Using Biomedical Data Science to Advance Precision Medicine and Digital Health

Official opening in summer of 2020.

Join us!

The Aran Lab integrates multidimensional biomedical data — including genomics and clinical data — to advance precision medicine and improve therapeutic strategies.

The core themes of the lab are:

  • Developing computational methods to understand cellular heterogeneity in complex tissues.
  • Incorporating cutting-edge technologies to study cellular dynamics in the tumor-microenvironment affecting response to immunotherapies.
  • Investigating real-world evidence and developing machine-learning models to improve clinical decision-making.

The lab is affiliated with the Faculties of Biology and Computer Science and the Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering at the Technion - Israel Institute of Technology, Haifa, Israel.

The Team

Principal Investigator

Researchers

Collaborators

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Abraham (Avi) Tsur

Sheba Medical Center

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Mallar Bhattacharya

Associate Professor, UCSF

Research

The lab focuses on the discovery of predictive biomarkers, improving existing treatments, and developing novel therapeutic strategies. The lab will develop novel computational and experimental cancer immunology methodologies for characterizing the interactions of the tumor and its microenvironment, and specifically focus on the mechanisms enabling immune resistance. By incorporating publicly available datasets with self-generated data, from bulk and single-cell profiling of multiple ‘omics’ types, mass spectrometry cytometry, immune repertoires, and other cutting-edge technologies, we will adequately portray the cellular dynamics of cancer initiation, progression, and response to treatment. The lab branches to both basic and clinical research, and collaborates with computer scientists, bioengineers, basic experimental researchers and clinicians.

Cancer Immunology

The recent breakthroughs in cancer immunology and the development of a newer generation of cancer immunotherapies have opened a brand-new chapter in the war on cancer. The tumor microenvironment composition has a major effect on the response to immunotherapy agents. Thus, an improved understanding of the interactions between the tumor, its microenvironment, and its proximal surroundings is crucial for improving existing treatments and the design of novel immunotherapy strategies.

Cancer Metastasis

Metastasis is the primary cause of mortality in most cancers, yet today, metastatic spread is still poorly understood. In recent years, there is increasing evidence that metastatic colonization depends not just on the inherent properties of cancer cells, but also on properties of the microenvironment in distant sites. Understanding how disseminated cells evade and corrupt the immune system during the metastatic colonization will be pivotal in developing new therapeutic methods to combat metastasis.

Clinical Informatics

Clinicians have been using Electronic Health Records (EHR) for over a decade for organizing and preserving patient information. However, only recently, these rich and valuable datasets became widely accessible for research. EHR analysis is expected to drive future precision medicine efforts and improve healthcare quality. Our lab is collaborating with leading hospitals and research institutions and will enjoy unique access to one of the largest health care datasets in the world.

Single-cell RNA-seq

Until recently, genomic analyses have been performed on heterogeneous populations of cells and thus observed signals represented a combination of the unique characteristics of each individual cell. In the last few years, single-cell techniques combined with high-throughput technologies have revolutionized the field, allowing for high-dimensional analysis of isolated subpopulations of individual cells and enabling an unprecedented level of granularity in characterizing gene expression changes in disease models. Researchers can now address core challenges that bar advancement in the field of onco-immunology, enabling the mapping of the variable spectrum of immune, stromal, and other cell states and ascertaining which of these features predict or explain clinical responses to anticancer agents.

Software

Here are some representative tools developed before the inception of the lab.

SingleR

Reference-Based Single-Cell RNA-Seq Annotation - Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently. SingleR is used by thousands of researchers across the world.

xCell

xCell is a webtool that performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. Over 20,000 researchers world-wide have now used xCell.

News

Azrieli Faculty Fellowship

Thank you Azrieli Foundation for awarding the Azrieli Faculty Fellowship to Dvir. This award will support the lab in the next three years.

Lab opening - August 2020

The lab will be situated on the 8th floor of the Emerson building at the Technion.

Join us!

Always looking for talented and curious candidates at the postdoctoral, predoctoral, and undergraduate levels.

The lab will physically open in August 2020!

Senior Researcher/Lab manager


Seeking an experienced, highly motivated senior researcher to help build and manage the experimental (wet) lab. The senior researcher/lab manager will demonstrate experience in primary cell isolation techniques, cell culture, immunocytochemistry, RNA-Seq, single-cell RNA-Seq, flow cytometry, and have excellent leadership skills.

The Senior Researcher/Lab manager will be fully supported to pursue research initiatives and will assist in writing grant applications and papers. The responsibilities include managing and coordinating research efforts with other collaborators as appropriate for multidisciplinary research. To plan, execute, and follow-up on high level regular and ad hoc meetings of investigators and management. Independently conceive, plan, and conduct research projects based on reviews of scientific literature and recent advances in related fields, organizing and executing all techniques involved. Contribute novel ideas of major methodological significance to the research projects, designing key experiments, and developing new techniques. Will perform complex data analysis using various statistical tools. Will author or co-author scientific journal manuscripts and book chapters and report directly to funding agencies and journal editors. Prepare and implement research study budgets based on the analysis of data. Perform other duties as needed.

QUALIFICATIONS

  • Advanced degree in molecular biology or related area and/or equivalent experience/training.
  • Senior-level research experience.
  • Experience in human cell isolation.
  • Strong ability to think creatively and independently on concepts requiring advanced analytical skills.
  • Exceptional experience and knowledge in developing hypotheses, designing and conducting experiments, analyzing data, writing manuscripts, and publishing results in peer-reviewed journals, including all interactions with Reviewers and Editors.
  • Demonstrated leadership skills and employee supervision associated with planning work assignments, training others and establishing priorities.
  • Strong oral and written communication skills. Ability to facilitate in written and verbal communication with clinical researchers, laboratory technicians, statisticians, bioinformatics experts and administrative personnel.
  • Strong ability to work collaboratively with internal and external peers and managers.
  • Thorough knowledge of administrative, budgetary, human resources and financial principles and practices.
  • Strong interpersonal skills and ability to work with diverse groups to achieve results.
  • Demonstrated ability to develop and adapt new techniques.

If interested, please send the following to aran.lab.technion@gmail.com:

  • A short research statement on your goals
  • Your CV
  • Contact information for three references

PhD and Master’s students


The lab is opening in the summer of 2020 and is seeking highly motivated students to develop and study novel approaches in translational bioinformatics, or the application of analytic and interpretive methods to optimize the transformation of genome-scale data of many types into proactive, predictive, preventative, and participatory health.

Ideal candidates will have:

  • Strong background in bioinformatics, computational biology, biostatistics, and genomics.
  • Strong problem-solving skills, creative thinking, and the ability to build new software tools as needed are required.
  • Applicants must possess good communication skills and be fluent in both spoken and written English.
  • A background in molecular biology or medicine or pharmacology will be a strong plus. Prior experience with genetic, drug, or clinical databases, machine-learning, deep-learning, text-mining and knowledge representation is a plus.

To apply, please send your CV and research interests to aran.lab.technion@gmail.com.

Postdoctoral researchers


We are looking for fully-funded postdoctoral researcher to work on some exciting projects. Candidates are expected to have a track record of bioinformatics and or clinical informatics analysis.

There is also an option of co-advising postdoctoral researchers with other computational or experimental labs. An example might be an experimental postdoc with their own biological question for which there are no current analysis tools.

If interested, please send the following to aran.lab.technion@gmail.com:

  • A short research statement on your goals
  • Your CV
  • Contact information for three references

Contact

  • LS&E - Technion Life Sciences and Engineering Infrastructure Center, Haifa, 94305
  • Floor 8, right side of hall