About
42
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Introduction
I am interested in improving accessibility and interpretation of research results using open source software technologies such as Solr search platform, and Weka Machine Learning library.
Current institution
Additional affiliations
April 2015 - present
April 2015 - present
March 2006 - January 2012
Publications
Publications (42)
Developing computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand...
The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science and society with a growing range of biotechnology applications in sectors such as biomedicine, energy, and food. Shotgun sequencing and metagenomics can now be used to catalog the diversity of ocean mi...
Life has been evolving in the oceans much longer than it has on land, resulting in highly diverse ocean organisms—particularly microbes like bacteria and archaea. Ocean microbes perform crucial functions that influence the health of the ocean and ultimately impact Earth’s climate. To understand the diversity and functions of marine organisms, scien...
Background
Identifying variants associated with diseases is a challenging task in medical genetics research. Current studies that prioritize variants within individual genomes generally rely on known variants, evidence from literature and genomes, and patient symptoms and clinical signs. The functionalities of the existing tools, which rank variant...
Late-stage drug development failures are usually a consequence of ineffective targets. Thus, proper target identification is needed, which may be possible using computational approaches. The reason being, effective targets have disease-relevant biological functions, and omics data unveil the proteins involved in these functions. Also, properties th...
More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. H...
Deep learning has massive potential in predicting phenotype from different omics profiles. However, deep neural networks are viewed as black boxes, providing predictions without explanation. Therefore, the requirements for these models to become interpretable are increasing, especially in the medical field. Here we propose a computational framework...
Biomedical knowledge is represented in structured databases and published in biomed- ical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that...
Bone is the most common site of distant metastasis from malignant tumors, with the highest prevalence observed in breast and prostate cancers. Such bone metastases (BM) cause many painful skeletal-related events, such as severe bone pain, pathological fractures, spinal cord compression, and hypercalcemia, with adverse effects on life quality. Many...
T-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immune response by activating and helping other immune cells, me...
Reliable quantification of cellular treatment effects in many bioassays depends on the accuracy of cell colony counting. However, colony counting processes tend to be tedious, slow, and error-prone. Thus, pursuing an effective colony counting technique is ongoing, and varies from manual approaches to partly automated and fully automated techniques....
Background
The accurate identification of the exon/intron boundaries is critical for the correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) demarcate these boundaries. Therefore, deriving accurate computational models to predict the SS are useful for functional annotation of genes and genomes, and for finding alte...
Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information,...
Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for ru...
In cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurode...
Polyadenylation signals (PAS) are found in most protein-coding and some non-coding genes in eukaryotes. Their accurate recognition improves understanding gene regulation mechanisms and recognition of the 3′-end of transcribed gene regions where premature or alternate transcription ends may lead to various diseases. Although different methods and to...
During cellular division DNA replicates and this process is the basis for passing genetic information to the next generation. However, the DNA copy process sometimes produces a copy that is not perfect, that is, one with mutations. The collection of all such mutations in the DNA copy of an organism makes it unique and determines the organism's phen...
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcr...
The European Bioinformatics Institute (EMBL-EBI-https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present th...
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT...
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis
tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and
to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry d...
Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.
Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers,...
The EMBRACE ( European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standa...
The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination
of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life
sciences. The project concluded that in order for web services to achieve widespread adoption, standar...
This paper describes a new rule induction system, rila, which can extract frequent patterns from multiple connected relations. The system supports two different rule selection strategies, namely the select early and select late strategies. Pruning heuristics are used to control the number of hypotheses generated during the learning process. Experim...
The EMBRACE project is a network of European partners providing services which integrate the major data resources and analysis software tools using web services and emerging grid technologies. Prototype services are available for the core data resources and the most commonly used tools for sequence analysis. Data access uses the WSDbFetch and BioMa...
In this paper we describe the improved version of a novel rule induction algorithm, namely ILA. We first outline the basic algorithm, and then present how the algorithm is enhanced using the new evaluation metric that handles uncertainty in a given data set. In addition to having a faster induction than the original one, we believe that our contrib...
Many-to-many relations are often observed between real life objects. When many-to- many relations are between objects in the same class the data mining process becomes more complicated than mining objects when there are no such recursive relations. Mining objects re- lated to other objects in the same class requires construction and execution of re...
The EMBRACE project is a network of European partners providing services which integrate the major data resources and analysis software tools using web services and emerging grid technologies. Prototype services are available for the core data resources and the most commonly used tools for sequence analysis. Data access uses the WSDbFetch and BioMa...
This paper describes a rule discovery system that has been developed as part of an ongoing research project. The system allows
discovery of multi-relational rules using data from relational databases. The basic assumption of the system is that objects
to be analyzed are stored in a set of tables. Multi-relational rules discovered would either be us...
In this paper we describe the ILA-2 rule induction algorithm, which is the improved version of a novel inductive learning algorithm ILA . We first outline the basic algorithm ILA, and then present how the algorithm is improved using a new evaluation metric that handles uncertainty in the data. By using a new soft computing metric, users can reflect...
Radiant panel heating and cooling systems for sensible space conditioning have several attributes. These include, but are not limited to, energy savings potential and ability to favorably tie-in with moderate temperature, low-intensity energy sources like solar systems and heat pumps. In order to predict and incorporate such attributes of panel sys...
