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Postdoctoral in Protein Structure Prediction & High-Performance Computing

Arizona State University

Arizona State University

Phoenix, AZ, USA
Posted on Wednesday, June 5, 2024

Arizona State University: Office of the University Provost Downtown: College of Health Solutions

Location

Phoenix, AZ

Open Date

Oct 05, 2023

Description

The College of Health Solutions (CHS) at Arizona State University (ASU) is seeking to fill a postdoc vacancy in protein structure prediction and high-performance computing. The candidate will work in the lab of Dr. Judith Klein-Seetharaman. Please see the Klein-Seetharaman Lab’s website (https://sites.google.com/asu.edu/jks-structural-biology) for more information about current projects. In addition to the CHS appointment, the candidate will have an affiliation with ASU’s Biodesign Center for Applied Structural Discovery which houses the first compact X-ray light source (CXLS) in a university setting.

The successful candidate will have a strong computer science background, possibly with experience in both molecular (wet lab) and computational (dry lab) techniques for both methodological and applied research in structural and/or systems biology. Examples of methodological research could be the design and development of assays for detection of ligand binding to proteins at large scale or software for improving prediction of ligand binding to proteins in different conformational states or assembly of structures of multidomain protein complexes including membrane proteins and their lipid membrane environments. Examples of applied research could be the experimental validation of computational predictions and collection of experimental datasets to improve performance of computational models, or the use of existing software and tools to analyze large-scale protein-ligand docking experiments. We currently have hundreds of thousands of docking results obtained by high-performance computing in need of analysis, and are in the process of scaling up the data collection to billions of docking results with over 1.3 million ligands to the entire human structural proteome. This position is expected to demonstrate progress towards a K99/R00 application and publish at least 3 manuscripts (1 as lead author) within the first 12 months of position.

Responsibilities include the development and use of machine learning and artificial intelligence methodology in the context of biological data. Bioinformatics and computational analysis of protein structure-ligand predictions. Innovative technique development for advancing the accuracy and biological significance of computational predictions. Development of high-throughput assays for detecting protein-protein or protein-ligand binding and/or conformational changes. Assisting in the mentoring of a group of undergraduate and graduate students. Preparation of first-author, peer-reviewed publications, and presentation of results at international conferences.

At ASU and the College of Health Solutions, we work to maximize opportunities for people from diverse backgrounds, abilities, and perspectives. We value and encourage inclusive excellence as outlined in our ASU Charter and strive to foster a welcoming and inclusive environment for all faculty, staff, and students — which we believe is critical to our success as a community. All individuals who can strengthen our academic community are encouraged to apply and will be considered without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other basis protected by law.

About the College of Health Solutions

The College of Health Solutions is committed to translating scientific health research and discovery into practice to improve health outcomes through education, research, and service. We equip students with the knowledge and skills to influence healthier lifestyle choices; develop creative interventions to improve the health of people and populations; analyze and translate large amounts of health data into solutions; and maximize the technology, science, business, and application of diagnostics. Through teaching, academic programs, service and research, all faculty at the College of Health Solutions address one or more of our three major areas of focus: 1) The systems of health care and the health needs of populations; 2) Health and human performance of individuals across the lifespan; 3) Personalized interventions through precision health. Across these areas, we work to address complex and difficult health problems which require transformative collaboration, translational research, and innovation. We are particularly interested in making an impact on populations with significant health disparities.

Our research programs encompass basic science, discovery science, clinical trials, intervention science and measurement of health outcomes. In all cases, our faculty use interdisciplinary approaches to address the complex systems that underpin health problems. We are highly collaborative, transparent and team-oriented. Our innovative organizational structure includes translational teams that move science from labs into communities with evidence-based interventions that make a difference, as well as affinity networks where teams of people work together to improve methodologies and processes. All our programs, in and out of the classroom, are designed with the goal of improving the health of people and communities.

Current training programs include behavioral health, biomedical diagnostics, biomedical informatics, exercise science, health promotion, health sciences, kinesiology, medical studies, nutrition, population health, the science of health care delivery, and speech and hearing science. Our programs are offered at the ASU Downtown Phoenix, Tempe, Polytechnic, West and Lake Havasu campuses, as well as on Mayo Clinic’s campus in north Phoenix.

About Arizona State University

Arizona State University is a new model for American higher education, an unprecedented combination of academic excellence, entrepreneurial energy, and broad access. U.S. News & World Report ranks ASU #1 in the U.S. for innovation for nine years in a row. ASU has been named a Hispanic-Serving Institution (HSI) by the U.S. Department of Education, a major milestone in its enterprise-wide commitment to increase the diversity of its student body. This New American University is a single, unified institution comprising multiple differentiated campuses positively impacting the economic, social, cultural, and environmental health of the communities it serves. Its research is inspired by real world application blurring the boundaries that traditionally separate academic disciplines. ASU serves 144,800 students across all campuses and on-line as of the Fall 2023 semester. ASU champions intellectual and cultural diversity and welcomes students from all fifty states and more than one hundred nations across the globe.

For more information about ASU and the College of Health Solutions, visit http://about.asu.edu/ and https://chs.asu.edu.

Qualifications

Required Qualifications

  • Doctorate (e.g., PhD, ScD) in computer science, language technologies, computational biology, bioinformatics, genomics, proteomics, molecular biology, biochemistry, biophysics, structural biology, systems biology, evolutionary biology, or related fields
  • Existing research focus in multi-omics data analysis
  • Demonstrated ability to work, collaborate, and communicate effectively with diverse colleagues, community partners, and staff in a multicultural environment.
  • Demonstrated ability to progress towards a K99/R00 application and publish at least 3 manuscripts (1 as lead author) within the first 12 months of position.
  • Shows support of ASU’s commitment to inclusive excellence as outlined in the ASU charter

Desired Qualifications

  • Expertise in machine learning and artificial intelligence;
  • Expertise in protein structure prediction;
  • Experience with molecular dynamics simulations;
  • Expertise in experimental -omics data collection and analysis;
  • Experience in protein-ligand binding;
  • Experience developing pipelines for analysis of biological data;
  • Experience with programming and use of bioinformatics libraries and packages via Python and R.
  • Background, knowledge, and/or research that could be conducted or relevant to the needs of Arizona's diverse populations.
  • Potential for high impact research
  • Evidence of participation in translational, trans-disciplinary, and team science initiatives

Application Instructions

Application deadline December 1, 2023. Applications will continue to be accepted on a rolling basis for a reserve pool. Applications in the reserve pool may then be reviewed in the order in which they were received until the position is filled.

To apply, submit the following:

  • A letter of interest including the name of the position for which you are applying, your qualifications, and professional experience, and an example(s) of how your work has exemplified Arizona State University’s Charter and its values of Inclusive Excellence
  • Research statement;
  • Curriculum vitae;
  • Copies of up to three publications;
  • Information for three professional references (their position, title, e-mail, phone number). References will not be contacted until the candidate progresses to the latter stages of the search process.

Informal inquiries and questions can be directed to Prof. Judith Klein-Seetharaman, jkleinse@asu.edu.