Gluconeogenesis unraveled: A proteomic Odyssey with machine learning.

The metabolic pathway known as gluconeogenesis, which produces glucose from non-carbohydrate substrates, is essential for maintaining balanced blood sugar levels while fasting. It's extremely important to anticipate gluconeogenesis rates accurately to recognize metabolic disorders and create efficient treatment strategies. The implementation of deep learning and machine learning methods to forecast complex biological processes has been gaining popularity in recent years.

Fermatean fuzzy Linguistic term set based on linguistic scale function with Dombi aggregation operator and their application to multi criteria group decision -making problem.

The selection of an industrial location is a challenging multiple-criteria decision-making (MCDM) problem that depends on taking a variety of locations as well as incompatible and inconsistent criteria. This paper proposed a comprehensive framework for the strategic selection of industrial locations, considering both quantitative and qualitative aspects. Decision-makers (DMs) have to deal with ambiguous information throughout this process due to a complex decision environment or their insufficient knowledge.

DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features.

In the domain of genome annotation, the identification of DNA-binding protein is one of the crucial challenges. DNA is considered a blueprint for the cell. It contained all necessary information for building and maintaining the trait of an organism.

iAcety-SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest.

Acetylation is the most important post-translation modification (PTM) in eukaryotes; it has manifold effects on the level of protein that transform an acetyl group from an acetyl coenzyme to a specific site on a polypeptide chain. Acetylation sites play many important roles, including regulating membrane protein functions and strongly affecting the membrane interaction of proteins and membrane remodeling. Because of these properties, its correct identification is essential to understand its mechanism in biological systems.

iTAGPred: A Two-Level Prediction Model for Identification of Angiogenesis and Tumor Angiogenesis Biomarkers.

A crucial biological process called angiogenesis plays a vital role in migration, growth, and wound healing of endothelial cells and other processes that are controlled by chemical signals. Angiogenesis is the process that controls the growth of blood vessels within tissues while angiogenesis proteins play a significant role in the proper working of this process. The balancing of these signals is necessary for the proper working of angiogenesis.

The βTubulin, Rad50-ATPase and enolase cis-regulatory regions mediate male germline expression in Tribolium castaneum.

Genetics-based pest management processes, including the sterile insect technique, are an effective method for the control of some pest insects. However, current SIT methods are not directly transferable to many important pest insect species due to the lack of genetic sexing strains. Genome editing is revolutionizing the way we conduct genetics in insects, including in Tribolium castaneum, an important genetic model and agricultural pest.

DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning.

DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e.

iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments Chou's 5-steps Rule and Pseudo Components.

Background: The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological pro-cesses. Thus its identification is necessary to understand its mechanism.

iMethylK_pseAAC: Improving Accuracy of Lysine Methylation Sites Identification by Incorporating Statistical Moments and Position Relative Features into General PseAAC Chou's 5-steps Rule.

Background: Methylation is one of the most important post-translational modifications in the human body which usually arises on lysine among the most intensely modified residues. It performs a dynamic role in numerous biological procedures, such as regulation of gene expression, regulation of protein function and RNA processing. Therefore, to identify lysine methylation sites is an important challenge as some experimental procedures are time-consuming.

Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment.

Glycosylation of proteins in eukaryote cells is an important and complicated post-translation modification due to its pivotal role and association with crucial physiological functions within most of the proteins. Identification of glycosylation sites in a polypeptide chain is not an easy task due to multiple impediments. Analytical identification of these sites is expensive and laborious.

iProtease-PseAAC(2L): A two-layer predictor for identifying proteases and their types using Chou's 5-step-rule and general PseAAC.

Proteases are a type of enzymes, which perform the process of proteolysis. Proteolysis normally refers to protein and peptide degradation which is crucial for the survival, growth and wellbeing of a cell. Moreover, proteases have a strong association with therapeutics and drug development.

iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition.

Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious.

Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of .

Transcriptomic studies of have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues.

SPrenylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins.

The protein prenylation (or S-prenylation) is one of the most essential modifications, required for the association of membrane of a plethora of signalling proteins with the key biological process such as protein trafficking, cell growth, proliferation and differentiation. Due to the ubiquitous nature of S-prenylation and its role in cellular functions, any defect in the biosynthesis or regulation of the isoprenoid leads to the occurrence of a variety of diseases including neurodegenerative disorders, metabolic issues, cardiovascular diseases and one of the most fatal diseases, cancer. This depicts the strong biological significance of S-prenylation, thus, the timely and accurate identification of S-prenylation sites is crucial and may provide with possible ways to understand the mechanism of this modification in proteins.

SPalmitoylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-palmitoylation sites in proteins.

S-Palmitoylation is a uniquely reversible and biologically important post-translational modification as it plays an essential role in a variety of cellular processes including signal transduction, protein-membrane interactions, neuronal development, lipid raft targeting, subcellular localization and apoptosis. Due to its association with the neuronal development, it plays a pivotal role in a variety of neurodegenerative diseases, mainly Alzheimer's, Schizophrenia and Huntington's disease. It is also essential for developmental life cycles and pathogenesis of Toxoplasma gondii and Plasmodium falciparum, known to cause toxoplasmosis and malaria, respectively.

pSSbond-PseAAC: Prediction of disulfide bonding sites by integration of PseAAC and statistical moments.

The structure of protein gains additional stability against various detrimental effects by the presence of disulfide bonds. The formation of correct disulfide bonds between cysteine residues ensures proper in vivo and in vitro folding of the protein. Many cysteine residues can be present in the polypeptide chain of a protein, however, not all cysteine residues are involved in the formation of a disulfide bond, and therefore, accurate prediction of these bonds is crucial for identifying biophysical characteristics of a protein.

iPhosY-PseAAC: identify phosphotyrosine sites by incorporating sequence statistical moments into PseAAC.

Protein phosphorylation is one of the most fundamental types of post-translational modifications and it plays a vital role in various cellular processes of eukaryotes. Among three types of phosphorylation i.e.

iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition.

Nucleosome is a central element of eukaryotic chromatin, which composes of histone proteins and DNA molecules. It performs vital roles in many eukaryotic intra-nuclear processes, for instance, chromatin structure and transcriptional regulation formation. Identification of nucleosome positioning via wet lab is difficult; so, the attention is diverted towards the accurate intelligent automated prediction.

iPhosT-PseAAC: Identify phosphothreonine sites by incorporating sequence statistical moments into PseAAC.

Among all the post-translational modifications (PTMs) of proteins, Phosphorylation is known to be the most important and highly occurring PTM in eukaryotes and prokaryotes. It has an important regulatory mechanism which is required in most of the pathological and physiological processes including neural activity and cell signalling transduction. The process of threonine phosphorylation modifies the threonine by the addition of a phosphoryl group to the polar side chain, and generates phosphothreonine sites.

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides.

The molecular structure of macromolecules in living cells is ambiguous unless we classify them in a scientific manner. Signal peptides are of vital importance in determining the behavior of newly formed proteins towards their destined path in cellular and extracellular location in both eukaryotes and prokaryotes. In the present research work, a novel method is offered to foreknow the behavior of signal peptides and determine their cleavage site.

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.

Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests.

Bi-PSSM: Position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane proteins.

Mycobacterium is a pathogenic bacterium, which is a causative agent of tuberculosis (TB) and leprosy. These diseases are very crucial and become the cause of death of millions of people every year in the world. So, the characterize structure of membrane proteins of the protozoan play a vital role in the field of drug discovery because, without any knowledge about this Mycobacterium's membrane protein and their types, the scientists are unable to treat this pathogenic protozoan.

Next-Generation Insect-Resistant Plants: RNAi-Mediated Crop Protection.

Plant-mediated RNA interference (RNAi) shows great potential in crop protection. It relies on plants stably expressing double-stranded RNAs (dsRNAs) that target essential genes in pest insects. Practical application of this strategy is challenging because producing sufficient amounts of stable dsRNA in plants has proven to be difficult to achieve with conventional transgenesis.

Functional analysis of the ABCs of eye color in Helicoverpa armigera with CRISPR/Cas9-induced mutations.

Many insect pigments are localized in subcellular pigment granules, and transport of pigment precursors from the cytoplasm is accomplished by ABC proteins. Drosophila melanogaster has three half-transporter genes (white, scarlet, and brown, all affecting eye pigments) and Bombyx mori has a fourth (ok). The White, Brown, Scarlet and Ok proteins each have one transmembrane and one cytoplasmic domain and they heterodimerize to form functional transporters with different substrate specificities.