Postings

07.11.2022. PhD Studentship in Barcelona

A funded PhD studentship is available in Dr Nataša Pržulj’s lab, funded by La Caixa foundation, so it comes with the most competitive stipend in the EU.
The application deadline is January 25th, 2023. The advert is at https://fundacionlacaixa.org/en/inphinit-doctoral-fellowships-incoming ,
to see it filter by host organization being “BSC” at https://finder-fellowships.lacaixafoundation.org/finder and then choose “PhD student
in Explainable Machine Learning for Biomedical Data to Aid Precision Medicine.

01.11.2022. Job posting

Seeking to recruit a Postdoctoral Research Scientist in the lab of Dr. Aleksandar Obradovic at the Department of Medicine, Division of Experimental Therapeutics, Columbia University Irving Medical Center in New York, NY.

Looking for an enthusiastic individual experienced in computational analysis of transcriptional data and interested in cancer immunotherapy research. The lab’s over-arching research goal is to identify mechanisms of resistance to immunotherapy treatment and prioritize combination-therapy approaches to overcome these mechanisms. This work builds on multiple datasets of bulk and single-cell RNA-Sequencing as well as multi-omic studies across clinical trials of immunotherapy in kidney, prostate, head and neck, as well as other tumor types. Ongoing work is highly collaborative with senior faculty in the Department of Systems Biology as well as the Center for Translational Immunology, and the lab maintains close connections to clinical collaborators running immunotherapy trials at Columbia, Fred Hutch, MSK, and Vanderbilt.

The ideal candidate should have a quantitative background (Bioinformatics, Computational Biology, Biostatistics, Statistics, Computer Science, or Applied Mathematics), be highly motivated to solve biological problems, and have experience analyzing large-scale transcriptomic data. Interest in or experience with wet lab tissue processing techniques is a plus. A Ph.D. in computational biology, bioinformatics, statistics, biostatistics, computer science, or related area is preferred, but a Ph.D. in biology is also acceptable if the candidate has experience with quantitative methods. The candidate should have good knowledge of at least one programming language for implementing computational models and algorithms (R and/or python preferred), and familiarity with machine learning concepts. This position is a union position and has a starting salary of $60,000. The candidate will be directly mentored and trained in computational techniques by Dr. Aleksandar Obradovic.

Research Projects and Directions will include the following:

• Developing and optimizing computational tools for analysis of single-nucleus and multi-modal single-cell data (scRNA-Seq, snRNA-Seq, CITE-Seq, TCR-Seq, and 10X Visium spatial
transcriptomic)

• Generating and expanding on a Precision Medicine database of immunogenic drug effects
(transcriptional effects of large-scale drug library on sorted immune cell types, immune effects
of radiation therapy)

• Analysis of clinical trial data identifying shared characteristics of immunotherapy non-
responders and matching resistance mechanisms to candidate drugs.

Application Instructions
If interested, please submit an application or inquiries by e-mail to Dr. Aleksandar Obradovic (azo2104@cumc.columbia.edu). Please include a cover letter with a CV describing previous research, research interests, and future goals.

Aleksandar Obradovic, PhD
Associate Research Scientist, Department of Medicine, Division of Experimental Therapeutics, Columbia University Irving Medical Center MD Candidate, Columbia College of Physicians and Surgeons Medical Scientist TrainingProgram
azo2104@cumc.columbia.edu

31.10.2022. Post-doctoral Researcher in Computer and Biomedical Data Science (R2-R3)

Professor Nataša Pržulj is looking for several post-docs to work in Machine Learning (ML) and network data science algorithms for mining molecular (“omics”) and medical data to improve precision medicine. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. Sample papers from the lab can be viewed at Google Scholar. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj.

The successful candidates will address developing and applying sophisticated Machine Learning and network data science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining algorithms efficiently for the data to uncover new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitating rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The researcher will work in a highly sophisticated HPC environment of BSC, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas.

Key Duties

  • Conduct high-quality research
  • Write and publish research papers in high impact peer-reviewed journals and conferences
  • Present research at national and international conferences and meetings
  • Collaborate with various research groups across Europe and elsewhere
  • Help supervise PhD and MSc students
  • Participate in grant writing and organizational activities
  • Participate in educational and outreach activities

Requirements

  • Education
    • PhD in Computer Science, Mathematics, Physics, Bioinformatics, or a related field
  • Essential Knowledge and Professional Experience
    • Good publication record for the career stage
    • Fluency in spoken and written English
  • Additional Knowledge and Professional Experience
    • Desired at least 2 years of working experience
  • Competences
    • Good technical skills including at least several of the following: algorithms, data analysis, graph, network and complexity theory, scientific computing, statistics, machine learning, programming in C, C++, a scripting language and Matlab, using a parallel computing environment, bioinformatics, network biology, network medicine, network analytics, medical informatics.

Conditions

  • The position will be located at BSC within the Life Sciences Department
  • We offer a full-time contract, a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible working hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures
  • Duration: Open-ended contract due to technical and scientific activities linked to the project and budget duration
  • Salary: we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona
  • Starting date: asap

Applications procedure and process

All applications must be made through BSC website (https://www.bsc.es/join-us/job-opportunities/40322lsiconbir2-3) and contain:

  • A full CV in English including contact details
  • A Cover Letter with a statement of interest in English, including two contacts for further references – Applications without this document will not be considered

14.12.2021. Call for PhD studies in Weiqun Peng’s group

The Peng group is seeking enthusiastic graduate students to join
Aiming to understand the fundamental principles of living systems at the scales ofmolecule, genome and cell, we conduct highly interdisciplinary research inthe areas of computational biophysics and biology, bioinformatics andsystems biology. Specifically, our research focuses include:

1) theinformation-encoding and processing at the molecular and genetic levels,gene regulatory circuits underlying specific biological processes

2)Emergent complexity of genome, maintenance and development of cellidentity

3) Spatial architecture of the genome and its functionalsignificance in gene regulation.

We employ a combination of multi-omicsdata analytics, machine learning, model simulation and theoreticalapproaches. We collaborate closely with leading experimental groups andpublish in high-impact journals including Nature, Science, Cell, NatureImmunology, Nature Communications, Cancer Cell (Google Scholar: https://scholar.google.com/citations?user=Jf4lfF0AAAAJ&hl=en). Past groupmembers were well placed in both academia and industry.

Interested students are encouraged to contact dr Peng at wpeng@gwu.edu for more information.

—

20.02.2021. Open positions at Barcelona Supercomputing Center – Centro Nacional de Supercomputación

Barcelona Supercomputing Center – Centro Nacional de Supercomputación (BSC-CNS) has open positions for