Hamid Ismail

North Carolina Agricultural and Technical State University | NC A&T · Department of Computational Science and Engineering

Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite predictor 1.0 (RF-Phos 1.0), to predict phosphorylation sites given...

Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite (RF-Phos 2.0) predictor, to predict phosphorylation sites given only...

Protein post-translational modifications (PTMs) introduce new functionalities and play a critical role in the regulation of protein functions. Characterizing these modifications, especially PTM sites, is essential for unraveling complex biological systems. However, traditional experimental approaches, such as mass spectrometry, are time-consuming a...

The mapping from codon to amino acid is surjective due to the high degeneracy of the codon alphabet, suggesting that codon space might harbor higher information content. Embeddings from the codon language model have recently demonstrated success in various downstream tasks. However, predictive models for phosphorylation sites, arguably the most stu...

Recent advancements in natural language processing have highlighted the effectiveness of global contextualized representations from Protein Language Models (pLMs) in numerous downstream tasks. Nonetheless, strategies to encode the site-of-interest leveraging pLMs for per-residue prediction tasks, such as crotonylation (Kcr) prediction, remain large...

O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling....

Phosphorylation is one of the most important post-translational modifications and plays a pivotal role in various cellular processes. Although there exist several computational tools to predict phosphorylation sites, existing tools have not yet harnessed the knowledge distilled by pre-trained protein language models. Herein, we present a novel deep...

This book contains the latest material on the subject, covering next-generation sequencing (NGS) applications and meeting the requirements of a complete semester course. This book digs deep into analysis, providing both concept and practice to satisfy the exact need of researchers seeking to understand and use NGS data reprocessing, genome assembly...

Bioinformatics: A Practical Guide to Next Generation Sequencing Data Analysis contains the latest material in the subject, covering NGS applications and meeting the requirements of a complete semester course. This book digs deep into analysis, providing both concept and practice to satisfy the exact need of researchers seeking to understand and use...

Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments provides the basics of bioinformatics and in-depth coverage of NCBI databases, sequence alignment, and NCBI Sequence Local Alignment Search Tool (BLAST). As bioinformatics has become essential for life sciences, the book has been written specifically to address the need of...

Machine learning has become one of the most popular choices for developing computational approaches in protein structural bioinformatics. The ability to extract features from protein sequence/structure often becomes one of the crucial steps for the development of machine learning-based approaches. Over the years, various sequence, structural, and p...

I ntroduction: Mycosis Fungoides (MF) is the most common subtype of cutaneous T-cell lymphomas. Prior Studies have identified Black race as a risk factor for earlier age at diagnosis, more advanced stages at time of diagnosis and poor prognosis in patients with MF. Data examining differences in racial disparities outcomes over time are limited. Obj...

Galectins are part of a conserved family of β-galactoside-binding proteins that contribute to critical biological events during mammalian gestation and increasingly recognized for a possible role in the immune response of the cow. The objective of this study was to evaluate the effect of Galectins on signal transduction and cell activation in cow b...

This review provides insight into the importance of understanding NETosis in cows, sheep, and goats in light of the importance to their health, welfare and use as animal models. Neutrophils are essential to innate immunity, pathogen infection, and inflammatory diseases. The relevance of NETosis as a conserved innate immune response mechanism and th...

Phosphorylation, which is mediated by protein kinases and opposed by protein phosphatases, is an important post-translational modification that regulates many cellular processes, including cellular metabolism, cell migration, and cell division. Due to its essential role in cellular physiology, a great deal of attention has been devoted to identifyi...

Dietary phytochemicals have both nutritional and health benefits for farm animals. Research on the immunomodulatory effects of phytochemicals may aid in developing novel therapeutic agents and provide insights into the regulation of gene expression. Eugenol (4-allyl-2-methoxyphenyl) is the active ingredient in clove oil that has been studied for it...

Gum arabica (GA) is a well-known traditional herbal medication from Acacia Senegal. Previous studies have shown that GA has physiological and therapeutic effects on animals. Anemia is a reduction below normal in the number of red blood cells. Infection by parasites, such as Haemonchus contortus, can result in anemia when there is a reduction below...

Gastrointestinal nematodes and other pathogens pose a major problem for goat production by reducing animal performance and welfare. Plants such as Acacia Senegal are useful as dietary sources for natural prophylaxis. Gum Arabica (GA) from A. Sengal has antimicrobial, anti-inflammatory properties that need to be explored in goats. The objective of t...

Inflammation is a complex but defensive biological response of living tissue to infection that can be triggered by exogenous injury and infectious agents such as bacteria and viruses. Inflammation is part of the innate immune response acting as the first line of defense against pathogens and disease. The inflammatory response acts as a double-edged...

The objective of this study was to compare galectin gene (LGALS) expression and secretion in cow, sheep and goat blood. Ruminants succumb to infectious and metabolic diseases. Galectins (Gals) are a family of β –galactoside binding proteins that have a conserved carbohydrate recognition domain increasingly recognized for their role in inflammation....

Infectious and metabolic diseases are the significant hindrance to animal production. Galectins (Gal) are β-galactosidase binding proteins that can modulate inflammation following external and internal secretion from the cell. Galectin 9 is a tandem repeat member of Gal involved in cell activation, pathogen destruction and immunosuppression. Bindin...

Background: The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computational tool to classify the newly identified BL enzymes into one of its classes. There are two types of...

The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to...

The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computational tool to classify the newly identified BL enzymes into one of its classes. There are two types of classificatio...

The objective of this study was to investigate the effect of crude cowpea polyphenol extract (CPE) on the expression of genes involved in the inflammatory response in bovine blood in vitro. Plant-derived polyphenols in animal feeds are being used as alternatives to antibiotics to treat and prevent invading microbes. These compounds have antioxidant...

The aim of this study was to evaluate the expression of galectins in cow blood and to evaluate their modulation in periparturient cows at different stages of lactation. Galectins are multipotent, evolutionarily conserved, carbohydrate- binding proteins that, by crosslinking cell surface glycoconjugates, trigger a cascade of transmembrane signaling...

In this study, galectin gene expression pre- and postpartum was evaluated in blood. St. Croix sheep are a breed of hair sheep that are parasite resistant and prolific and so are of interest for production. Immunosuppression during the periparturient period occurs in every organ in the sheep's body to enable the ewe support fetal growth and prevent...

The objective of this study was to evaluate the effect of probiotics (FASTtrack microbial pack) on the expression of Toll-like receptors (TLR) in goats. Probiotics are viable microorganisms that have positive effects on growth performance, nutrient synthesis, the microbial ecosystem, absorption, and the reduction in the incidence of intestinal infe...

The objective of this study was to assess the molecular impact of probiotic administration on genes involved in homeostasis and immunity in goat blood. Following initial screening for infection, one-week post weaning, female SpanishXBoer goats were drenched daily with the recommended doses of FASTtrak microbial pack (Conklin Company Inc., Shakopee,...

Use of probiotic supplements as a non-chemical approach to promote health has increased in animal production. The present study evaluated the effect of oral probiotic administration on growth and global gene expression profile in dairy cows. Lactating Holstein-Friesian cows received a daily dose (50 ml) of a commercial probiotic (containing Lactoba...

Probiotic supplements are beneficial for animal health and rumen function; and lipopolysaccharides (LPS) from gram negative bacteria have been associated with inflammatory diseases. In this study the transcriptional profile in whole blood collected from probiotics-treated cows was investigated in response to stimulation with lipopolysaccharides (LP...

Protein hydroxylation is an emerging posttranslational modification involved in both normal cellular processes and a growing number of pathological states, including several cancers. Protein hydroxylation is mediated by members of the hydroxylase family of enzymes, which catalyze the conversion of alkyne group at select lysine or proline residues o...

Sericea Lespedeza (SL), is a high-quality, low input forage that suppresses gastro-intestinal parasites in goats. The effect of dietary SL on the expression of genes involved in innate immunity in goats has not been established. The objective of this study was to evaluate the impact of a diet containing SL on the expression of genes involved in inn...

Neutrophils are the first line of defense and central to many disease processes in animals. A study was conducted to determine the expression on 84 genes involved in innate and adaptive responses. The modulation by extracts of the mushroom Coriolus versicolor was also determined. Blood was collected from adult female SpanishXBoer (N=10) goats, befo...

Protein sequence-driven features are numeric vectors extracted from amino acid residues of protein sequences for their ability to capture some information that can be used for knowledge discovery in both supervised and unsupervised machine learning. Extracting features from protein sequences is always a challenge for many researchers, who need feat...

Gastrointestinal nematodes in goats have developed resistance to chemical anthelmintics resulting in the need for alternative control strategies. One approach to this problem is the incorporation of condensed tannin- rich (CT) forages that suppress gastrointestinal parasites in goats. In this study, the effect of supplementing goat diets with seric...

Machine learning algorithms have been widely used in bioinformatics to develop computational tools and the usage is still growing due to the growth of the volume of data and availability of computational resources, and invention of newer machine learning algorithms. The important task in this implementation is to fit models to experimentally pre-cl...

The supplementary Tables (1, 2, 3, 4, and 5) show the accuracy, precision, sensitivity, specificity, F1-score, Matthew's correlation coefficient (MCC), and the area under the curve based on 10-fold cross validation for models trained with sequences of window-sizes of 7, 11, 15, 19, and 21, respectively.

prediction has been investigated in the field of bioinformatics. This has become necessary due to the challenges associated with experimental methods. Previously, we developed a random forest-based method, termed Random Forest-based Phosphosite predictor (RF-Phos 1.0), to predict phosphorylation sites in proteins given only the amino acid sequence...

It is estimated that about 30% of the proteins in the human proteome are regulated by phosphorylation. Phosphorylation site prediction has in recent year been investigated in the field of bioinformatics. This has become necessary since due to the challenges associated with experimental methods. Here, we report an improved method, termed Random Fore...

Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite predictor 1.0 (RF-Phos 1.0), to predict phosphorylation sites given...

The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to...

The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to...

The objective of this study was to evaluate resistance and resilience to gastrointestinal parasites in goats following supplementation with probiotics. Improving resistance and resilience to gastro-intestinal parasites is essential to combating the threat to the small ruminant industry from anthelmintic resistance. Following initial screening for i...

The objective of this study was to evaluate resistance and resilience to gastrointestinal parasites in goats following supplementation with probiotics. Improving resistance and resilience to gastro-intestinal parasites is essential to combating the threat to the small ruminant industry from anthelmintic resistance. Following initial screening for i...

The effects of a water extract of Sericea lespedeza (SL)(a high tannin plant), bacterial lipopolysaccharide (LPS) from gram negative bacteria, nystatin (NYS), and peptidoglycan (PGN) (both from gram positive bacteria) on transcription of Toll-like receptor 2 (TLR2) in bovine blood was investigated.Toll-like receptors (TLRs) are pattern recognition...

This study was conducted to evaluate the effect of a water extract of Sericea Lespedeza (SL) on gene activation in ruminant (cow, sheep and goat)blood. Sericea Lespedeza (SL), a high tannin containing legume has been shown to be a useful component of feed for control of gastro intestinal nematodes in goats. Blood was collected from Four (N=4) BoerX...

The Goat Capra hiricus is the first domesticated ruminant and is globally distributed. Evidence exists for genomic diversity, cell specific gene expression profiles are lacking. Gene expression in goat neutrophils can impact the response to bacterial pathogens and is associated with inflammatory diseases. The objectives of this study were to determ...

Evaluation of the impact of dietary sericea lespedeza on rumen microflora and innate immunity in goats. A. Abdalla*1, H. Ismail1, S. Ibrahim1, N. Whitley1, M. Worku1, 1North Carolina A&T University, Greensboro,. Gastrointestinal nematodes have developed resistance to chemical anthelmintics resulting in the need for alternative control strategies s...

The Wnt proteins are secreted members of the wingless family of signaling molecules. These proteins bind to 2 receptors on the cell surface, single transmembrane low density lipoprotein receptor-related proteins 5 and 6 (LRP5/6) and 7 transmembrane Frizzled receptors. There is accumulating evidence that the Wnt/Frizzled pathway may play a distinct...

The effect of tomato on diseases of economic importance continues to be of broad interest. To evaluate these relationships, the effect of crude extracts of Cherokee purple tomato on pro-inflammatory genes and cytokines were evaluated. Neutrophils from three Holstein Fresian cows were treated with Phosphate Buffered Saline (PBS) or E. coli O111-B4 L...

A study was conducted to identify bone morphogenetic protein 15 (BMP-15) in goat genomic DNA, to evaluate its role in fertility. Bone morphogenetic protein 15 is a growth factor and a member of the TGFβ superfamily that is recognized by the bone morphogenetic protein receptor. It is specifically expressed in oocytes and is important for ovulation a...

Previous studies in our lab have reported the identification and expression of Wingless (Wnt) 1 and Frizzled in the goat. Wnt ligands conduct their functions in canonical Wnt signaling by binding to 2 receptors, the single transmembrane low density lipoprotein receptor-related proteins 5 and 6 (LRP5/6) and 7 transmembrane Frizzled receptors. Polymo...

Co-grazing of parasite resistant and susceptible animals may aid in onfarm control of parasite load and offer a system for reducing production losses in goats. An experiment was conducted to evaluate the effect of nematode infection in goats co-grazed with St Croix sheep reported to be parasite resistant under fall and summer grazing conditions. St...

The effect of tomato on diseases of economic importance continues to be of broad interest. To evaluate these relationships, the effect of crude extracts of Cherokee purple tomato on pro-inflammatory genes and cytokines were evaluated. Neutrophils from three Holstein Fresian cows were treated with Phosphate Buffered Saline (PBS) or E. coli O111-B4 L...

Zoonoses and the occurrence of antibiotic residues in milk are inherent concerns especially for small scale dairy producers in developing countries and where raw milk is desired for consumption globally. The mastitis model of inflammation is applicable to the study of pathogens causing economic and public health concerns. Factors in milk modulate h...

The objective of this study was to determine how Nramp1 expression may be associated with disease states in the goat. Natural resistanceassociated macrophage protein (Nramp1) is expressed exclusively in professional phagocytes. Expression of Nramp1 affects host innate immunity to intracellular bacteria because of its ability to transport divalent c...

The objective of this study was to assess the expression of galectin-11 in neutrophils isolated from cow and goat blood. Galectin-11 isolated form sheep infected with Haemonchus contortus is a member of a family of proteins that consists of β-galactoside binding lectins. Host galectins have been shown to be active participants in the recruitment of...

The objective of this study was to determine how Nramp1 expression may be associated with disease states in the goat. Natural resistance associated macrophage protein (Nramp1) is expressed exclusively in professional phagocytes. Expression of Nramp1 affects host innate immunity to intracellular bacteria because of its ability to transport divalent...

The objectives of this study were to identify members of the wingless (Wnt) signaling pathway (Wnt gene family) in the goat genome and to evaluate expression of genes involved in Wnt signaling in blood. The Wnt gene family encodes secreted members of the wingless family of signaling molecules that control cell fate, specification, proliferation, po...