PhD OpPortunities

We invite qualified candidates to apply for a PhD position in the Biological & Environmental Science & Engineering Division. Active projects are listed below.

Development of a novel Stimulated Raman Scattering microscopy system

  • Professor Carlo Liberale

    An innovative high-speed broadband Stimulated Raman Scattering system will be designed and  implemented in our laboratory, in the framework of a recently awarded grant, in collaboration with the  Politecnico di Milano (Italy). We are looking for ambitious and self-motivated candidates to work on the set up and application of the Stimulated Raman Scattering system, in a collaborative and interdisciplinary project involving radiation-matter interaction, nonlinear optics, ultrashort laser pulses, detectors, electronic instrumentation and finally investigation of lipid dysregulation in cancer.


    Priority will be given for applicants with a master degree in Electrical Engineering, Optics/Optical Engineering, Physics or a related field .


    Applications should include: a CV; a cover letter that summarizes the research experience and areas of interests of the applicant; contact information of at least 2 professional references.  To Apply for the PhD postion, please email to carlo.liberale@kaust.edu.sa and fill out an online application using the "Apply Here" button below.

    Apply Here

Novel Micro-optical structures on optical fiber tip with two-photon lithography

  • Professor Carlo Liberale

    Optical fibers are nowadays an ubiquitous core element of telecommunication systems, new laser technologies and biomedical devices. Manufacturing techniques for optical fibers have been developed and refined in order create manifold geometries and optical properties (e.g. Dual clad fibers, fiber bundles, Photonic Crystal Fibers, to name a few). Yet the capability to fabricate complex miniaturized structures integrated with optical fibers to realize important optical functions (like beam shaping, beam deflection, fiber optical tweezers, etc.) has been demonstrated only very recently. The project will focus on the fabrication of optical wave-guiding structures on the tip of optical fibers exploiting to flexibility, resolution and 3D fabrication capability of Laser Direct Writing based on Two-Photon Lithography (TPL)​​​


    Priority will be given to applicants with a master degree in Electrical Engineering, Optics/Optical Engineering, Physics or a related field.


    Applications should include: a CV; a cover letter that summarizes the research experience and areas of interests of the applicant; contact information of at least 2 professional references.  To Apply for the PhD postion, please email to carlo.liberale@kaust.edu.sa and fill out an online application using the "Apply Here" button below.

    Apply Here

Modeling differentiation of human embryonic stem cells and induced pluripotent stem cells into endodermal derivatives

  • Professor Antonio Adamo

    The Laboratory of Stem Cells and Diseases (STEMD-Lab) is seeking a highly motivated candidate to develop a project based on the use of human embryonic stem cells (hES) and induced pluripotent stem cells (iPSCs) to derive glucose sensitive differentiated cell types (i.e. beta-cells, hepatocytes and adipocytes). The proposed project is aimed at studying the epigenetic and transcriptional role played by key transcription factors and epigenetic modifiers in the regulation of glucose homeostasis in physiological and pathological conditions as well as upon exposure to extreme environmental stimuli.


    Priority will be given to students with good communication skills, strong self-motivation, ability to work in a team, and desire to carry out research in an interdisciplinary and international environment .  A strong background in cellular and molecular biology and excellent academic qualifications are mandatory.


    Applications including a CV, a one page statement on your motivation, past research experience and contact for two academic references should be sent to: antonio.adamo@kaust.edu.sa

    APPLY HERE

Developing programmable DNA-guided endonucleases for genome engineering

  • ​Professor Magdy Mahfouz

    Bacterial and archaeal species are rich with proteins used for DNA processing or host defense. We aim to engineer some of these proteins and test their ability to generate double strand breaks in a programmed and site-specific fashion. These catalytic activity assays will be conducted in vitro and in vivo in bacterial, mammalian, and plant cells. We look for candidates with broad expertise in molecular biology techniques preferably in protein purification and in vitro activity assays. Ample opportunities exist for training in molecular biology, synthetic biology, biotechnology, genetics, and plant molecular biology. Ambitious and self-motivated candidates are encouraged to apply.


    Priority will be given to candidates with BS and or MS in biology, biochemistry, genetics, microbiology, and plant molecular biology.


    Please send your CV, summary of research interests and technical portfolio in molecular biology, three references to Magdy Mahfouz magdy.mahfouz@kaust.edu.sa

    Apply Here

Molecular Genetics of Durable Disease Resistance in Wheat

  • Professor Simon Krattinger

    https://www.kaust.edu.sa/en/study/faculty/simon-krattinger

    The identification of agriculturally important genes in wheat had long been limited by its large genome, which is five times larger than the human genome. However, recent progress in wheat genomics, including the development of several rapid gene isolation strategies, will allow us to isolate and study the effect of genes much more rapidly in the future. In addition, the advancements in wheat genomics allow us nowadays to capture the sequence information of many different wheat cultivars and wild wheat relatives, which makes comparative analyses and genome-wide association studies feasible. The role of this PhD position is to incorporate these genomic advancements, as well as to develop novel approaches for gene identification and isolation. In particular, this position will focus on the cloning of several broad-spectrum stripe rust resistance genes in wheat.

    We are seeking an outstanding young scientist who has recently been awarded a MSc degree or equivalent in genetics, molecular biology, plant biology, agronomy or equivalent. Applicants must have a strong and demonstrated background in molecular plant genetics, including topics such as map-based cloning, genome-wide association studies, or high-throughput phenotyping (preferably disease resistance). Experience in cereal research is preferable.

    For questions relating to the position, kindly contact Prof. Simon Krattinger, simon.krattinger@kaust.edu.sa. Please send your application as single PDF-File by e-mail. Applications should include: full CV and publication list, a statement of research interests not exceeding one page, and three academic references. Applications are accepted from December 2018 until the position is filled. Position start date is April 1st 2019.

    apply here

Bioinformatics

  • Professor Manuel Aranda

    We are currently seeking a highly motivated candidate with strong bioinformatics background to pursue Ph.D. Our group applies functional and comparative genomics techniques to investigate the molecular basis of symbiosis and adaptation in corals and related cnidarian model organisms.  The respective projects are focused on NGS data analysis and include RNAseq, genome and transcriptome assembly as well as bisulfite and ChIP-Seq data.

    The successful candidate will join the Group of Prof. Manuel Aranda at the Red Sea Research Center of the King Abdullah University of Science and Technology (KAUST) [https://coralsymbiomics.kaust.edu.sa/Pages/Home.aspx]. Strong computational skills in the areas of Perl or Python programing as well as the proficient use of open source software for data processing and analysis of NGS data are required.

     

    Scope:

    • Handle and analyze NGS data (Illumina, PacBio)
    • Develop, assess, and adapt new technologies, protocols, and software
    • Write proposals and manuscripts for publication
    • Attend international conferences and events

    Requirements:

    • Masters or Undergraduate degree with emphasis in bioinformatics AND molecular biology OR genetics
    • Must have bioinformatics skills and strong understanding of basic biology, genomics, high-content data analysis, and genome databases
    • Experience in programming, databases and Unix/Linux (Python or Perl, R,)
    • Experience with bioinformatics software such as assemblers, mappers, and general tools
    • Basic statistics and Next-gen sequencing pipeline experience

    Locale:

    KAUST is a dynamic new university campus and campus community in Saudi Arabia that opened in September 2009. The campus is located directly at the Red Sea, near Jeddah. More information is available at www.kaust.edu.sa.

     

    Compensation:

    The position includes a highly competitive stipend, accommodation, annual leave, and health insurance.

     

    To apply:

    Please send cover letter summarizing your qualifications and interests, a curriculum vitae, and the names and contact information for 2 references to manuel.aranda@kaust.edu.sa, arun.nagarajan@kaust.edu.sa. Applications that do not fulfill requirements outlined above will not be considered.

     

    Deadline:

    Open till filled

    apply here


Visiting student internship Opportunities

The Visiting Student Research Program is an opportunity for exceptionally qualified international baccalaureate and post-baccalaureate students to conduct research with faculty mentors in selected areas of basic and applied research projects. The duration of the program ranges from between four and six months, depending on the research project.  Active projects are listed below.


An iPSCs-based approach to model Type Two Diabetes in-vitro


  • Faculty Name: Professor Antonio Adamo


    Internship Project Description

    Studying the transcriptional and epigenetic mechanisms dysregulated in patients affected by metabolic disorders such as insulin resistance (IR) and type 2 diabetes mellitus (T2DM) is essential to derive efficient pharmacological approaches. We are seeking an outstanding student to work on a project focused on the study of the role of histone modifiers to the onset of metabolic disorders.

    Deliverables/Expectations

    The selected candidate will use human stem cells and terminally differentiated glucose sensitive cell types and will acquire skills in molecular biology techniques including Chromatin Immuno-precipitation (ChIP), quantitative real-time PCR (Q-PCR) and next generation sequencing (NGS)

    Field of Study

    Molecular and Cellular Biology and/or Bioinformatics

    Apply Here

Exploring gene functions in an obligate intracellular parasite Theileria using CRISPR-Cas9 technologies

  • Faculty Name: Professor Arnab Pain


    Internship Project Description

    Background: Theileria is a unique and remarkable apicomplexan parasite capable of transforming its host leukocyte into a disseminating cancer-like tumour and it is the only known example of natural reversible transformation of mammalian host leukocytes by an eukaryotic parasite. T. annulata is the causative agent of the cattle disease called tropical theileriosis, which is of major economic importance in countries in Northern Africa, The Middle East and Asia. Importantly, the tumor-like phenotype is reversed upon drug-induced parasite death. Moreover, virulent macrophages can be attenuated by multiple in vitro passages, and upon attenuation, they lose both adhesion and invasiveness. Transfection systems are available for several important species of protozoa, including the apicomplexan parasites Toxoplasma gondii, Eimeria tenella and Plasmodium spp. However, such approaches are not available for Theileria spp.

    Objectives: In this study, we aim to test the feasibility of new delivery systems to create genetic tools for the study of T. annulata genes. The CRISPR‐Cas9 system is a powerful tool for gene editing in various cells and organisms, but delivery of CRISPR‐Cas9 plasmids into cells or tissues is challenging, because the vectors encoding both Cas9 and sgRNA are handicapped by both a strong negative charge and a large size.

    Methodology: In order to achieve our objective, we propose to develop nanoparticles to deliver the CRISPR genome-editing system into T. annulata-infected leukocytes and specifically modify expressed parasite genes. This study will be performed in active collaboration with KAUST experts in the nanomaterials field


    Deliverables/Expectations

    This study will fill a technology gap in Theileria research by enabling systematic and genome-wide functional studies of parasite gene functions, and facilitating assessment of many aspects of the biology of this unique host-apicomplexan parasite interaction. Moreover, defined vaccines created by genetically manipulating parasite genes and validation of antigens will become a possibility.

    Field of Study

    Microbiology, Molecular Biology, Cell biology, Parasitology

    Apply Here

Compositional biases in the genomes of human malaria parasites

  • Faculty Name: Professor Arnab Pain


    Internship Project Description

    Genomic sequence variation is available from around two and a half thousand natural isolates of the human malaria parasite, Plasmodium falciparum. P. falciparum displays an extreme composition of its genome, where almost 80 percent of all bases are A or T, yet little is known about the evolutionary driving forces behind this highly biased composition. Preliminary analysis of subsets of natural isolates showed a strong bias in the direction of genomic changes between the reference genome sequence and the isolates. This project aims at analyzing this pattern in closer detail. This includes a comprehensive analysis of all available data, and a specific analysis of the observed genomic changes in terms of where the changes reside in the genome. Changes can occur in both non-coding and protein-coding regions, and within the latter changes may or may not cause differences in the encoded proteins. Such changes are referred to as non-synonymous and synonymous changes, respectively. The available data has been extensively analyzed by the scientific community in terms of population structures and selection patterns, but not from a purely compositional point of view

    Deliverables/Expectations

    An account of the genomic changes in natural P. falciparum isolates, along with their positions in the genome. An analysis of any compositional biases apparent in this data

    Field of Study

    Bioinformatics, molecular evolution

    Apply Here

Roles of novel miRNAs in leukocyte transformation – using Theileria-leukocyte transformation as a model

  • Faculty Name: Professor Arnab Pain


    Internship Project Description

    Background: Theileria is a unique and remarkable apicomplexan parasite capable of transforming its host leukocyte into a disseminating cancer-like tumour and it is the only known example of natural reversible transformation of mammalian host leukocytes by an eukaryotic parasite.  T. annulata is the causative agent of the cattle disease called tropical theileriosis, which is of major economic importance in countries in Northern Africa, The Middle East and Asia. Importantly, the tumor-like phenotype is reversed upon drug-induced parasite death. Moreover, virulent macrophages can be attenuated by multiple in vitro passages, and upon attenuation, they lose both adhesion and invasiveness. T. annulata-mediated transformation of host B cells and macrophages is associated with a major modulation of host cell gene expression involving major transcription factors genes such as NF-κB, c-Myc and AP and other genes involved in host signaling pathways and many protein-encoding genes such as MMP9, RASGRP1, GZMA and non-coding RNAs such as miR126, miR155 have been functionally implicated in Theileria-mediated leukocyte transformation and dissemination. With the availability of next generation sequencing technologies (such as Illumina miRNA-seq), it is possible to obtain an unbiased and comprehensive catalogue of miR gene expression and an understanding of their perturbations due to T. annaulata-mediated leukocyte transformation. In a recent study, miRNA-seq was used to define the miR-expression landscapes of T. annulata-transformed B-cell and macrophage cell lines and we have identified several oncogenic miRs relevant to cellular transformation and dissemination. Bioinformatic comparisons of the miR expression catalogues has identified several candidate novel miR-like sequences whose expresson is modulated during infection.

    Objectives: In this study, we aim to functionally verify the existence of potential novel miRs relevant to infection and functionally characterize their roles in Theileria-mediated transformation of bovine host host cells and eventually explore if these miRs are indeed also present and expressed in human and play any role in cell proliferation and dissemination during tumorigenesis. 

    Methodology: We propose to bioinformatically re-analyse the miRnome datasets generated previously by our group to look for novel miRs and quantify their expression landscapes by Q-RT-PCR and finally test their functional roles and cellular targets by routine cell biology techniques with inhibitors and over expression of novel miR candidates. Finally, we will be screening a panel of human cancel lines to check for their existence in the context of human cancer progession and dissemination phenotype.

    This study will be performed in active collaboration with KAUST experts in the tumorigenesis field.

    Deliverables/Expectations

    This study is expected to discover previously unknown miRs and their cellular targets / functions not only in Theileria-mediated leukocyte transformation and dissemination but also thei potential roles in mammalian cell proliferation and dissemination.

    Field of Study

    Microbiology, Molecular Biology, Cell biology, Parasitology

    Apply Here

​ Development of a novel Stimulated Raman Scattering microscopy system

  • Faculty Name: Professor Carlo Liberale


    Internship Project Description

    Microscopy techniques based on vibrational spectroscopy are poised to be part of the next generation of microscopes for biological applications based on their unique chemical contrast and sub-cellular resolution for non-invasive, non-destructive and label free imaging of biological samples as live cells. The project will focus on the development of a fast and low-noise detection system in a setup for microscopic vibrational spectroscopy based on Stimulated Raman Scattering, which is one of the most advanced and sensitive methods for label-free microscopy for bio-imaging. The system will be applied to vibrational imaging of cancer stem cells to unveil their specific bio-chemical signatures

    Deliverables/Expectations

    Learn Coherent Raman Scattering techniques. Design, assemble and test circuitry for multiplexed and low-noise detection in a Stimulated Raman Scattering microscopy setup based on femtosecond broadband laser sources. Demonstrate fast and high S/N ratio imaging with multiplex (broadband) Stimulated Raman Scattering microscopy.

    Field of Study

    Electrical Engineering, Physics


    Apply Here

Novel Micro-optical structures on optical fiber tip with two-photon lithography

  • Faculty Name: Professor Carlo Liberale

    Internship Project Description

    Optical fibers are nowadays an ubiquitous core element of telecommunication systems, new laser technologies and biomedical devices. Manufacturing techniques for optical fibers have been developed and refined in order create manifold geometries and optical properties (e.g.
    Dual clad fibers, fiber bundles, Photonic Crystal Fibers, to name a few). Yet the capability to fabricate complex miniaturized structures integrated with optical fibers to realize important optical functions (like beam shaping, beam deflection, fiber optical tweezers, etc.) has been demonstrated only very recently.

    The project will focus on the fabrication of optical wave-guiding structures on the tip of optical fibers exploiting to flexibility, resolution and 3D fabrication capability of Laser Direct Writing based on Two-Photon Lithography (TPL).​

    Deliverables/Expectations

    Learn Two-Photon Lithography. Design structures using wave-optics propagation software. Fabricate structures on optical fibers. Measurements to assess optical function of fabricated structures.

    Field of Study

    Electrical Engineering, Physics

    Apply Here

Plant-Beneficial Microbe Interaction

  • Faculty Name: Professor Heribert Hirt


    Internship Project Description

    Abiotic stresses are the most important factors for hampering plant growth and yield world-wide. However, beneficial microbes can help plants to enhance stress tolerance of plants. DARWIN 21 is a large scale project to isolate and study the interaction how rhizophere microbes contribute to enhance the capacity of plants under the most difficult abiotic stress conditions (http://www.darwin21.net/index.htm).

    In this project, the student will characterize several rhizosphere microbes and investigate whether they can confer plant resistance to different abiotic stresses. The student will learn how to apply techniques in microbiology, molecular biology and plant biology.

    Deliverables/Expectations

    Isolation and characterization of bacterial strains. Analysis of beneficial microbes on plant physiology. Sequencing and bioinformatics to analyze microbial genomes, transcriptome and proteome analysis of beneficial microbes and plants.

    Field of Study

    Microbiology, Genomics, Plant biology, Bioinformatics

    Apply Here

A Mobile Application for Measuring Contact Angles


  • Faculty Name: Professor Himanshu Mishra


    Internship Project Description

    Small drops of liquids are ubiquitous in our daily life, for example, morning dew on flowers, leaves and spider webs are some common examples.  Typically, the interface at the solid-liquid-gas contact line forms a contact angle that represents the mechanical equilibrium of the interfacial tensions. In a lab setting, contact angle have been traditionally measured by taking images and using a goniometer. These days, however, image-processing software are routinely employed for accurate and quick estimation of contact angles. Unfortunately, due to the bulkiness of contact angle instruments and their cost proprietary software, experiments are limited to confines of laboratories that can afford them. We would like to change this trend by using smart phones.

    We propose to develop a software application for smartphones, which will take input from the mobile camera and calculate contact angles, base diameters, and drop volumes in real-time for real world experiments. The application would be developed in Android as well as iOS platforms. The application will have a user-friendly interface to obtain the contact angles and save and share data. Both specialists and amateur scientists will welcome such an application.

    Deliverables/Expectations

    Develop a software application for smartphones (Android as well as iOS platforms), which will take input from the mobile camera and calculate contact angles, base diameters, and drop volumes in real-time for real world experiments. 
    Develop a user-friendly interface to obtain the contact angles and save and share data.

    Field of Study

    Computer Science, Electrical engineering, Information Technology​

    Apply Here

Chemistries in Electrosprays

  • Faculty Name: Professor Himanshu Mishra


    Internship Project Description

    When a polar or non-polar liquid passes through a narrow metallic capillary (~0.1 mm), connected to electrical voltage (~3 kV), the liquid breaks into what is known as an electrospray. Electrosprays are exploited in analytical techniques, such as Electrospray Ionization Mass Spectrometry (ESIMS), to characterize ionic or neutral species in the solution. Recently, we observed that the rate of polymerization of isoprene (C5H8) was dramatically enhanced in electrosprays in comparison to reactions in condensed phase and oil-water emulsions. However, the underlying mechanisms are unclear. We would like to understand the effects of electrical voltage, temperature, capillary diameters, gas flow rates, etc., factors on the rates of reactions.

    Deliverables/Expectations

    The VSRP intern will work with a senior graduate student and learn the following skills:
    Laboratory experiments: ESIMS, voltage sources, identifying reactions of interest
    Theory: basic electrostatics, data analysis, data plotting
    We expect the intern to be driven by curiosity, hard working, and thrive in a multicultural work environment.​

    Field of Study

    Engineering, Physics, Chemistry, Applied Math

    Apply Here

Wetting Transitions in Doubly Reentrant MicroTextures

  • Faculty Name: Professor Himanshu Mishra


    Internship Project Description

    Our research Group has recently reported on surface microtextures comprising of doubly reentrant cavities that render common surfaces omniphobic, i.e. an ability to sustain non-wetting states. Remarkably, omniphobicity of our microtextures is not compromised even if there is minor surface damage or if surfaces are immersed in wetting liquids. To further assess the suitability of those microtextures for marine applications, we are investigating the role of capillary condensation, liquid imbibition along corners, and gas dissolution on wetting transitions in our microtextured surfaces on immersion.​

    Deliverables/Expectations

    The VSRP intern will work with senior Group members and learn the following skills:
    Laboratory experiments: contact angle cells, immersion studies, imaging (optical and confocal), microfabrication and IIID printing
    Theory: data analysis, data plotting
     We expect the intern to be driven by curiosity, hard working, and thrive in a multicultural work environment.​

    Field of Study

    Engineering, Physics, Chemistry, Applied Math

    Apply Here

Evaporation of liquid marbles

  • Faculty Name: Professor Himanshu Mishra


    Internship Project Description

    Interestingly, when a drop of water is rolled on a powder made of hydrophobic particles, the particles adsorb onto the liquid-vapor interface, creating what are known as ‘liquid marbles’. Liquid marbles can roll around; collide gently, etc., without releasing water.

    Recently, we observed that the rates of evaporation of water from liquid marbles could be higher or lower in comparison to bare water drops depending on the choice of hydrophobic particles.  To understand what factors control these phenomena, we will conduct systematic experiments and theoretical analysis.

    Deliverables/Expectations

    The VSRP intern will work with a senior graduate student and learn the following skills:
    Laboratory experiments: wet chemistry (silanation of glass beads), optical imaging
    Theory: data analysis, data plotting
    We expect the intern to be driven by curiosity, hard working, and thrive in a multicultural work environment

    Field of Study

    Engineering, Physics, Chemistry, Applied Math

    Apply Here

Learning Generative Causal Models from Sparse Temporal Observations during Cellular Reprogramming

  • Faculty Name: Professor Jesper Tegner


    Internship Project Description

    Recent work on stem cells and different mature specialized cells in different systems/organs  (neurons, blood cells,) has revealed a stunning plasticity and capacity of reprogramming cells. For example, mature cells can be reprogrammed into pluripotent stem cells, and exciting work on engineered design of tissues and organs (organoids) are underway. On the one hand the community has since the sequencing of the human genome produced very efficient tools to read off the corresponding molecular events accompanying reprogramming and engineering of cells. Recently, the discovery of the CRISPR techniques has equipped us with unprecedented opportunities for precise writing or editing of the genomes. These developments in fundamental biology and biotechnology are currently opening new tools and perspectives of vital significance for drug development, regenerative medicine, synthetic biology, and personalized medicine. Yet, in essence all these efforts require and would be greatly facilitated if we could advance from correlative data-analysis to a predictive discovery of which interventions (edits, engineering) are producing which effects. Thus, we are facing the fundamental problem on how to discover causal relations from data, or in other words, can we derive quantitative predictive laws from data?
    We offer internships for several highly motivated bachelor (B.Sc.) or master (M.Sc.) students who will explore this fundamental question primarily from a computational standpoint. This includes using high-performance simulations of dynamical models, and design of algorithms in a controlled in-silico environment.  For example, to identify (a) efficient algorithms for generation of ensembles of dynamical models, (b) use supervised deep learning algorithms for pattern discovery in large-scale simulation data-sets, (c) to perform deep data-driven analysis of computational models in biology, (d) pursue investigations of transfer entropy and related techniques for system identification. These tools will be tested utilizing rich and recent molecular data on cellular reprogramming.

    Deliverables/Expectations

    Individual projects will be tailored and narrowly designed from the above palette according to interest of the student, technical proficiency, and level of study. The project is suitable for candidates fascinated by dynamical causal systems, be it computational or those we find in the natural world, i.e. living cells. We expect you (a) to bring enthusiasm, creativity, and hard work, (b) give lab seminars on your work, and (c) produce a final written report. In return this facilitates your critical thinking, presentations skills, and scientific writing. Your research, in collaboration and with support of team members, may lead to scientific publications. We publish avidly in both bioscience and computational sciences, not for the fame but rather as steps aiming to and motivated both by our quest of asking fundamental questions of relevance to human nature and discovery of transformative intelligent technologies inspired from nature. You will get a good hands-on perspective on the frontiers in dynamical systems and bioscience using state-of-the-art simulation and machine learning tools.

    Field of Study

    computer science, mathematical modeling, machine learning, systems biology, bioscience

    Apply Here

Deep Learning and Machine Intelligence for Single Cell Genomics

  • Faculty Name: Professor Jesper Tegner


    Internship Project Description

    Single cell biology and genomics in particular are currently transforming the biosciences. Single cell RNA sequencing (scRNAseq), method of the year 2013 (Nature Methods), has now matured and large amounts of scRNAseq are now available. These data, characterizing living systems at an unprecedented level of resolution, hold the promise to set the stage for a fundamental quantitative understanding of living systems with special reference to genomic regulation and collective computation. Yet, there are a number of open problems on how to think about these data and how to pragmatically analyze them.
    In parallel, we have witnessed a rapid development in machine learning. The rise of computation, such as supercomputers (shaheen@KAUST) and GPU based techniques, in conjunction with data explosion (often referred to as big data), has fuelled the development of new techniques aiming for machine intelligence. In particular, techniques inspired from livings systems, such as deep convolutional networks, currently experience a renaissance. Driving forces include not only data and computation but also the availability of suite of open source platforms (e.g. Theano, Caffe, Torch7, TensorFlow) supporting machine-learning algorithms. These algorithms represent industry standard for processing images, speech, text, and runs on the majority of services and devices provided by Google, Amazon, Facebook, to name a few big players, as well as a numerous startups.
    We offer internships for several highly motivated bachelor (B.Sc.) or master (M.Sc.) students who will identify (a) appropriate supervised deep learning architectures and training algorithms for scRNAseq data, (b) explore generative adversarial network (GANs) techniques for estimation of high-dimensional data distribution in the single cell gene expression space. This work will be used to develop new techniques and to address open problems in single cell genomics such as pseudo-temporal ordering of single cell data, clustering of data, investigate representations, transfer learning, and unsupervised feature discovery.

    Deliverables/Expectations

    Individual projects will be tailored and narrowly designed from the above palette according to interest of the student, technical proficiency, and level of study. The project is suitable for candidates fascinated of living systems, interested in cutting edge bioscience, and artificial intelligence for science and not for discovering cats in YouTube. We expect you (a) to bring enthusiasm, creativity, and hard work, (b) give lab seminars on your work, and (c) produce a final written report. In return this facilitates your critical thinking, presentations skills, and scientific writing. Your research, in collaboration and with support of team members, may lead to scientific publications. We publish avidly in both bioscience and computational sciences, not for the fame but rather as steps aiming to and motivated both by our quest of asking fundamental questions of relevance to human nature and discovery of transformative intelligent technologies inspired from nature. You will also get a good hands-on perspective at the frontier of bioscience and machine intelligence in an interdisciplinary research group and environment.

    Field of Study

    computer science, bioscience, machine learning, systems biology, artificial intelligence​

    Apply Here

Improving coral thermal tolerance through association with acclimatized Symbionts

  • Faculty Name: Professor Manuel Aranda


    Internship Project Description

    Corals have shown capable of coping with increasing temperatures; however strong inter-species and intra-species variation is evident. Different thermal tolerances between members of the same species have been attributed partially to the associated zooxanthellae. The Red Sea offers a unique environment to understand these associations as host and symbiont live in higher annual temperatures than counterparts elsewhere. Using the coral model organism Aiptasia pallida, a small anemone, we investigate whether Symbiodinium from anemones of the Red Sea can improve heat stress resilience of individuals from geographically distant locations.

    Deliverables/Expectations

    Bleaching and re-infecting anemones with different strains of Symbiodinium cultured in the lab
    Quantification of phenotypic changes between host-symbiont combinations during and after heat stress exposure
    RNA extraction and gene expression analysis of interesting and informative biomarkers
    Perform further analysis on data obtained.
    Write a (short) manuscript of these analyses​.

    Field of Study

    Biological Sciences, Marine Sciences

    Apply Here

High resolution remote sensing of agricultural systems for improved water and food security

  • Faculty Name: Professor Matthew McCabe


    Internship Project Description

    A range of high-resolution (1-10m) space based commercial systems have recently become available for earth observation. There is considerable capacity to develop products on various terrestrial surface features from these, including vegetation health and stress, land cover changes and even digital surface models. Here we will explore some of these opportunities using high-resolution commercial as well as government based satellite systems, with a focus on applications in precision agriculture.

    Deliverables/Expectations

    Skill development in programming (Python, Matlab); analysis and interpretation of high-resolution satellite imagery; derivation of geospatial data sets for food and water security assessment; knowledge development related to remote sensing, water resources, agricultural systems, machine learning and big data analysis.

    Field of Study

    Computer science, civil and environmental engineering, statistics, applied math

    Apply Here

Anaerobic membrane bioreactor as a decentralized municipal wastewater treatment technology

  • Faculty Name: Professor Peiying Hong


    Internship Project Description

    This project looks into scaling up anaerobic membrane bioreactors to treat municipal wastewaters. A pilot-scale anaerobic membrane bioreactor will be constructed and operated to treat municipal wastewater. Reactor performance will be evaluated along with the effluent quality.

    Deliverables/Expectations

    The deliverables are to come up with a process reactor design for the scaled-up anaerobic membrane bioreactor; a lab-scale anaerobic membrane bioreactor will be operated to treat municipal wastewater; reactor performance will be assessed; effluent quality will be measured; effluent will be used to irrigate agricultural crops; crop yield and health will also be evaluated in collaboration with Professor Ikram Blilou’s group.

    Field of Study

    Chemical or Process Engineering ​

    Apply Here

Screening for Carotenoid-Derived Signaling Molecules

  • Faculty Name: Professor Salim AlBabili


    Internship Project Description

    The project focuses on novel signaling molecules involved in plant development and response to environmental stress. It includes studies on the activity of selected carotenoid-metabolizing enzymes and the identification of their enzymatic products. Biological activity of products will be investigated by developmental assays using Arabidopsis and rice and by determining the effect of these compounds on the transcript levels of selected genes including strigolactone biosynthesis genes. These studies will be complemented by geno- and phenotyping of mutants disrupted in the corresponding genes.

    Deliverables/Expectations

    Identification of new bioactive compounds/Better understanding of the regulation of strigolactone biosynthesis. Significant contribution to a publication

    Field of Study

    Plant Biochemistry and Development

    Apply Here

Structural Landscape of Genetic Diseases


  • Faculty Name: Professor Stefan Arold


    Internship Project Description

    Advances in gene sequencing have led to the production of a wealth of data linking gene mutations to patient phenotypes. Structural biology can often reveal the underlying molecular basis of a particular protein mutation but existing tools only look at one gene at the time. This project aims at producing a software tool that allows performing this structure-function analysis on a large scale and thus to analyze structural mechanisms of diseases from big data resources

    Deliverables/Expectations

    Creation of several modules to compute/retrieve sequence-and structure-based properties and integrate them in 3D (structure) space;  Conversion and cleanup of high-quality human mutation data from clinical collaborator; Integration and correlation of both.

    Field of Study

    Computer science, bioinformatics 

    Apply Here

Structural Biology of Immune Signalling

  • Faculty Name: Professor Stefan Arold


    Internship Project Description

    In the Arold lab, we use biochemistry, biophysics and structural methods such as X-ray crystallography, small angle X-ray scattering, nuclear magnetic resonance and cryo-electron microscopy to reveal the 3D structure of protein complexes involved in controlling the immune system. The student will be embedded in a team of structural biologists and help with protein production and biochemistry, crystallization screens and EM particle picking. Some prior wet-lab experience would be a plus.

    Deliverables/Expectations

    Recombinant production and purification of proteins. Biophysical protein assays. Structure determination of proteins or protein-ligand complexes.

    Field of Study

    Computer science, bioinformatics 

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Virtual Reality for multi-domains protein

  • Faculty Name: Professor Stefan Arold


    Internship Project Description

    The goal of this project is to enhance our understanding of protein structure and function in two complementary ways. Firstly, we wish to enhance our existing tool for visualisation and manipulation of protein structures in a true 3D virtual reality. Secondly, we wish to produce an interactive tool that allows scientists to build natural or synthetic multi-domain proteins by combining their known protein domains and the (natural or synthetic) regions linking these domains into a ‘3D nanomachine’.

    Deliverables/Expectations

    1) Using A-Frame, Javascript, and Python, improve our existing visualisation and manipulation tool. New features can be: support of multimers, integration of the tool developed in point 2)
    2) To produce a python wrapper/pipeline from currently separate softwares to allow producing 3D molecular models from protein sequence and known structures of (isolated) protein domains.

    Field of Study

    Computer sciences, bioinformatics, biosciences 

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Polymeric membranes for liquid separation

  • Faculty Name: Professor Suzana Nunes


    Internship Project Description

    Development of polymeric membranes for different separations, aiming at applications in the chemical industry or water treatment.  The project will involve polymer modification or crosslinking, morphology control and characterization, and filtration performance evaluation. 

    Deliverables/Expectations

    Membranes with controlled porosity and different chemical functionalizations
    Morphology imaging (electron microscopy)

    Field of Study

    Chemistry, chemical engineering, polymer science

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Fouling in Membrane Filtration Systems


  • Faculty Name: Professor TorOve Leiknes


    Internship Project Description

    In the last decades the use of membrane systems for fresh water production has increased strongly to supply the growing water demand due to increasing human population, industrial and agricultural activity, economic growth and urbanization. Fouling represent one of the major drawbacks of membrane systems. In this project, we aim to explore different techniques in order to study the fouling developed in the system and relate with the membrane performance decrease. ​

    Deliverables/Expectations

    ​The student will learn various approaches to characterize the fouling developed in membrane filtration systems. He/She will learn different techniques (i.e. Confocal, Flow Cytometry, ATP, SEM, LCOCD etc). Several experiments will be run in order to relate the fouling developed in the system with the overall performance.

    Field of Study

    Environmental science and engineering

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Development of algorithms to decipher the complexity of chromation organization

  • Faculty Name: Professor Wolfgang Fischle


    Internship Project Description

    Cells control gene expression by means of dynamic changes in chromatin. Different functional chromatin states are the result of highly combinatorial patterns of DNA- methylation, histone modifications, sequence specific DNA - binding proteins and chromatin accessory factors. The advent of large-scale, high- throughput experiments has resulted in the generation of an immense array of genome association data ( enrichment profiles) of chromatin components. Computational epigenetics is an interdisciplinary area of research that involves the development of computational methods to analyze and conceptionalize large scale epigenomic data. 

    At the Chromatin Biochemistry lab, we are developing computational methods for integrative analysis of Big-Data from ,odENCODE (1) to better understand the complexity of (epi) gennomic information. Decoding the increasingly large volumes of Bid-Data sets involves deciphering signal patterns and to systematically quantify the localization of these signal intensities.

    Deliverables/Expectations

    Develop (or assist/apply) computational method for segmentation of genomes using a combination of epigenomic datasets
    Application of machine learning techniques to predict the​ 3D architecture of epigenomic segments
    Maintain good log (CVS), submit progress in writing and present results
    Final report summarizing and explaining all project work.

    Field of Study

    ​computational biology, bioinformatics, informatics

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Development of a 3D colorectal cancer model based on 3D bioprinted organoids for drug screening applications

  • Faculty Name: Professor Charlotte Hauser


    Internship Project Description

    Colorectal cancer is one of the main cancer types which often leads to metastasis and ultimately cause the death of the patient. Early detection and improved treatments for colorectal cancer can prevent the death of the patients. To detect colorectal cancer at an early stage and to develop an effective treatment, in vitro 3D models are required. This project involves the 3D bioprinting of a colorectal cancer cell line for the development of an in vitro 3D colorectal cancer model. Ultrashort peptides will be used as bioinks to perform 3D bioprinting of the colorectal cancer cell line. After 3D bioprinting, the 3D constructs will be analyzed using fluorescence microscopy for the formation of the organoids. The formation of the organoids in the 3D constructs will help to create a functionally relevant model for colorectal cancer to compare with the in vivo situation.

    Deliverables/Expectations

    Formation of 3D bioprinted organoids related to colorectal cancer

    Field of Study

    Biomedical Engineering

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Investigation on the sequence-structure-function relationship of pathogenic, destructive human tau aggregates abundantly found in patients with chronic traumatic encephalopathy (CTE) and Alzheimer’s to explore synthetic small peptide inhibitor compounds.

  • Faculty Name: Professor Charlotte Hauser


    Internship Project Description

    Compelling evidence suggests that tauopathies like Alzheimer’s (AD) disease with deleterious impact on memory, cognition and motion are age-related, since they are commonly found in the elderly population. However, repetitive traumatic brain injuries found in young football and boxing athletes, military veterans below their 40s or in abused victims show similar neuropathological symptoms like memory loss, suicidality, confusion, depression, anxiety and debilitation due to chronic traumatic encephalopathy (CTE). The premature, often suicidal,  death cases of multiple US National Football League (NFL) players were found to be caused by CTE demonstrating an abnormally high level of toxic tau aggregates.  Our study aims to identify the sequence-structure-function relationship of pathogenic tau isoforms, and investigate newly designed small molecule peptide inhibitors in suitable in vitro and in vivo models. We will sequence the isolated CTE and AD subject-related tau protein isoforms and study post-translational modifications, particularly the phosphorylation signature of the tau isoforms, seen as a key factor for tau pathologies. Structure-function studies will be complemented at KAUST with sophisticated NMR and dynamic simulation studies. Thus, regarding structural cross-connectivity within tau isoforms that are expressed in CTE and AD subjects, new avenues with suitable therapeutic disease​ intervention strategies for CTE and AD will be explored. Building on our expertise in synthetic peptide chemistry and our current understanding of amyloidogenesis, we will explore the suitability of designed peptide amyloid inhibitors that in case of success could be further tested in clinical trials.

    Deliverables/Expectations

    chemical synthesis of peptides, supramolecular chemistry of peptide self-assembly into nanofibers, peptide-based inhibitors for tau and amyloid beta aggregation​

    Field of Study

    Biochemistry and Biomedical engineering

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Salinity tolerance of plants

  • Faculty Name: Professor Mark Tester


    Internship Project Description

    Soil salinity is a major abiotic stress constraining crop production. We are investigating how some plants are able to cope with salt stress, to then inform research on other crops to make them more tolerant to salinity stress. Quinoa (Chenopodium quinoa) tastes good, is highly nutritious and is a very salt tolerant crop; however, we are yet to discover the mechanisms for its high salt tolerance. This is one species that we are currently studying. We are also looking at mechanisms of tolerance in wild relatives of domesticated crops, in particular wild tomatoes and wild barley.

    Deliverables/Expectations

    Lots of good research / lots of hard work and fun.

    Field of Study

    Biology and Computer Science

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Molecular hospitality seen by NMR spectroscopy

  • Faculty Name: Professor Mariusz Jaremko


    Internship Project Description

    Supramolecular chemistry is the domain of chemistry beyond that of molecules that focuses on the chemical systems made up of a discrete number of assembled molecular subunits or components stabilized usually by weak interactions as van der Waals or electrostatic forces, or hydrogen bonding. Cyclodextrins (CD), one group of so called host molecules, are macrocyclic oligosaccharides composed of several glucosidic units. Other molecules called guests can enter their cavity forming inclusion complexes. In aqueous solutions, CDs can form guest/host inclusion complexes with many partially or fully lipophilic molecules. The inclusion CD complexes are widely used in modification of solubility and stability of pharmaceuticals, food and cosmetic additives, or enzyme simulation studies. Many physicochemical methods have been used to study the formation of weak inclusion complexes in solid and liquid states. There is no doubt that some methods are better suited to study such complexes than others, and among the nonseparation methods nuclear magnetic resonance spectroscopy is one of the most widely used because it delivers a wealth of highly reliable information at the atomic resolution level.

    Deliverables/Expectations

    Within the framework of the proposed project the participating student will learn about the supramolecular chemistry of cyclodextrin as well as extend own knowledge on the different host-guest interactions. The main method of the study of mentioned phenomena will be the Nuclear Magnetic Resonance (NMR) spectroscopy

    Field of Study

    chemistry, bioscience, physics, or engineering background

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Spatio temporal analysis of expression of genes controlling assymetric stem cell division and tissue patterning in plants

  • ​Faculty Name: Professor Ikram Blilou

    Internship Description

    BIRDs nuclear factors have been described to regulate root growth through association with the transcription factors SCARECROW and SHORTROOT, however their function in other organs remain to be elucidated. Here we propose to dissect network function in lateral roots and leaves. We will determine their physical associations spatially and during different developmental stages. We will also assess whether their target are regulated similarly.

    Objectives: In this project we aim to dissect how BIRD proteins regulate leave tissue patterning and map their localization in different mutant backgrounds. In addition, we will dissect binding sites in different target genes and alter specific binding by site directed mutagenesis.

    Technologies: confocal imaging microscopy, site directed mutagenesis, promoter activities using dual luciferase, plant phenotyping, cloning using gateway technology

    Deliverables/Expectations

    Map the expression of the genes at different developmental stages and dissect thein binding motifs

    Field of Study

    Plant Biology

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Effect on plant growth and microbial food safety arising from treated anaerobic effluent irrigation

  • Faculty: Professor Peiying Hong

    Internship Description

    Currently, about 70% of the global freshwater supplies are withdrawn for agricultural irrigation. Food production is water-thirsty and with the projected increase in global human population from the current 7 billion to 9.7 billion in 2050, the amount of water to be channeled into food production is expected to increase in the near future. Intensive mining of non-renewable groundwater supplies for food production is unsustainable. Alternative water resources like treated wastewater should be considered so as to alleviate the demand on groundwater and surface water.

     

    One of the barriers towards safe water reuse is the wastewater treatment process. In particular, existing wastewater treatment plants have to be retrofitted with membrane filtration to ensure a substantial removal of emerging contaminants.  However, existing membrane bioreactors are generally aerobic systems which incur high energy costs. In contrast, anMBRs have several advantages. First, anMBRs generate energy that can be harvested to operate the process as a decentralized system. This is significant as most agricultural fields are off the infrastructure grid. Second, anMBRs do not produce a large amount of sludge and hence diminish the need for solid disposal. Third, the membrane separation unit improves effluent quality. Fourth, anMBRs produce effluents that retain the original concentration of nitrogen and phosphorus. This nutrient-rich effluent can be used to irrigate and fertilize the crops.

     

    This project therefore hypothesized that crop yield obtained from treated anaerobic effluent would be maintained at a comparable rate as that obtained from groundwater or partial desalinated water, without the need to add further N and P fertilizers. It is further hypothesized that the high quality effluent, being collected post membrane filtration, would not detrimentally impact food safety. The proposed project aims to demonstrate the validity of both hypotheses. 

    Deliverables/Expectations

    Growing of lettuce or tomato plants over a 2 month period to assess impact on leafing, flowering and fruiting process. Characterize microbial community in crops and soils exposed to treated wastewater 


    Field of Study

    Applied microbiology; environmental sciences

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Interaction between cells and magnetic nanoparticles for synergic magnetic and plasmonic-based hyperthermia studies

  • Faculty: Professor Andrea Falqui


    Internship Description

    It is known that promoting nanoparticles uptake from cells could bring to several applications. Among these application, two are based on the capability of nanostructured object to produce heat. In fact, if the nanoparticles are magnetic and showing a non-null hysteresis loop from room temperature to more than 45 degrees, they are able to produce heat once put in an oscillating magnetic field of proper strength and frequency. As well, a similar effect could be obtained irradiating gold nanoparticles with light of proper wavelength. The main aim of this project is then promoting the nanoparticles uptake from glioblastoma STEM cells, being the glioblastoma the most aggressive brain tumor. To enhance the heating effect, the cells will be treated with bot magnetic and gold nanoparticles, then submitted to a concomitant alternative magnetic field and light irradiation, in order to get a synergic response from the two heating nanopopulations. If possible, also a control cell line (healthy astrocytes) will be submitted to the same treatment to compare the nanoparticles uptake with that observed in the glioblastoma STEM cells. The effect of the nanoparticles uptake will be measured from a macroscopic point of view (i.e., by studying the possible temperature increase) and the cell overall structure and ultrastructure will be investigated, before and after the treatment with the nanoparticles, by both confocal and electron microscopy imaging.
    If successful, the student will be proposed to pursue this study in the framework of a Kaust PhD course.

    Deliverables/Expectations

    At the end of the internship the student is expected to know: the basics of cells culture, how to give them the nanoparticles, how to measure the specific absorption rate of the sole magnetic nanoparticles, the basics of cells preparation in view of light and electron microscopy, the basics of light and electron microscopy cells imaging.
    Twice per month the student will participate to a meeting with the PI and his team, in order to show and discuss his/her progress in the research project. Besides, at the end of the internship period, he/she will write a short, referenced report about the results he/she will get.​ 

    Field of Study

    Physics, Physical engineering, Physics engineering

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Conjugated polymers for metabolite sensing

  • ​Faculty: Professor Sahika Inal


    Internship Description

    Detecting analytes and quantifying minute changes in their concentrations in bodily fluids, in the living tissue or at single cell level is one of the biggest endeavors of the biomedical engineers. We tackle this challenge by integrating biofunctionalized organic mixed conductors in customized electronic devices so that they have high sensitivity, specificity and speed. The work includes developing and testing organic electrochemical transistors (OECTs) based on various mixed conductors and evaluating their performance for biosensing.

    Deliverables/Expectations

    OECT fabrication and characterization

    Sensor analytical characteristics

    Screening different materials

    Field of Study

    Materials Science, Physics, Chemical Engineering

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