Bioinformatics
bioinformatics
MedUni PhD Recruitment
Medical University of Vienna invites applications for all currently open Ph.D. positions within their 18 Ph.D. programs. We encourage ambitious and creative young scientists to develop their original research project in the field of Behavioural Biology, Biochemistry, Biophysics, Bioinformatics & Machine Learning, Cancer, Cardiovascular Systems, Drug Targets & Drug Development, Endocrinology & Metabolism, Biomedical Engineering, Mathematics & Statistics, Immunology, Medical Physics, Mental Health, Molecular and Cellular Biology, Neuroscience and Public Health with the assistance of our renowned and international scientists . Benefit from a well-established and connected network within the science community and built important relations with your peers at our university. On top of it, become an expert in your field! All project information can be found online under https://www.meduniwien.ac.at/web/en/studies-further-education/phd-doctoral-programmes/phd-programme-un094/phd-opportunities/ Apply online till 20.11.2022
Navin Pokala
The Department of Biological and Chemical Sciences at New York Institute of Technology seeks outstanding applicants for a tenure-track position at the Assistant Professor level to develop a research program in the broadly defined fields of biostatistics, bioinformatics or computational biology that complements existing research programs and carries potential to establish external collaborations. The successful candidate will teach introductory and advanced courses in the biological sciences at the undergraduate level, notably Biostatistics. The Department has undergraduate programs in Biology, Chemistry, and Biotechnology at the New York City and Long Island (Old Westbury) campuses. New York Tech emphasizes interdisciplinary scholarship, research, and teaching. Department faculty research interests are diverse, including medicinal and organic chemistry, neuroscience, cell and molecular biology, genetics, biochemistry, microbiology, computational chemistry, and analytical chemistry. Faculty in the Department have ample opportunity to collaborate with faculty at the New York Tech’s College of Engineering and Computer Sciences and College of Osteopathic Medicine.
Dr Clyde Francks
A postdoctoral position (2 years duration) on brain imaging genomics is available at the Language and Genetics Department of the Max Planck Institute, Nijmegen, the Netherlands. We seek a postdoctoral researcher to investigate links between gene expression in the human cerebral cortex and inter-individual variations in brain and behaviour. The position will be embedded within the Imaging Genomics group of the host department, and will be carried out in collaboration with leading researchers at the Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen. The successful candidate will join an innovative research program that is seeking to characterize the brain’s molecular infrastructure for language, and integrate this with data on individual differences in brain and behaviour. This is an initiative of the Language in Interaction (LiI) consortium, sponsored by a major grant from the Netherlands Organisation for Scientific Research. We recently generated a unique gene expression dataset using spatial transcriptomics from regions of the human cerebral cortex that are important for language. The postdoctoral scientist will take the lead on integrative analyses linking gene expression to genetic association, making use of large-scale resources such as the UK Biobank (currently data from over 30,000 individuals with brain image and genetic data – including common single nucleotide polymorphisms and rare genetic variants) and the international GenLang Consortium (data from up to 34,000 individuals on reading- and language-related abilities together with genetic data). One major goal is to apply a recently-optimized pipeline for measuring white matter tracts in biobank-scale diffusion tensor imaging data, and subsequently to apply genetic techniques such as genome-wide association analysis, partitioned heritability analysis, and polygenic score analysis. The project therefore offers the possibility to learn state-of-the-art techniques in both brain image analysis and genetic analysis.
Department of Biological and Chemical Sciences
The Department of Biological and Chemical Sciences at New York Institute of Technology seeks outstanding applicants for a tenure-track position at the Assistant Professor level to develop a research program in the broadly defined fields of biostatistics, bioinformatics or computational biology that complements existing research programs and carries potential to establish external collaborations. The Assistant Professor will be responsible for our NY campus locations. The Department has undergraduate programs in Biology, Chemistry, and Biotechnology at the New York City and Long Island (Old Westbury) campuses. New York Tech emphasizes interdisciplinary scholarship, research, and teaching. Department faculty research interests are diverse, including medicinal and organic chemistry, neuroscience, cell and molecular biology, genetics, biochemistry, microbiology, computational chemistry, and analytical chemistry. Faculty in the Department have ample opportunity to collaborate with faculty at the New York Tech’s College of Engineering and Computer Sciences and College of Osteopathic Medicine. The successful candidate will teach introductory and advanced lecture and laboratory courses in the biological sciences at the undergraduate level, notably Biostatistics. Interested candidates should apply here: https://internal-nyit.icims.com/jobs/2681/assistant-professor%2c-tenure-track%2c-computational-quantitative-biology/job?iis=Social+Networks&iieid=pt1645617395656e37e8
Prof. Dr. S.E. Fisher
The successful candidate will join an innovative research program that is characterizing individual variation in language skills at behavioural, neurobiological, and genetic levels, an initiative of the Language in Interaction (LiI) consortium, sponsored by a major grant from the Netherlands Organisation for Scientific Research. The LiI consortium has developed a computer-based test battery to assess core skills underlying speaking and listening across a broad spectrum of abilities, and has already applied this to hundreds of young adults from the general population, a subset of whom are also tested with functional MRI. In parallel, saliva sampling has been used to collect DNA. The postdoctoral scientist will take the lead on the genetic aspects of the project. Specifically, they will process and analyse genome-wide genotype data from this unique resource, and use methods for analyzing polygenic contributions to human traits in order to trace genetic links to cognitive skills, childhood learning disorders, and MRI-based measures of brain structure/function, integrating with independent datasets available at the Language and Genetics department. The project will be further scaled up by applying online versions of the LiI battery to large pre-existing population-based cohorts with available genome-wide genotypes. The postdoctoral scientist will also foster connections to ongoing work by GenLang, an international network of researchers carrying out genetic association meta-analyses of multiple speech/language/reading-related cohorts across the world.
Emily Osterweil
The Osterweil lab is recruiting a motivated individual to fill a Wellcome Trust funded postdoctoral position in the Centre for Discovery Brain Sciences at the University of Edinburgh. We are studying mRNA translation in specific neural circuits, and investigating how disruptions lead to autism and intellectual disability. Our work uses cutting-edge molecular techniques, including cell type-specific TRAP-seq, ribosome profiling and single-cell RNA-seq, and combines them with electrophysiology and behavior to assess how circuit-specific changes in translation alter learning in autism models. This approach continues to identify novel therapeutic strategies. The post requires relevant experience in Neuroscience research, with a PhD either obtained or expected within 6 months of the start of the contract. The applicant must have experience with molecular biology and a working knowledge of RNA-seq analysis and/or related bioinformatics processing. This is a full-time post. Interested applicants should send a CV and letters of reference to Emily.osterweil@ed.ac.uk. Lab website: https://www.osterlab.org/
Dr Emily Osterweil
The Osterweil lab is recruiting a motivated individual to fill a postdoctoral position in cellular neuroscience and bioinformatics. You will be joining the exceptional group of scientists in the Centre for Discovery Brain Sciences and the Simons Centre for the Developing Brain at the University of Edinburgh, recently ranked as the 16th best university in the world. You will be working in Edinburgh, one of the world’s most liveable cities with access to world-class cultural activities, UNESCO Heritage sites and unparalleled outdoor experiences. The laboratory’s research sits at the interface of cellular neuroscience and disease, seeking to address the role of mRNA translation in autism-related neurodevelopmental disorders. You will use cutting edge approaches such as TRAP-seq, Ribo-seq and scRNA-seq to discover how alterations in specific neural circuits contribute to disruptions in circuit function and behavior in animal models of autism. This Wellcome Trust funded position will use these approaches to answer critical questions about how ribosome expression changes mRNA translation in hippocampal and cortical circuits, and how this process may be targeted for therapeutic intervention in mouse models of autism. The post requires relevant experience in bioinformatics analysis of RNA-seq datasets, and experience with scRNA-seq datasets is desired. Candidates must have a PhD in cell biology, neuroscience or a related topic either obtained or expected within 6 months of the start of the contract. This is a full-time post, and start date is flexible. Applications will be reviewed on a rolling basis with a soft deadline of Aug 21. Interested applicants should send a CV and letters of reference to Emily.osterweil@ed.ac.uk. Lab website: https://www.osterlab.org/ University of Edinburgh: https://www.ed.ac.uk/ Simons Centre for the Developing Brain: https://www.sidb.org.uk/ Centre for Discovery Brain Sciences: https://www.ed.ac.uk/discovery-brain-sciences Further Reading 1) Thomson SR*, Seo SS*, Barnes SA✝, Louros SR✝, Muscas M, Dando O, Kirby C, Hardingham GE, Wyllie DJA, Kind PC, and Osterweil EK. Cell type-specific translation profiling reveals a novel strategy for treating fragile X syndrome. Neuron. 2017 Aug 2; 95(3):550-563.e5. doi: 10.1016/j.neuron.2017.07.013. 2) Stoppel LJ, Osterweil EK, and Bear MF. The mGluR Theory of fragile X syndrome. Fragile X Syndrome: From Genetics to Targeted Treatment. Willemsen, R. & Kooy, F. (Eds.). Academic Press, 2017. ISBN: 0128045078, 9780128045077. 3) Asiminas A*, Jackson AD*, Louros S†, Till SM†, Spano T, Dando O, Bear MF, Chattarji S, Hardingham GE, Osterweil EK, Wyllie DJA, Wood ER, and Kind PC. Sustained correction of associative learning deficits following brief, early treatment in a rat model of Fragile X Syndrome. Science Translational Medicine. 2019 May 29;11(494). pii: eaao0498. doi: 10.1126/scitranslmed.aao0498.
Dr Guillermina López-Bendito
The López-Bendito Lab is interested in understanding and uncovering the principles underlying the development of sensory circuits with emphasis on the role of the thalamus in the development of cortical sensory maps. Furthermore, we are developing strategies for circuit restoration in sensory deprived mice. We are seeking for two (2) highly motivated postdoctoral scientists to investigate the cellular and molecular mechanisms involved in sensory circuit glia-to-neuron reprogramming. This 3-years project funded by La Caixa Foundation aims to understand the rules for region-specific reprogramming with the ultimate goal of recovery sensory thalamocortical circuits in sensory deprived mice. Applicants should have a proven track record and an independent working style.
Dr Nathan Skene
Using machine learning to predict cell-type specific effects of genetic variants which influence genome regulation. This PhD project is focused on using machine learning techniques to develop novel classifiers for predicting how changes in DNA sequences alter genomic regulatory features. Many regulatory proteins recognise particular DNA sequences known as motifs, for instance, EcoRI only binds to GAATTC. DNA sequences can be converted into a machine interpretable format, using one-hot encoding. The candidate will use publicly available and inhouse datasets of genomic regulatory features to train models. Machine learning techniques will be used to predict the cell-type specific regulatory effects of genetic variants. We will provide several true-positive datasets, wherein the effect of genetic mutations on particular regulatory features has been measured. These will form validation datasets to evaluate how well the trained classifier works. We are interested in how improvements in the machine learning approach (e.g. use of transfer learning, recurrent attentional networks or graph convolution networks) can be used to improve upon existing methods. The candidate will use these techniques to identify causal pathways and candidate drug targets for neurodegenerative diseases.
Birkan Tunc
We are seeking postdoctoral fellows with interest and experience in computational approaches for quantifying human social behavior. This research is conducted at the University of Pennsylvania and the Center for Autism Research at Children’s Hospital of Philadelphia, as a part of multiple NIH grants. The applicant will be part of a big multidisciplinary team that develops AI tools to study human behavior (facial and bodily movements) during social interactions. Our research is a unique blend of machine learning, computer vision, cognitive science, bioinformatics, and mental health conditions. The fellow will be responsible for all or some of the following tasks, depending on the expertise: - Developing computer vision techniques (e.g., face analysis, body movement analysis, gesture analysis) - Developing signal processing methodologies to analyze biological and behavioral signals (e.g., head movements, joint movements) - Developing time series analysis techniques to extract patterns in biological and behavioral signals (e.g., coordination and causality in movements of multiple people) - Validating developed tools using in-house clinical data, as well as publicly available datasets - Performing pattern recognition on collected data (i.e., classification, regression, clustering, feature learning)
Birkan Tunc
We are seeking postdoctoral fellows with interest and experience in computational approaches for quantifying human social behavior. This research is conducted at the University of Pennsylvania and the Center for Autism Research at Children’s Hospital of Philadelphia, as a part of multiple NIH grants. The applicant will be part of a big multidisciplinary team that develops AI tools to study human behavior (facial and bodily movements) during social interactions. Our research is a unique blend of machine learning, computer vision, cognitive science, bioinformatics, and mental health conditions. The fellow will be responsible for all or some of the following tasks, depending on the expertise: Developing computer vision techniques (e.g., face analysis, body movement analysis, gesture analysis), Developing signal processing methodologies to analyze biological and behavioral signals (e.g., head movements, joint movements), Developing time series analysis techniques to extract patterns in biological and behavioral signals (e.g., coordination and causality in movements of multiple people), Validating developed tools using in-house clinical data, as well as publicly available datasets, Performing pattern recognition on collected data (i.e., classification, regression, clustering, feature learning)
N/A
The Faculty of Computer Science of HSE University invites applications for full-time, tenure-track positions of Assistant Professor in all areas of computer science including but not limited to artificial intelligence, machine learning, computer vision, programming language theory, software engineering, system programming, algorithms, computation complexity, distributed and parallel computation, bioinformatics, human-computer interaction, and robotics. The successful candidate is expected to conduct high-quality research publishable in reputable peer-reviewed journals with research support provided by the University.
Xiaohui Xie
The Department of Computer Science at the University of California, Irvine (CS@UCI) invites applicants for a tenure-track/tenured faculty position at the assistant, associate, or full rank starting July 1, 2023. This faculty search targets applicants with research background in bioinformatics, broadly defined to be in the general area of applying computational and/or machine learning methods to study biology and/or medicine.
Pol Solé Navais
Miscarriage is the most common pregnancy complication, with over 23 million pregnancies ending in miscarriage every year. Chromosome abnormalities – aneuploidies – are observed in half of all miscarried fetuses, but not all fetuses with chromosome abnormalities miscarry, with some surviving until, or even after birth. This project aims to quantify the contribution of the fetal genome in miscarriage, particularly among fetuses with normal chromosome counts. The postdoc fellow will lead a project using large-scale genetic data from miscarriage fetuses and their mothers (including calling of aneuploidies) and contribute to ongoing efforts in this field (GWAS, meta-analyses, etc). Apply here: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=35562
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Advertising a PhD position for Bioinformatics Machine Learning in Dresden, Germany. The ideal candidate has experience with building and evaluating a wide array of machine learning models and an interest in working with data from molecular biology: protein and DNA sequences and structures. The candidate will get a German working contract with standard social security contributions and with the income rate ruled by the TVL system. Here, a PhD student will be allocated to a TVL group E13 65% (Level 1 if first time in the German system).
The role of CNS microglia in health and disease
Microglia are the resident CNS macrophages of the brain parenchyma. They have many and opposing roles in health and disease, ranging from inflammatory to anti-inflammatory and protective functions, depending on the developmental stage and the disease context. In Multiple Sclerosis, microglia are involved to important hallmarks of the disease, such as inflammation, demyelination, axonal damage and remyelination, however the exact mechanisms controlling their transformation towards a protective or devastating phenotype during the disease progression remains largely unknown until now. We wish to understand how brain microglia respond to demyelinating insults and how their behaviour changes in recovery. To do so we developed a novel histopathological analysis approach in 3D and a cell-based analysis tool that when applied in the cuprizone model of demyelination revealed region- and disease- dependent changes in microglial dynamics in the brain grey matter during demyelination and remyelination. We now use similar approaches with the aim to unravel sensitive changes in microglial dynamics during neuroinflammation in the EAE model. Furthermore, we employ constitutive knockout and tamoxifen-inducible gene-targeting approaches, immunological techniques, genetics and bioinformatics and currently seek to clarify the specific role of the brain resident microglial NF-κB molecular pathway versus other tissue macrophages in EAE.
Epilepsy genetics 2023: From research to advanced clinical genetic test interpretation
The presentation will provide an overview of the expanding role of genetic factors in epilepsy. It will delve into the fundamentals of this field and elucidate how digital tools and resources can aid in the re-evaluation of genetic test results. In the initial segment of the presentation, Dr. Lal will examine the advancements made over the past two decades regarding the genetic architecture of various epilepsy types. Additionally, he will present research studies in which he has actively participated, offering concrete examples. Subsequently, during the second part of the talk, Dr. Lal will share the ongoing research projects that focus on epilepsy genetics, bioinformatics, and health record data science.
Linking GWAS to pharmacological treatments for psychiatric disorders
Genome-wide association studies (GWAS) have identified multiple disease-associated genetic variations across different psychiatric disorders raising the question of how these genetic variants relate to the corresponding pharmacological treatments. In this talk, I will outline our work investigating whether functional information from a range of open bioinformatics datasets such as protein interaction network (PPI), brain eQTL, and gene expression pattern across the brain can uncover the relationship between GWAS-identified genetic variation and the genes targeted by current drugs for psychiatric disorders. Focusing on four psychiatric disorders---ADHD, bipolar disorder, schizophrenia, and major depressive disorder---we assess relationships between the gene targets of drug treatments and GWAS hits and show that while incorporating information derived from functional bioinformatics data, such as the PPI network and spatial gene expression, can reveal links for bipolar disorder, the overall correspondence between treatment targets and GWAS-implicated genes in psychiatric disorders rarely exceeds null expectations. This relatively low degree of correspondence across modalities suggests that the genetic mechanisms driving the risk for psychiatric disorders may be distinct from the pathophysiological mechanisms used for targeting symptom manifestations through pharmacological treatments and that novel approaches for understanding and treating psychiatric disorders may be required.