Pharmacokinetics-Pharmacodynamics Modeling and Evaluation of Tumor Response to Bortezomib Proteasome Inhibitor in Waldenstrom Macroglobulinemia.

Background: Waldenstrom's macroglobulinemia (WM), also known as lymphoplasmacytic lymphoma, is a type of non-Hodgkin's lymphoma in which the malignant cells produce many macroglobulin proteins. It originates from B cells and develops in the bone marrow, where Wm cells combine to produce distinct types of blood cells, resulting in reduced volumes of red blood cells, white blood cells, and platelets, making it harder for the body to fight diseases. Chemoimmunotherapy is being used for the clinical management of WM, but new targeted agents, the BTK inhibitor ibrutinib and the proteasome inhibitor bortezomib, have shown significant improvements in patients with relapsed/refractory WM.

Gene expression profiling utilizing extremely sensitive CDNA arrays and enrichment-based network study of major bone cancer genes.

Background: The gene interaction network is a set of genes interconnected by functional interactions among the genes. The gene interaction networks are studied to determine pathways and regulatory mechanisms in model organisms. In this research, the enrichment study of bone cancer-causing genes is undertaken to identify several hub genes associated to the development of bone cancer.

Insights into the Dynamic Fluctuations of the Protein HPV16 E1 and Identification of Motifs by Using Elastic Network Modeling.

Background: Cancers of cervix, head and neck regions have been found to be associated with Human Papilloma Virus (HPV) infection. E1 protein makes an important papillomavirus replication factor. Among the ORFs of papillomaviruses, the most conserved sequence is that of the E1 ORF.

Computational Method for Classification of Avian Influenza A Virus Using DNA Sequence Information and Physicochemical Properties.

Accurate and fast characterization of the subtype sequences of Avian influenza A virus (AIAV) hemagglutinin (HA) and neuraminidase (NA) depends on expanding diagnostic services and is embedded in molecular epidemiological studies. A new approach for classifying the AIAV sequences of the HA and NA genes into subtypes using DNA sequence data and physicochemical properties is proposed. This method simply requires unaligned, full-length, or partial sequences of HA or NA DNA as input.

Computational Analysis of Domains Vulnerable to HPV-16 E6 Oncoprotein and Corresponding Hot Spot Residues.

Background: Human Papilloma Virus (HPV) is the primary cause of cancers in cervix, head and neck regions. Oncoprotein E6 of HPV-16, after infecting human body, alters host protein- protein interaction networks. E6 interacts with several proteins, causing the infection to progress into cervical cancer.

Molecular Docking Studies Reveal Rhein from rhubarb () as a Putative Inhibitor of ATP-binding Cassette Super-family G member 2.

Background: ATP-binding cassette Super-family G member 2 protein is an active ATPbinding cassette transporter with the potential to combat cancer stem cells.

Objective: Due to the lack of potential ATP-binding cassette Super-family G member 2 inhibitors, we screened natural inhibitors, which could be a safe source to control multidrug resistance by blocking the regulation of ATP-binding cassette Super-family G member 2 protein.

Methods: Three-dimensional structure of ATP-binding cassette Super-family G member 2 protein downloaded from the protein databank and chemical structures of 166 selected compounds of the training dataset were retrieved from PubChem.

System-based strategies for p53 recovery.

The authors have proposed a systems theory-based novel drug design approach for the p53 pathway. The pathway is taken as a dynamic system represented by ordinary differential equations-based mathematical model. Using control engineering practices, the system analysis and subsequent controller design is performed for the re-activation of wild-type p53.

Evaluation of the whole body physiologically based pharmacokinetic (WB-PBPK) modeling of drugs.

The Physiologically based pharmacokinetic (PBPK) modeling is a supporting tool in drug discovery and improvement. Simulations produced by these models help to save time and aids in examining the effects of different variables on the pharmacokinetics of drugs. For this purpose, Sheila and Peters suggested a PBPK model capable of performing simulations to study a given drug absorption.

Construction and analysis of protein-protein interaction network correlated with ankylosing spondylitis.

Background: Ankylosing spondylitis, a systemic illness is a foundation of progressing joint swelling that for the most part influences the spine. However, it frequently causes aggravation in different joints far from the spine, and in addition organs, for example, the eyes, heart, lungs, and kidneys. It's an immune system ailment that may be activated by specific sorts of bacterial or viral diseases that initiate an invulnerable reaction that don't close off after the contamination is recuperated.

ChromBiSim: Interactive chromatin biclustering using a simple approach.

Unlabelled: Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics.

Mathematical Modeling of E6-p53 interactions in Cervical Cancer.

Background: Cervical cancer is the third most common cancer in women throughout the world. The human papillomavirus (HPV) E6 viral protein plays an essential role in proteasomal degradation of the cancer suppressant protein p53. As a result, p53 negative regulation and apoptosis relevant activities are abrogated, facilitating development of cervical cancer.

On p53 revival using system oriented drug dosage design.

We propose a new paradigm in the drug design for the revival of the p53 pathway in cancer cells. It is shown that the current strategy of using small molecule based Mdm2 inhibitors is not enough to adequately revive p53 in cancerous cells, especially when it comes to the extracting pulsating behavior of p53. This fact has come to notice when a novel method for the drug dosage design is introduced using system oriented concepts.

ChromClust: A semi-supervised chromatin clustering toolkit for mining histone modifications interplay.

Mining patterns of histone modifications interplay from epigenomic profiles are one of the leading research areas these days. Various methods based on clustering approaches and hidden Markov models have been presented so far with some limitations. Here we present ChromClust, a semi-supervised clustering tool for mining commonly occurring histone modifications at various locations of the genome.

MCaVoH: A toolkit for mining, classification and visualization of human microbiota.

Human body is the home for a large number of microbes. The complexity of enterotype depends on the body site. Microbial communities in various samples from different regions are being classified on the basis of 16S rRNA gene sequences.