genomics

Contributions to In Silico Genome Annotation

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B3 L5 R5209

Abstract Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation while identifying functions of these regions are considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and time-consuming. This study contributes to genome annotation by introducing

Novel Computational Methods that Facilitate Development of Cyanofactories for Free Fatty Acid Production by Olaa Motwalli

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B3 L5 R5209

Abstract Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of FFA production for it to be commercially viable. Thus, new chassis strains that require less engineering are needed

VSIM: Visualization and Simulation of Genomes for Premarital Testing

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B3 L5 R5209

Abstract Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data. We have developed VSIM an automated and easy to use web application for interpretation and visualization of a variety of genomics data, it identifies the candidate disease variants by referencing to four databases Clinvar, GWAS, DIDA, and PharmGKB, and predicted the pathogenic variants. Moreover, it investigates the attitude towards

AI4GH Seminar Series - VSIM: Visualization and Simulation of Genomes for Premarital Testing

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B2 R5220

Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data.

Large-scale Text and Data Integration for Cancer Genomics Research

Prof. D, Rebholz-Schuhmann (University Cologne, Germany​)​

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B19 L3 H2

Abstract This talk will give an overview of data and text mining in the life science domain, but will also point out the use of semantic technologies for other domains. Such solutions cover the integration of heterogeneous data sources based on Semantic Web standards (e.g., TCGA, Cosmic, others), the development of smart technologies (e.g., stream processing), graph and literature analytics, and open data initiatives. Application domains are biomedical solutions in cancer genomics and targeted projects together with industrial partners exploiting Semantic Web technologies in general. The

Digital Health: promises and pitfalls

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B9 L3 R3223

This talk will try to clarify some misconceptions about what digital health (DH) is, and what it should not be.

Making the silent genes speak

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Regulating an overlooked set of genes may help biologists manipulate cells to find new therapy options.

Honey bee behavior is in the genes

1 min read ·
An integrated set of genetic mechanisms controls whether bees behave as foragers or nurses.

Exploring protein form to find function

1 min read ·
Existing systems for predicting protein structure are outperformed by a newly developed method.

Enhancing understanding of genetic regulation

1 min read ·
Researchers round up clues to track down enhancers.

Student life: studying and working at the Computational Bioscience Research Center (KAUST)

1 min read ·
For Ph.D. students Arturo Magana Mora, Haitham Ashoor and Olaa Motwalli, April 2017 was a particularly nerve-wracking month. After years of hard work and sleepless nights, they finally defended their thesis, bringing them one step closer to graduation.

Mining Red Sea bacteria for industrial potential

1 min read ·
Genome sequencing of two Red Sea bacteria highlights their potential as industrial workhorses.

Azza Althagafi defends her Master's thesis

1 min read ·
Azza Althagafi, a student under the supervision of Assistant Professor Robert Hoehndorf, defended her Master's thesis on November 1, 2018.

Studying COVID-19’s envelope protein

1 min read ·
A likeness between genes of the SARS and COVID-19 viruses could inform research into potential treatments.

Simulating evolution to understand a hidden switch

1 min read ·
Some organisms evolve an internal switch that can remain hidden for generations until stress flicks it on.

Sarah Alghamdi

Ph.D. Student, Computer Science
Sarah Alghamdi is a Ph.D. candidate in the Bio-Ontology Research Group (BORG) at King Abdullah University of Science and Technology (KAUST) under the supervision of Professor Robert Hoehndorf. Research Interests Sarah's research interests include applications of artificial intelligence and using statistical methods to genomics and healthcare. Professional Profile Program Committee for the International Conference of Biomedical Ontology (ICBO 2022) Program Committee for the International Society of Molecular Biology (ISMB 2022) - Bio-Ontology track 2018-2021: Teaching Assistant positions: CS

Olaa A. Motwalli

Research Interests Olaa Motwalli is a Ph.D. student in Computational Science and a member of the Computational Bioscience Research Center (CBRC) at KAUST. She obtained her Bachelor's degree in Computer Science at King Abdul Aziz University in Jeddah and obtained her Master's degree in Computer and Software Engineering at Widener University in the USA. Her research interests are mainly the development and computational support for the design of sustainable biofuel production via microbial cell factories through machine learning, graph mining, and algorithm development, genome-scale metabolic

Jesper Tegner

Professor, Bioscience
Jasper Tegner is an M.D./Ph.D., innovator and professor with over 350 publications, dedicated to exploring the interconnected mechanisms underlying life, intelligence and the mind. His research aims to advance fundamental progress in artificial intelligence by moving beyond engineering to understand the intrinsic modes of operation within cells, between cells and within the brain.

Hajime Ohyanagi

Research Interests ​My original question in biology is the Origin and History of Eukaryotes. I also love to understand the possibility of Genomic Breeding in the imminent global food security issue. To these ends, currently, I aim to determine the biological significance in big data of marine and crop genomics, by the means of diverse bioinformatics methodologies. Professional Profile 2015-present: Technical Specialist, KAUST, Thuwal, Saudi Arabia 2015-present: Visiting Research Scientist, National Agriculture and Food Research Organization, Tsukuba, Japan 2013-present: Visiting Research

Hammad Naveed

Postdoctoral Research Fellow, Structural and Functional Bioinformatics
Hammad Naveed worked as a Postdoctoral research fellow at Prof. Xin Gao's Structural and Functional Bioinformatics Group (SFB) at King Abdullah University of Science and Technology (KAUST) during 2013-2015. Hammad is an Associate Professor in the Computer Science Department at the National University of Computer & Emerging Sciences, Pakistan. Previously he was a Research Assistant Professor at the Toyota Technological Institute at Chicago, University of Chicago 2014-2017. Hammad Naveed received his Ph.D. in Bioinformatics from the University of Illinois at Chicago in 2012. He spent the