Yaqoub Ashhab

Yaqoub Ashhab
Palestine Polytechnic University · Palestine-Korea Biotechnology Center

Ph. D

About

48
Publications
20,465
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,094
Citations
Citations since 2016
13 Research Items
315 Citations
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
Additional affiliations
September 2006 - present
Palestine Polytechnic University
Position
  • Research Director
January 1999 - August 2005
Hadassah Medical Center
Position
  • PostDoc Position
January 1999 - August 2005
Hebrew University of Jerusalem
Position
  • PostDoc Position

Publications

Publications (48)
Article
Full-text available
The aim of this paper is to evaluate improvement in the classification of protein sequence data by introducing clustering as a prepossessing step. Clustering analysis was introduced to discover any possible sub-clusters that might have different patterns within the same protein class. A classification learning algorithm is then applied to each clus...
Article
Background: Brucellosis is a global zoonotic disease ranked by WHO as being among the top seven neglected zoonoses. After implementing a livestock vaccination strategy in 1998, the incidence rate of human brucellosis in Palestine dropped significantly. However, in 2015 the disease re-emerged with alarming incidence rates similar to those in the pe...
Article
Brucellosis is an endemic disease in many developing countries and ranked by the World Health Organization among the top seven “neglected zoonoses”. Although a Palestinian brucellosis control program was launched in 1998, the disease reemerged after 2012. Interestingly, a similar reemerging pattern was reported in the neighboring Israeli regions. T...
Article
Full-text available
One of the most effective strategies for eliminating new and emerging infectious diseases is effective immunization. The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) warrants the need for a maximum coverage vaccine. Moreover, mutations that arise within the virus have a significant impact on the vaccination strate...
Preprint
Full-text available
Brucellosis is an endemic disease in many developing countries and ranked by the World Health Organization among the top seven “neglected zoonoses”. Although a Palestinian brucellosis control program was launched in 1998, the disease reemerged after 2012. Interestingly, a similar reemerging pattern was reported in the neighboring Israeli regions. T...
Article
Full-text available
Because of their potent adjuvanticity, ease of manipulation and simplicity of production Gram-negative Outer Membrane Vesicles OMVs have the potential to become a highly effective vaccine platform. However, some optimization is required, including the reduction of the number of endogenous proteins, the increase of the loading capacity with respect...
Article
Full-text available
Single Tube Nested PCR (ST-nPCR) is of value to clinical laboratories with limited settings for the detection of fastidious microorganisms. The detection sensitivity of ST-nPCR is dependent on ensuring minimal leftovers of outer primers during the second round of the reaction. In this work, we investigated various approaches to optimize the perform...
Article
Full-text available
The objective of this work is to present a novel evolutionary-based approach that can create and optimize powerful string kernels using Genetic Programming. The proposed model creates and optimizes a superior kernel, which is expressed as a combination of string kernels, their parameters, and corresponding weights. As a proof of concept to demonstr...
Article
Full-text available
Brucellosis is a zoonotic infectious disease caused by bacteria of the genus Brucella . Brucella melitensis , Brucella abortus , and Brucella suis are the most pathogenic species of this genus causing the majority of human and domestic animal brucellosis. There is a need to develop a safe and potent subunit vaccine to overcome the serious drawbacks...
Article
Full-text available
Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology...
Data
Support materials for executing the experiments. A compressed (.zip) file that contains all the needed scripts for executing any experiment of this work is provided. The similarity matrix is also included. The README file contains the needed details to run these scripts. (ZIP)
Article
Brucella melitensis Rev.1 is an avirulent strain that is widely used as a live vaccine to control brucellosis in small ruminants. Although an assembled draft version of Rev.1 genome has been available since 2009, this genome has not been investigated to characterize this important vaccine. In the present work, we used the draft genome of Rev.1 to p...
Code
An implementation of protein descriptors in R. These descriptors combine the advantages of being fixed length and including partial sequential effect: Various length of protein sequences are described with fixed length vectors that are suitable for machine learning algorithms, and still includes partial sequential effect.
Article
Abstract 1. The aim of this work was to compare a group of virulence-associated characteristics of Escherichia coli isolates from broiler chickens that had died with signs of colibacillosis against E. coli isolates from ready-to-market chicken meat in the West-Bank. 2. The isolates were investigated to determine the virulence factor profile, phylog...
Article
Full-text available
SslE, the Secreted and surface-associated lipoprotein from Escherichia coli, has recently been associated to the M60-like extracellular zinc-metalloprotease sub-family which is implicated in glycan recognition and processing. SslE can be divided into two main variants and we recently proposed it as a potential vaccine candidate. By applying a numbe...
Article
Full-text available
Caspases are a family of cysteinyl proteases that regulate apoptosis and other biological processes. Caspase-3 is considered the central executioner member of this family with a wide range of substrates. Identification of caspase-3 cellular targets is crucial to gain further insights into the cellular mechanisms that have been implicated in various...
Data
Detailed results of the performance comparison. This table shows the prediction results of CAT3 versus CASVM and Cascleave for 16 caspase substrates (17 cleavage sites) that were not originally included in the training of CAT3. The cleavage position(s) in all these substrates were confirmed by site directed mutagenesis.
Data
Full-text available
Heat-map representing caspase-3 cleavage pattern. This heat-map represents the scores of the 20 amino acids in the scoring matrix 'A' (see establishment of scoring matrices in the Methods' section). The colour intensities reflect the magnitude of amino acid scores. The blue scale denotes the positive scores, while the yellow to red scale denotes th...
Data
Chart representing biological processes among predicted substrates. This figure shows the graphical representation of the enriched GO terms: Biological Process among the 3013 predicted caspase-3 substrates. The red bars indicate the gene count (Y-axis) per each GO term: Biological Process (X-axis). The blue dotted line shows the p-value for each GO...
Data
List of the significantly enriched cellular component GO terms. This table shows the full list of the significantly enriched terms of GO: Cellular Component among the 3013 predicted caspase-3 substrates.
Data
Prediction results of non-caspase-3 substrates. The three Excel sheets show the prediction results for 25 non-caspase-3 substrates (17 cleavage sites for caspase-1, 12 cleavage sites for caspase-8 and 5 cleavage sites for caspase-9). The Pub Med ID reference and the CAT3 score for each cleavage site are shown.
Data
List of the significantly enriched biological process GO terms. This table shows the full list of the significantly enriched terms of GO: Biological Process among the 3013 predicted caspase-3 substrates.
Data
Full-text available
Full list of caspase-3 substrates. This table shows the description of the obtained 227 caspase-3 substrates. The cleavage evidence refers to the experimental method through which cleavage was identified. SDM stands for site directed mutagenesis, while proteomics refers to experiments of high-throughput proteomic screening.
Data
List of predicted potential human caspase-3 substrates. This table shows the list of 3320 human proteins that were predicted to be caspase-3 substrates. Several proteins have more than one predicted site leading to a total of 4903 potential cleavage sites. Only cleavage sites of scores ≥ 45 are shown.
Data
Installation files for CAT-3 tool. This compressed folder contains a total of 6 files: final_CAT3.exe, process.exe, algmodule.pm, and submodules.pm that are needed for CAT3 software to work on Windows operating system. The two files: Single_sequence-test.txt and Multiple_sequences-test.txt are provided for testing purposes. To install CAT-3 v1.0 on...
Chapter
Full-text available
Bioinformatics and genomics sciences are becoming indispensable to develop our knowledge in vital fields such as medicine, food and agriculture, and biodiversity. Unlike other science and technology disciplines, research and development in bioinformatics does not require prohibitive resources. As the accessibility of most biological databases in t...
Article
Major risk factors of oral squamous cell carcinoma (OSCC) are environmental and can lead to DNA mutagenesis. Mismatch repair (MMR) system functions to repair small DNA lesions, which can be targeted for promoter hypermethylation. We therefore wanted to test whether hypermethylation of MMR genes (hMLH1, hMSH2) could contribute to oral carcinogenesis...
Article
Natural killer (NK) cells are part of the innate immune system, capable of killing tumor and virally infected cells. NK cells induce apoptosis in the target cell by either granule- or receptor-mediated pathways. A set of inhibitory and activation ligands governs NK cell activation. As transformed cells often attempt to evade NK cell killing, up-reg...
Article
Full-text available
Livin is a member of the Inhibitor of Apoptosis Protein family which inhibits apoptosis induced by a variety of stimuli. We previously identified Livin and demonstrated that following apoptotic stimuli, Livin is cleaved by effector caspases to produce a truncated form with paradoxical pro-apoptotic activity. In the present study, we reveal that whi...
Article
Autoimmune thyroid diseases are characterized by lymphocytic infiltration of the thyroid gland. Chemokines are crucial in the recruitment of lymphocytes and might play an important role in the pathogenesis of autoimmune thyroid disease. The aim of this study was to test the feasibility of analysing by one-tube reverse-transcriptase polymerase chain...
Article
Full-text available
Human CCL4/macrophage inflammatory protein (MIP)-1beta and CCL3/MIP-1alpha are two highly related molecules that belong to a cluster of inflammatory CC chemokines located in chromosome 17. CCL4 and CCL3 were formed by duplication of a common ancestral gene, generating the SCYA4 and SCYA3 genes which, in turn, present a variable number of additional...
Article
Inhibitor of Apoptosis proteins (IAP) comprise a family of intracellular proteins that play an essential role in the regulation of apoptosis. IAP family members are defined by one or more repeats of a highly conserved anti-apoptotic domain termed the baculovirus IAP repeat (BIR), located at the amino-terminus. In addition, some IAPs contain a conse...
Article
Central nervous system involvement is a well recognized complication of systemic non-Hodgkin lymphoma. Most central nervous system recurrences occur within the first 2 years after the initial diagnosis and are considered to represent clonally related recurrence of systemic disease. The authors attempted to investigate the clonal relation between th...
Article
Apoptosis is a crucial biological process that prevents uncontrolled cell proliferation and eliminates harmful cells. Resistance to apoptotic stimuli is a hallmark feature of various cancers. One of the mechanisms through which tumor cells are believed to acquire resistance to apoptosis is by overexpression of inhibitor of apoptosis proteins (IAPs)...
Article
Full-text available
Mammalian heparanase (endo-beta-glucuronidase) degrades heparan sulfate proteoglycans and is an important modulator of the extracellular matrix and associated factors. The enzyme is preferentially expressed in neoplastic tissues and contributes to tumour metastasis and angiogenesis. To investigate the epigenetic regulation of the heparanase locus,...
Article
Full-text available
Inhibitor of apoptosis protein (IAP) is a family of intracellular proteins that plays an essential role in the regulation of apoptosis. Recently, we and others discovered a new member of this family, termed Livin. Many studies have focused on the inhibitory effect of IAPs on caspases. Here, we describe a novel regulatory mechanism by which Livin is...
Article
AU-rich elements (AREs) are found in 3′ untranslated regions (3′ UTR) of many highly unstable mRNAs for mammalian early-response genes. The minimal AU sequence core within the ARE is the heptamer WAUUUAW, although from a functional point of view, several pentanucleotides clustered in close proximity are the key sequence motif that mediates mRNA deg...
Article
A novel human Krüppel-associated box (KRAB) type zinc finger protein encoding gene, ZNF304, was obtained by AU-motif-directed display and RACE. This gene, which contains a tandem AU motif in the 3' untranslated region, has an ORF 1977-bp long that codes for a putative 659 residue protein with an amino-terminal KRAB domain and 13 carboxyl-terminal C...
Article
Using homology searches, we identified a novel human inhibitor of apoptosis (IAP) gene. This gene has two splicing variants that contain open reading frames of 298 and 280 amino acids and both contained a single copy of baculovirus IAP repeat (BIR) and RING domain. We refer here to the longer and shorter variants as Livin alpha and beta, respective...
Article
Full-text available
An adaptation of mixed oligonucleotide primed amplification of complementary DNA to detect the profile of CC chemokines in biological samples is presented. By introducing normalization, two correction coefficients, performing a single amplification reaction, and five parallel hybridizations, intrasample and intersample comparisons can be reliably m...
Article
A procedure suitable for cloning labile mRNAs that contain AU motifs is presented (AU-DD). These motifs are regulatory sequences within the so-called AU-rich elements (AREs) often found in 3' untranslated regions of genes such as cytokines, proto-oncogenes, and transcription factors. AU-DD is an AU-motif-directed differential display that permits t...
Article
According to the 'aberrant HLA expression' hypothesis, endocrine autoimmunity is driven by presentation of self antigens by target cells over-expressing HLA molecules. In autoimmune thyroid diseases (AITD), thyroid follicular cells (thyrocytes) over-express HLA class I and HLA class II molecules. Since efficient presentation of endogenous peptides...
Article
Decreased peripheral utilization of glucose is an important pathogenic mechanism in diabetes. Although it is universally acknowledged that insulin resistance plays a major role in the reduction of glucose consumption by peripheral tissues, and many defects have been described in the function of insulin receptors (see chapter by Olefsky), indirect c...
Article
Full-text available
Prediction of MHC class II binding peptides rep-resents a challenging problem in machine learning. Many researchers applied different machine learning tool for the prediction, these tools are: SVM, neural network, genetic programming, and HMM, but each has its own strengths and weaknesses. In this paper we used the Boosted decision tree algorithm f...

Questions

Question (1)
Question
I have ONLY to select between two options of real time PCR machines: Bio-Rad cfx96 touch or Rotor-Gene Q 5plex platform. In fact, I know the major technical differences like heating and cooling systems, number of channels..etc. However, my question is: Is there anybody who USED and compared both system and can tell the practical differences? The major tasks of our real time PCR machine will be diagnosis of infectious diseases with focus on multiplex targets.
Thanks in advance for your help! 

Network

Cited By