Subhadip Basu

• Ph.D.
• Professor (Full) at Jadavpur University

Protein-protein interactions (PPIs) are fundamental to the functioning of biological systems, regulating a myriad of cellular processes. Therefore, accurate prediction of PPIs is crucial for disease diagnosis and the development of novel therapeutic interventions. Computational techniques streamline the forecasting of PPIs and prove to be more cost...

Proteins interact with other proteins and bio-molecules to form a complex and execute key biological functions in a living organism, and respond to several environmental signals. Designing efficient predictive models for protein complexes is a challenging task with limited coverage in the contemporary literature. With this motivation, we have devel...

Monkeypox (Mpox), a zoonotic illness triggered by the monkeypox virus (MPXV), poses a significant threat since it may be transmitted and has no cure. This work introduces a computational method to predict Protein–Protein Interactions (PPIs) during MPXV infection. The objective is to discover prospective drug targets and repurpose current potential...

Proteins are considered indispensable for facilitating an organism’s viability, reproductive capabilities, and other fundamental physiological functions. Conventional biological assays are characterized by prolonged duration, extensive labor requirements, and financial expenses in order to identify essential proteins. Therefore, it is widely accept...

The traditional method of drug reuse or repurposing has significantly contributed to the identification of new antiviral compounds and therapeutic targets, enabling rapid response to developing infectious illnesses. This article presents an overview of how modern computational methods are used in drug repurposing for the treatment of viral infectio...

Large-scale protein-protein interaction (PPI) network of an organism provides key insights into its cellular and molecular functionalities, signaling pathways and underlying disease mechanisms. For any organism, the total unexplored protein interactions significantly outnumbers all known positive and negative interactions. For Human, all known PPI...

Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development, and chemical-induced cell death (Elmore in Toxicol Pathol 35:495–516, 20). Apoptosis proteins are strongly related to many diseases like neurodegene...

The main focus of this paper is to estimate the class of 3D point cloud gestures, using some statistical descriptors. To check the performance of proposed descriptors, we have evaluate it on a public 3D hand gesture dataset. We used several classification techniques with the different feature combinations and find that the random forest classifier...

Audio and video conferencing apps like Google meet, Zoom, Mobile call conference are becoming more and more popular. Conferencing apps are used not only by professionals for remote work, but also for keeping social relations. Present situation demands understanding of these platforms in details and extract useful features to recognize them. Identif...

Biclustering of biologically meaningful binary information is essential in many applications related to drug discovery, like protein–protein interactions and gene expressions. However, for robust performance in recently emerging large health datasets, it is important for new biclustering algorithms to be scalable and fast. We present a rapid unsupe...

This paper presents an unique audio database, we named it Multivariate Audio Database (MAuD), where audio data has been collected in real life scenarios. MAuD contains 229 audio files, each of duration approx 5 minutes, collected across different conferencing apps, spoken languages, background noises and discussion topics. Various audio conferencin...

Large scale protein-protein interaction (PPI) network of an organism provides key insights into its cellular and molecular functionalities, signaling pathways and underlying disease mechanisms. For any organism the total number of unexplored protein interactions significantly outnumbers all known positive and negative interactions. For Human, all k...

SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that...

This paper describes the effect of analysis window functions on the performance of Mel Frequency Cepstral Coefficient (MFCC) based speaker recognition (SR). The MFCCs of speech signal are extracted from the fixed length frames using Short Time Fourier Analysis (STFA) technique where an appropriate analysis window function is required to extract fra...

Recent research has highlighted that a large section of druggable protein targets in the Human interactome remains unexplored for various diseases. It might lead to the drug repurposing study and help in the in-silico prediction of new drug-human protein target interactions. The same applies to the current pandemic of COVID-19 disease in global hea...

Protein function prediction is gradually emerging as an essential field in biological and computational studies. Though the latter has clinched a significant footprint, it has been observed that the application of computational information gathered from multiple sources has more significant influence than the one derived from a single source. Consi...

Proteins are vital for the significant cellular activities of living organisms. However, not all of them are essential. Identifying essential proteins through different biological experiments is relatively more laborious and time-consuming than the computational approaches used in recent times. However, practical implementation of conventional scie...

Understanding multi-lingual texts in any digital image calls for identifying the corresponding languages of the localized texts. India houses a multi-lingual ambience which necessitates the pursuit of an efficient model that is robust against various complexities and successfully identifies the language of Indic texts. This paper presents a deep le...

Protein–protein interaction network (PPIN) plays a major role in information processing and decision making in cells. The PPIN works as a skeleton for cell signaling and functionality. Understanding the flow of information in a cell can enhance our understanding of functional outcomes and flow of signals. To utilize the whole potential of PPIN, we...

Vision-based hand gesture recognition is perhaps the most widely used technique for human–computer interaction technology with special application toward sign languages used by differently abled people. Perhaps the most important step in such a gesture recognition system is feature extraction. In this paper, we use a novel fingertip detection mecha...

Detection and language identification of multi-lingual texts in natural scene images (NSI) and born-digital images (BDI) are popular research problems in the domain of information retrieval. Several methods addressing these problems have been evaluated over the years upon mostly NSI based standard datasets. However, datasets highlighting bi/triling...

Deaf and hearing-impaired persons communicate by means of signs and gestures. In course of time, this form of communication has evolved as natural languages with its own grammars and lexicons. Automatic hand gesture recognition is an important task in development of human computer interaction system for deaf mute community. In this paper, we report...

We develop a dynamic hand gesture recognition system on the gestures of seven days of the week in Indian Sign Language. We use Kinect V2 sensor, which is a low-cost RGB-D camera, to collect videos of gestures of two subjects and then perform key frame extraction, cropping of static regions, background subtraction, feature extraction and classificat...

Reliable hand gesture recognition is extremely relevant for automatic interpretation of sign languages used by people with hearing and speech disabilities. In this work, we present (i) new benchmark datasets of depth-sensor based, multi-oriented, isolated and static hand gestures of numerals and alphabets following the conventions of American Sign...

Proteins are not only the fundamental components of all living cells but are also considered to be the most abundant kind of molecules available in human body. Few among these proteins may be classified as essential proteins. An essential protein is a member of a densely connected or a highly interactive protein–protein interaction network. The ide...

Novel coronavirus (SARS-CoV2) replicates the host cell's genome by interacting with the host proteins. Due to this fact, the identification of virus and host protein-protein interactions could be beneficial in understanding the disease transmission behavior of the virus as well as in potential COVID-19 drug identification. International Committee o...

Three-dimensional segmentation and analysis of dendritic spine morphology involve two major challenges: 1) how to segment individual spines from the dendrites and 2) how to quantitatively assess the morphology of individual spines. To address these two issues, we developed software called 3dSpAn (3-dimensional Spine Analysis), based on implementing...

An array of features and methods are being developed over the past six decades for Speaker Identification (SI) and Speaker Verification (SV), jointly known as Speaker Recognition(SR). Mel Frequency Cepstral Coefficients (MFCC) is generally used as feature vectors in most of the cases because it gives higher accuracy compared to other features. The...

S-palmitoylation is a reversible covalent post-translational modification of cysteine thiol side chain by palmitic acid. S-palmitoylation plays a critical role in a variety of biological processes and is engaged in several human diseases. Therefore, identifying specific sites of this modification is crucial for understanding their functional conseq...

The entire world is witnessing the coronavirus pandemic (COVID-19), caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 promotes fatal chronic respiratory disease followed by multiple organ failure, ultimately putting an end to human life. International Committee...

With the gradual increase in the COVID-19 mortality rate, there is an urgent need for an effective drug/vaccine. Several drugs like Remdesivir, Azithromycin, Favirapir, Ritonavir, Darunavir, etc., are put under evaluation in more than 300 clinical trials to treat COVID-19. On the other hand, several vaccines like Pfizer-BioNTech, Moderna, Johnson &...

Since the past two decades, detecting text regions in complex natural images has emerged as a problem of great interest for the research fraternity. This is because these regions of interest serve as source of information that can be utilized for various purposes. However, these regions may contain texts in multiple languages. Hence, identifying th...

Although sex differences in the brain are prevalent, the knowledge about mechanisms underlying sex-related effects on normal and pathological brain functioning is rather poor. It is known that female and male brains differ in size and connectivity. Moreover, those differences are related to neuronal morphology, synaptic plasticity, and molecular si...

Numerous brain diseases are associated with abnormalities in morphology and density of dendritic spines, small membranous protrusions whose structural geometry correlates with the strength of synaptic connections. Thus, the quantitative analysis of dendritic spines remodeling in microscopic images is one of the key elements towards understanding me...

Background Bioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides access to an ever-increasing amount of high-quality images, there arises a need for their analysis in an automated, unbiased, and simp...

Scene text analysis involves detecting and processing text/words in natural scene images for serving various purposes. This problem domain intrigues the research fraternity due to challenges like dealing with noise, blur, heterogeneous intensity variation, etc. The ultimate goal is making detected scene word recognizable by any standard Optical Cha...

Recent years have witnessed an exponential surge in interest to explore the domain of scene text detection as well as analysis in natural scene images. However, owing to the complexities arising due to various factors, it can be said that existing techniques may fail at times while attempting to detect text components. This paper presents a system...

Recognition of unconstrained handwritten word images is an interesting research problem which gets more challenging when lexicon-free words are considered. Prerequisite for developing a lexicon-free handwritten word recognition technique is the segmentation of a word image into its constituent character set. Therefore, a competent character segment...

Detecting texts from natural scene images is currently becoming a popular trend in the field of information retrieval. Researchers find it interesting due to the challenges faced while processing an image. In this paper, a relatively simple but effective approach is proposed where bright texts on a dark background and dark texts on a bright backgro...

Vessel tree segmentation from CT scan angiogram images of the human brain is a challenging task. The complex geometry, interconnections, and fusion with soft tissues and bones make the segmentation process harder. The segmented cerebrovasculature plays a major role in the fast analysis of vascular geometry leading to an effective diagnosis of the d...

This book gathers outstanding research papers presented at the International Conference on Frontiers in Computing and Systems (COMSYS 2020), held on January 13–15, 2019 at Jalpaiguri Government Engineering College, West Bengal, India and jointly organized by the Department of Computer Science & Engineering and Department of Electronics & Communicat...

This book contains the latest research work presented at the International Conference on Computing and Communication Systems (I3CS 2020) held at North-Eastern Hill University (NEHU), Shillong, India. The book presents original research results, new ideas and practical development experiences which concentrate on both theory and practices. It includ...

Drug assistance to various harmful diseases is still not discoverable since functions of proteins responsible for the cause of these diseases are still unannotated. By the use of high throughput techniques, huge amount of protein sequence can be annotated rapidly using computational technique to formulate biological hypothesis rather than using cos...

Gait is a behavioural biometric which sometimes changes due to diseases but it is still a strong identification metric that is widely used in forensic works, state biometric preserve sectors, and medical laboratories. Gait analysis sometimes helps to identify person’s present mental state which reflects on physiological therapy for improved biologi...

The development of modern high throughput sequencing techniques has resulted in an exponential growth in meta-genomic sequence accumulation that could greatly enhance large-scale functional annotation. Processing of these large and redundant sequences has become a major challenge for researchers. Clustering by similarity is one of the major steps t...

Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of proteins that plays a crucial role in PPI prediction. Several machine learning approaches have been applied to...

Protein function prediction becomes more challenging to the research community as it can be characterized as multi-label, hierarchical multi-class classification problem. This problem becomes complicated in nature as it suffers from several hardships which can be mentioned as: 1) Multiple functional groups with different confidence degree can be in...

Background: Bioimaging techniques offer a robust tool for studying molec- ular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high resolution 3D microscopy provides access to an ever-increasing amount of high quality images, there arises a need for their analysis in an automated, unbiased and si...

Text detection in natural scene images is an interesting problem in the field of information retrieval. Several methods have been proposed over the past few decades for scene text detection. However, the robustness and efficiency of these methods are downgraded due to high sensitivity towards various complexities of an image. Also, in multi-lingual...

Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our...

Scene text analysis is a field of research that poses challenges to researchers owing to the background complexities, image quality, text orientation, text size, etc. The problem gets more complex when the image contains multi-lingual texts. Most scene text detection techniques approach the problem as either a feature-based or deep learning-based p...

COVID-19 has turned out to be a global pandemic within a very short period of time since its first origin in China in December 2019. With the gradual increase in the mortality rate all over the world, there is an urgent need for an effectual drug. Though no clinically approved vaccine or drug is available until now but scientists are trying hard to...

COVID-19 has created a global pandemic with high morbidity and mortality in 2020. Novel coronavirus (nCoV), also known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), is responsible for this deadly disease. International Committee on Taxonomy of Viruses (ICTV) has declared that nCoV is highly genetically similar to SARS-CoV epidemic...

The entire world has recently witnessed the commencement of coronavirus disease 19 (COVID-19) pandemic. It is caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It has exploited human vulnerabilities to coronavirus outbreak. SARS-CoV-2 promotes fatal chronic respiratory dis...

The dendritic spines play a crucial role in learning and memory processes, epileptogenesis, drug addiction, and postinjury recovery. The shape of the dendritic spine is a morphological key to understand learning and memory process. The classification of the dendritic spines is based on their shapes but the major questions are how the shapes changes...

Speaker Identification(SI) has numerous applications in real world. Traditional classifiers like Gaussian Mixture Models (GMM), Support Vector Machine (SVM), and Hidden Markov Models (HMM) were used earlier for SI. Features like Mel Frequency Cepstral Coefficient (MFCC), and Gammatone Frequency Cepstral Coefficients (GFCC) need to be generated firs...

Activity-dependent remodeling of excitatory connections underpins memory formation in the brain. Serotonin receptors are known to contribute to such remodeling, yet the underlying molecular machinery remains poorly understood. Here, we employ high-resolution time-lapse FRET imaging in neuroblastoma cells and neuronal dendrites to establish that act...

Among many of the fastest growing research fields, sign language recognition is one of the top. Deaf and dumb community uses sign language to express their ideas or views. Sign Language is a methodical coded language where meanings are assigned to every gestures. Many techniques have been developed with the advancement of science and technology to...

Speaker Identification(SI) is the task of identifying a speaker from his voice (audio signal) by comparing against a set of known voices. Speaker Identification becomes challenging when voices were recorded in different environment, using various devices. Traditional classifiers like Gaussian Mixture Models (GMM), Support Vector Machine (SVM), Hidd...

Background: 3D segmentation and analysis of dendritic spines involve two major challenges: 1) how to segment individual spines in 3D from the dendrites and 2) how to quantitatively assess the 3D morphology of individual spines. We developed software named 3dSpAn to address these two issues by implementing a 3D multiscale opening algorithm in shared...

Network analysis is a powerful tool for modelling biological systems. We propose a new approach that integrates the genomic interaction data at population level with the proteomic interaction data. In our approach we use chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data from human genome to construct a set of genomic inter...

Due to the cursive nature, segmentation of handwritten Bangla words into characters and also recognition of the same sometimes become a very challenging problem to the researchers. Presence of comparatively large character set along with modifiers, ascendants, descendants, and compound characters makes the segmentation task more complex. As holisti...

The detailed architectural examination of the neuronal nuclei in any brain region, using confocal microscopy, requires quantification of fluorescent signals in three-dimensional stacks of confocal images. An essential prerequisite to any quantification is the segmentation of the nuclei which are typically tightly packed in the tissue, the extreme b...

Localization of text from camera captured images with complex background is now-a-days a growing demand of modern IT enable service. Most of the current text localization techniques are sensitive to text features like color, size, style and also to the background clutter. Among all the methods proposed in different literatures, Stroke Filter is muc...

Protein is one of the most essential components of a living cell. Any living organism requires a modest amount of protein to function well. With the advancement in science and technology, researchers have identified numerous protein sequences, while the functions of most of them still remains unannotated. So a considerable amount of research works...

Computational prediction of functional annotation of proteins is an uphill task. There is an ever increasing gap between functional characterization of protein sequences and deluge of protein sequences generated by large-scale sequencing projects. The dynamic nature of protein interactions is frequently observed which is mostly influenced by any ne...

The problem of scene text detection has been quite intriguing for the research fraternity due to wide scope of applications. In recent times, some robust technique like Maximally Stable Extremal Region (MSER) has been developed and have gained immense popularity in detection and localization of text components in the wild. However, the problem of a...

Analysis of pulmonary artery or vein tree has utmost importance in the study and clinical diagnosis of Chronic Obstructive Pulmonary Diseases (COPD). Due to difficulty in acquiring real life patient data and highly complex structure of artery/vein tree, design of imitated/approximate digital pulmonary phantoms for experimental purposes is an active...

Proteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale for a variety of species. The challenging problem is to massively determine the functions of proteins that are yet not characterize...

Similarity between sequence evolution and structural dynamics of proteins are of utmost importance in understanding the cellular and molecular mechanism in living organisms. Proteins those are similar in structure depict similar func-tionality. Amino acid composition based trigram representation becomes one of the key features to identify structura...

Ketamine is an N-methyl-D-aspartate receptor antagonist that has gained wide attention as a potent antidepressant. It has also been recently reported to have prophylactic effects in animal models of depression and anxiety. Alterations of neuroplasticity in different brain regions; such as the hippocampus; prefrontal cortex; and amygdala; are a hall...

The main purpose of scene text recognition is to detect texts in a given image. The problem of text detection and recognition in such images has gained great attention in recent years due to rising demand of several applications like visual based applications, multimedia and content-based retrieval. Due to low accuracies of existing scene text dete...

Categorizing spines into four subpopulations, stubby, mushroom, thin, or filopodia, is one of the common approaches in morphological analysis. Most cellular models describing synaptic plasticity, long-term potentiation (LTP), and long-term depression associate synaptic strength with either spine enlargement or spine shrinkage. Unfortunately, althou...

The biometric recognition of human through the speech signal is known as automatic speaker recognition (ASR) or voice biometric recognition. Plenty of acoustic features have been used in ASR so far, but among them Mel-frequency cepstral coefficients (MFCCs) and Gammatone frequency cepstral coefficients (GFCCs) are popularly used. To make ASR langua...

Detecting and localizing multi-lingual text regions in natural scene images is a challenging task due to variation in texture properties of the image and geometric properties of multi-lingual text. In this work, we explore the possibility of identifying and localizing text regions based on their degree of homogeneity compared to the non-text region...

Identification of script from multi-script text components of camera-captured images is an emerging research field. Here, challenges are mainly twofold: (1) typical challenges of camera-captured images like blur, uneven illumination, complex background, etc., and (2) challenges related to shape, size, and orientation of the texts written in differe...

Essential protein identification is an important factor to inspect the mechanisms of disease progression and to identify drug targets. With the advancement of high throughput genome sequencing projects, a bulk of protein data is available where the analysis of interaction pattern, functional annotation and characterization are necessary for detecti...

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Protein Function Prediction from Protein-Protein Interaction Network (PPIN) and physico-chemical features using the Gene Ontology (GO) classification are indeed very useful for assigning biological or biochemical functions to a protein. They also lead to the identification of those significant proteins which are responsible for the generation of va...

Generation of digital phantoms specific to the patients’ carotid vasculature is a complicated and challenging task because of its complex geometrical structure and interconnections. Such digital phantoms are extremely useful in quick analysis of the vascular geometry and modelling blood flows in the cerebrovasculature. All these analyses lead to ef...

We present a human protein cluster analysis by combining: 1) n-gram based amino acid frequency features, 2) optimal feature selection, 3) hierarchical clustering and 4) advanced partitioning techniques. Our method qualitatively and quantitatively groups proteins with increasing sequence similarity into similar clusters by calculating the frequency...