Thank you for your interest in the Englander Institute for Precision Medicine at Weill Cornell Medicine. We are looking for skilled talent to join our team. Please find descriptions of current opportunities below, and follow the application instructions. We look forward to speaking with you.
Bioinformatics Analyst (Genomics and Clinical data)
At the Englander Institute for Precision Medicine (EIPM), our mission is to use Next Generation Sequencing (NGS) data to give late-stage cancer patients therapeutic options to prolong and better their quality of life. In just four years we have built a CLIA-approved genomics test that has already been used on over 800 patients. As a Bioinformatics Analyst at IPM, you will be able to immediately impact and build data products aimed at expanding the scope of our genomics platform. You will get to create new ways of improving aspects of the genomics platform such as sample collection, sequencing, genomic data analysis, and reporting. You will also get to work with a diverse team of software engineers, bioinformaticians, researchers, and physicians, and create products that deepen our understanding of how cancers evolve and the best treatment options for them.
The Bioinformatics Analyst will perform statistical and integrative data analysis for genomics and clinical data for the Institute for Precision Medicine (EIPM). You will arm IPM with data and insights to help enhance the clinical sequencing portfolio. You’ll be focused on improving our Exome analysis pipeline (SNVs, CNVs, translocations, and viral detection) for our EXaCT-2 clinical test. You should be passionate about finding inefficiencies in how we generate clinically actionable insights, and enjoy brainstorming and building workflow solutions.
- Conducting and maintaining systematic documentation of clinical-enterprise software pipelines for compliance using (git/svn/etc.)
- Assisting in the development of new software tools and build pipelines for novel bioinformatics analyses
- Assisting in development and maintenance of genomic and clinical databases
- Creating web user interfaces for to explore large data stores, combining genomic and clinical data and statistical analyses to help other IPM team members understand insights form theses data stores
- Performing statistical and integrative data analysis on genomics and clinical data
- Driven and Self-motivated. Willingness to tackle and drive execution of challenging projects
- Ability to learn and deliver work in fast-paced and diverse environment
- Comfortable with communicating and working alongside a diverse team of scientists and medical professionals
- BS in Bioinformatics, Biomedical Engineering, Computer Science or Related Field
- Minimum 3 years experience working with next generation sequencing data and relevant tools (GATK, samtools, BWA, TopHat, STAR,etc.)
- Knowledge and proficiency of UNIX
- Proficiency in at least one scripting language : (R, Ruby, Python, Perl)
- Experience using Git/SVN
Bonus Points for:
- Demonstrated ability to run computationally intensive jobs on HPC and Cloud computing environments
- Previous experience in designing and building bioinformatics workflows
- Proficiency in programming in Java, C, C++
- Experience in web user interface applications and database design
- Knowledge of clinical IT systems (OMOP, HL7 messaging, etc.)
Please send cover letter, CV and contact information for at least two referees to:
Kenneth Wha Eng
Postdoctoral Associate in Computational Biology
The Elemento lab at the Englander Institute for Precision Medicine invites applications from highly motivated candidates for a postdoctoral position working on cutting-edge computational biology research.
We are looking for computational scientists to work on exciting research projects involving prostate cancer biology within the Prostate Cancer SPORE and in close collaboration with basic scientists and clinician scientists. The postdoctoral candidate is expected to exhibit resourcefulness and independence, developing new statistical models of high-dimensional data and implementing computational pipelines.
- Ph.D. level degree in the quantitative sciences
- Expertise in scientific programming, e.g. C, C++, Python, or R. Proficiency working in a Linux environment, with large data sets, computer clusters, and databases.
- Research publications in computational biology, machine learning or physics. The ideal candidate will have experience dealing with next-gen DNA sequencing data and/or cancer biology.
- Effective communication skills, both written and oral.
Please send cover letter and CV to:
Postdoctoral Position Opening in Dr. Giorgio Inghirami’s Laboratory in Department of Pathology and Laboratory Medicine (New York, NY)
A postdoctoral position is available at Weill Cornell Medicine to identify the mechanisms driving T-cell transformation.
Dr. Giorgio Inghirami’s laboratory focuses on studying the contribution of STAT3 and DNA epigenetic changes to the development and maintenance of T cell lymphoma. Target drugs and drug combinations are currently investigated in novel model systems, expected to be tested in preclinical models and used in patient-specific, precision medicine trials. Model systems in use include transgenic mice and patient-derived tumor xenografts (PDTX), 3-dimensional cancer spheroids derived from patient tumors and PDTX.
Dr. Giorgio Inghirami’s laboratory has previously demonstrated that Anaplastic Large Cell Lymphoma (ALCL) have a unique signature (Blood. 2012 Aug 9;120(6):1274-81; J Clin Oncol. 2010 Mar 20;28(9):1583-9; Blood. 2009 Mar 19;113(12):2776-90; J Clin Invest. 2006 Dec;116(12):3171-82) and there are addicted to STAT3 (Nat Med. 2012 Nov;18(11):1699-704; Nat Rev Cancer. 2008 Jan;8(1):11-23; Nat Med. 2005 Jun;11(6):623-9). Deregulated expression of STAT3 is mediated via multiple kinase fusions or somatic mutations of members of the JAK/STAT pathway (Leukemia. 2015 Jun;29(6):1390-401; Cancer Cell. 2015 Apr 13;27(4):516-32). More recently we have established a battery of PDTX from a variety of T-cell lymphoma demonstrating that they faithfully mimic donor patients’ samples and once tested in HTP drug screening display a phenotype that confirms clinical responses and predicts vulnerabilities (Curr Opin Hematol. 2017 Jul;24(4):384-392; Cancer Cell. 2016 Apr 11;29(4):574-586).
Dr. Giorgio Inghirami’s lab uses and develops biochemistry, molecular biology, and a large array of quantitative technologies to investigate how STAT3 reprograms and maintains the genomic landscape of T-cell neoplasms and sustains the growth and survival of these cells. We use Proteomics, WES, RNA-seq, ERBBS, ATACseq, ChIP, RIP and novel technologies to determine these effects using a combination of in vitro and in vivo models including transgenic/PDTX mice and human disease samples.
Projects will include in vivo and in vitro modeling of candidate genes to identify STAT3-mediated gene (coding and lncRNA) transcription and epigenetic changes that contribute to the development and maintenance of hematopoietic malignancies and characterization of candidate genes using in vitro and in vivo systems and pharmacological and genomic (CRISP/Cas9) platforms.
The candidate should be able to work independently and as part of a laboratory team, design experiments, collect/tabulate and analyze data, and present results to the PI and the laboratory team. Duties assigned to this position may involve organizing and implementing complex research plans, the development of research methodologies, as well as data collection, analysis, and evaluation. The Postdoctoral Researcher will assume general responsibility for scientific laboratory operations and provide supervision and guidance to junior technicians, students, and researchers. Evidence of scholarly ability (record of publication in peer-reviewed journals, etc.) and ability to communicate in written and spoken English are required.
We are currently seeking a highly motivated postdoctoral fellow with comprehensive knowledge and broad skills in cellular and molecular biology. The candidates should have proven proficiency in a variety of laboratory techniques e.g. cell culture and molecular biology assays (molecular cloning, cell proliferation assay, subpopulation analysis by FACS, stable and transient transfection, use of shRNA and viral constructs), preparation and analysis of nuclei acid (preparation of plasmids, PCR and qRT-PCR), chromatin immunoprecipitation (ChIP) assays, biochemical assays (WB, immunoblotting, Co-IP). Experience in gene regulation, transcription, RNA biochemistry, and/or protein-nucleic acid interaction is preferred. Experience in cancer in vitro and in vivo models, cell/molecular biology, cancer genetics or epigenetics is required. Prior experience in epigenetics is preferred but not required.
Minimum Degree Required:
- M.D. and/or Ph.D. in cancer biology, cell biology, molecular biology, or biochemistry
Please send cover letter and CV to:
Giorgio Inghirami, M.D.
Note: Combine cover letter, CV, and contact information for 3 references into one PDF file
Postdoctoral Fellow for Ongoing Research in Gastrointestinal Malignancies (New York, NY)
The laboratory of Dr. Manish Shah at Weill Cornell Medicine, New York, NY, is recruiting a postdoctoral fellow for ongoing research in gastrointestinal malignancies.
Dr. Shah’s clinical/translational laboratory focuses on understanding the implications of disease subtypes of gastrointestinal cancers and the mechanisms of resistance. We combine multi-disciplinary approaches to elucidate drug resistance mechanisms in gastric cancer towards a class of drugs called Taxanes. Other projects include an examination of the role of the microbiome and tumor microenvironment in etiology of esophagus cancer and gastric cancer.
This candidate will use genome-wide molecular techniques in combination with available in vitro cell line models and organoid culture models to understand the drivers of therapeutic resistance. This clinical/translational project will allow for a broad network of interactions with computational, clinical and basic researchers here at Weill Cornell and at other institutions.
The position will also work closely with the Englander Institute for Precision Medicine in its development of patient-derived models of cancer to define distinct molecular classes of cancer using genomic data from human samples, and investigate the potential to translate these findings to clinical relevance.
The position is open to graduating Ph.D. students and current postdoctoral fellows. Candidates must have a Ph.D. and a strong background in, molecular biology, cancer genomics or related fields. Experience working with Organoid models is preferred.
Please send details to:
Note: Combine cover letter, CV, personal statement a brief summary of research experience and contact information for 3 references into one PDF file
Prashant V. Thakkar, Ph.D.
Department of Hematology and Medical Oncology
Postdoctoral Scientist to lead computational analysis of genomics, epigenomics, transcriptomics profiles focusing on hematological malignancies and patient-derived xenografts
We are looking for an ambitious, driven post-doctoral scientist to lead computational analysis of genomics, epigenomics, transcriptomics profiles focusing on hematological malignancies and patient-derived xenografts. The work will take place in the context of a close and productive collaboration between two laboratories at Weill Cornell Medicine and in the Meyer Cancer Center: Dr. Olivier Elemento, whose group focuses on cancer genomics, precision medicine and cancer systems biology, Dr. Giorgio Inghirami who uses patient-derived xenografts to study deregulated pathways and treatment for hematological malignancies. The group has collectively advanced the field and published hundreds of papers in the past few years in the area of genomics (Whole-exome sequencing), epigenomics (ATAC-seq and RRBS), transcriptomics (RNA-Seq) applied to problems of high biomedical relevance. The post-doctoral scientist will perform computational analyses to integrate and interpret large multi-omics genome-wide biological datasets including, generate testable hypotheses, build predictive models that will further drive experimental discovery. In addition, the candidate will develop software and methods to help characterize and share genomics, epigenomics, transcriptomic profiles of patient-derived xenografts and help characterize their sensitivity to therapeutic agents. We are looking for a highly interactive candidate, who will be integrated into the Institute of Computational Biomedicine (ICB). The ICB hosts 6 research groups and over 100 scientists, together with a petabyte scale high-performance computing infrastructure. The ICB also has a large group of talented and experienced computational biologists with a strong focus on cancer genomics on whom the post-doctoral scientist can rely on intellectual input, support, and extensive computational resources.
- Lead computational analysis of Whole-Exome Sequencing, RNA-Seq, ChIP-Seq, ATAC-Seq, RRBS and WGBS data generated in hematological malignancies (primary tumors, cell lines, patient-derived xenografts), generate hypotheses regarding deregulated mechanisms, potential therapeutic targets, biomarkers of drug response, design follow-up experiments
- As needed develop novel methods and algorithms for normalization, analysis, and visualization of large multi-omics data
- Correlate/Integrate multiple omics datasets
- Collaborate closely with several other scientists in the PIs’ groups and elsewhere
- Present results at joint group meetings and other outlets write manuscripts
- A Ph.D. in Biology, Bioinformatics or Computer Science
- Strong publication record with at least one strong first author paper
- Strong background in bioinformatics with experience in analysis of next-generation sequencing data demonstrated by relevant publications.
- An ability to program in at least one widely used language (Perl, Python, Java, C++, etc.), proficiency in statistical software packages such as R / Bioconductor, ability to create compelling graphics and use state-of-the-art data visualization methods e.g. RMarkdown, Shiny, ggplot2, D3.js
- Strong focus and interest on biomedically relevant problems
- Track record of developing novel computational methodologies and publishing innovative software packages
- Demonstrated ability to lead projects and work both independently and collaboratively
- Excellent verbal and written communication skills demonstrated by a track record of publication, public speaking, and collaborative interactions.
Please send cover letter, CV and contact information for at least two referees to:
Olivier Elemento, Ph.D. email@example.com
Giorgio Inghirami, M.D. firstname.lastname@example.org
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