, of about 22 nucleotides in length, which modulate and sometimes degrade the target mRNAs thereby regulating a number of cellular functions. Recent research in this area establishes the involvement of miRNAs in various disease progressions, including certain types of cancer development. Further...

Parkinson's Disease (PD) is a progressive neurologic disorder that affects movement and balance. Recent studies have revealed the importance of microRNA (miR) in PD. However, the detailed role of miR and its regulation by Transcription Factor (TF) remain unexplored. In this work for the first time we have studied TF-miR-mRNA regulatory network as w...

Clustering algorithms are occasionally used on biological datasets to obtain statistically coherent groups of biomolecules. The biological coherence of such a group (e.g., a gene or protein cluster) might have different interpretations. Functional similarity is the most widely used form of biological coherence of a cluster. We often require to assi...

Predicting the transcription start sites (TSSs) of microRNAs (miRNAs) is important for understanding how these small RNA molecules, known to regulate translation and stability of protein-coding genes, are regulated themselves. Previous approaches are primarily based on genetic features, trained on TSSs of protein-coding genes, and have low predicti...

Details about the collection of brain-specific miRNAs, preparation of miRNA TSS dataset, and the construction of the methylation-based feature score. (PDF)

MicroRNAs (miRNAs) are a class of small noncoding RNAs that are known to have critical functions across various biological processes. Simultaneous activities of multiple miRNAs can be monitored from their expression profiles under various conditions. We often build up co-expression networks from such profiles. Unfortunately, due to the change of ex...

MicroRNAs (miRNAs) are a class of short non-coding RNAs, which show tissue-specific regulatory activity on genes. Expression profiling of miRNAs is an important step for understanding the pathology of Alzheimer's disease (AD), a neurodegenerative disorder originating in the brain. Recent studies highlight that miRNAs enriched in gray matter (GM) an...

In this work, we model the problem of mining quasi-bicliques from weighted viral-host protein-protein interaction network as a biclustering problem for identifying strong interaction modules. In this regard, a multiobjective genetic algorithm-based biclustering technique is proposed that simultaneously optimizes three objective functions to obtain...

MicroRNAs (miRNAs) are small endogenous non-coding RNAs of about 22 nt in length that take crucial roles in many biological processes. These short RNAs regulate the expression of mRNAs by binding to their 3'-UTRs or by translational repression. Many of the current studies focus on how mature miRNAs regulate mRNAs, however, very limited knowledge is...

Background / Purpose: Multiple expression analyses over different tumor types may lead to diverse types of relationships between microRNAs (miRNAs). We integrate knowledge from multiple co-expression networks using a supervised learning approach for obtaining robust functional relationships between miRNAs. Main conclusion: This type of approac...

A graph G=(V,E) is γ-quasi-complete (γ∈[0,1]) if every vertex in G is connected to at least γ·(|V|-1) other vertices. In this paper, we establish some relationships between the girth and the quasi-completeness of a graph. We also derive an upper bound 1 21 + r γ+1 41 + r γ 2 +2|E| γ-r|V| γ for the largest order γ-quasi-complete subgraph in a graph...

We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein...

Simultaneous overexpression or underexpression of multiple genes, used in various forms as probes in the high-throughput microarray experiments, facilitates the identification of their underlying functional proximity. This kind of functional associativity (or conversely the separability) between the genes can be represented proficiently using co-ex...

A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem of finding quasicliques that are almost complete subgraphs of a graph. In sparse and very lar...

Our culture is in the process of renegotiating what it thinks computation and computer really mean.

The diagnosis, prognosis and therapeutics of various kinds of cancers are challenging domains of research. Current landmark of cancer research at the molecular level mainly focuses on the regulation of genes for studying cancer pathways. Recent investigations highlight that there is a significant association of a class of short RNAs in the progress...

MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, eve...

MicroRNAs (miRNAs) are non-coding, short (21-23nt) regulators of protein-coding genes that are generally transcribed first into primary miRNA (pri-miR), followed by the generation of precursor miRNA (pre-miR). This finally leads to the production of the mature miRNA. A large amount of information is available on the pre- and mature miRNAs. However,...

Two genes are said to be coexpressed if their expression levels have a similar spatial or temporal pattern. Ever since the profiling of gene microarrays has been in progress, computational modeling of coexpression has acquired a major focus. As a result, several similarity/distance measures have evolved over time to quantify coexpression similarity...

Can game theory 'prove' that online robbery is irrational?

Very little is known to date about the regulation protocol between transcription factors (TFs), genes and microRNAs (miRNAs) associated with diseases in various organisms. In this paper, we focus on finding the activity of miRNAs through the HIV-1 regulatory pathway in humans at the systems level. For this, we integrate and study the characteristic...

Introduction Topology of PPI Networks Literature Survey Problem Discussion Theoretical Analysis Algorithmic Approach Empirical Analysis Conclusions Acknowledgment References

Some of the recent investigations in systems biology have revealed the existence of a complex regulatory network between genes, microRNAs (miRNAs) and transcription factors (TFs). In this paper, we focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. A putative TF of an miRNA is con...

The maximum clique problem is an important problem in graph theory. Many real-life problems are still being mapped into this problem for their effective solutions. A natural extension of this problem that has emerged very recently in many real-life networks, is its fuzzification. The problem of finding the maximum fuzzy clique has been formalized o...

A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem of finding quasicliques that are almost complete subgraphs of a graph. In sparse and very lar...

MicroRNAs (miRNAs) are small, non-coding RNAs that participate in the post-transcriptional regulation of messenger RNAs (mRNAs) by degrading or inhibiting translation. Some of the topical studies strongly suggest that the disorders in the normal activities of miRNAs might cause many diseases. Generally, such studies concern patient-specific express...

Courier problems comprise a set of recently proposed combinatorial optimization problems, which are inspired by some novel requirements in railway wagon scheduling. In these problems, scheduling strategies of some mobile couriers are considered. These mobile couriers initially reside at some fixed location. They are assigned some duties of commodit...

Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with tissues taken from similar organs of dif...

Simultaneous overexpression or underexpression of mul- tiple genes, used in various forms as probes in the high- throughput microarray experiments, facilitates the ident ifi- cation of their underlying functional proximity. This kind of functional associativity (or conversely the separabili ty) between the genes can be represented proficiently usin...

Despite the existence of a number of variations of genetic algorithms for the traveling salesman problem in literature, no efforts have been made to the best of our knowledge to characterize their performance. This paper presents a detailed comparative study on some of the solution methods for the traveling salesman problem using genetic algorithms...

An important problem of knowledge discovery that has recently evolved in various reallife networks is identifying the largest set of vertices that are functionally associated. The topology of many real-life networks shows scale-freeness, where the vertices of the underlying graph follow a power-law degree distribution. Moreover, the graphs correspo...

In this article an inherent characteristics of the non-prime numbers of recursively holding the divisibility property is studied. The recursive property applies to any number system by virtue drawing some necessary conclusions. 2000 Mathematics Subject Classification: 11A51, 11K16.

The maximum clique problem, into which many problems have been mapped effectively, is of great importance in graph theory. A natural extension to this problem, emerging very recently in many real-life networks, is its fuzzification. The problem of finding the maximum clique in a fuzzy graph has been addressed in this paper. It has been shown here,...

A new set of NP problems defined as Courier Problems that is motivated from the requirements in railway wagon scheduling is proposed. The general version includes many mobile couriers. The simplest version of this will consider a single courier. An algorithm to transform the single courier problem into a traveling salesman problem is presented.

In this paper we propose a simplified design and visualization approach. It can be used to implement Boolean functions given in the form of minterms primarily using 2-input universal NAND gates. Then it can be extended easily for NAND gates with any number of inputs. We name the novel approach μ-graph method. This basically presents a compact data...

We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein...