Positions available

Several positions available! Please read through for different job/project descriptions.

Human Gut Cell Atlas project is looking for a computational biologist

We are looking for a postdoctoral fellow to join as a computational biologist an interdisciplinary team aiming to create a cellular atlas of the human gut. In close collaboration with  Drs. Sebastian Pott, Eugene Chang,  and Matthew Stephens at UChicago, we are working to generate cellular and molecular maps of the intestine, particularly terminal ileum and ascending colon. We use these maps to compare against the aberrant mucosa in ileal and ileal-colonic Crohn’s Disease. We plan to leverage single cell data generated to also test response to pro-inflammatory stimuli and drugs in normal and patient-derived organoids as models to test cellular response to environmental and microbial triggers as well as drug efficacy. The ideal candidate will have a strong computational background and experience in analyzing single cell genomics assays, including scRNA-seq and scATAC-seq. We are looking for an individual excited to be part of a team that includes biologists, clinicians, and statisticians; the candidate should be highly collaborative and comfortable in a team setting. We strive to provide a collegial and inclusive environment that nurtures scientific creativity and rigor. If interested, please contact onibasu at uchicago.edu with a brief statement of research interest, CV, and two references with their email addresses.

 

Integration of silicon chip technologies with soft microfluidics: Post-doc or graduate student applications to work on microbial cell lysis and single cell genomics

In collaboration with Dr. Supratik Guha’s Lab, we are looking for a postdoctoral scientist or graduate student to work on a project that incorporates silicon nanotechnology into soft microfluidics for genomic analysis of microbes.  Initial research will develop promising experimental results we have obtained on microbial cell lysis using micromechanical impaction. Further opportunities exist in exploring the integration of photonic and electrical functionalities via microelectronics or photonics for spectroscopic analyses of microbial lysates.  The candidate should have strong nanofabrication skills.  Microfluidics experience is desirable.  While prior experience in biological research is not necessary, the candidate should have a strong in interest in biological research and genomics, in particular.  This is a collaboration between Basu lab in the Biological Sciences Division, and Professor Guha’s lab at the Pritzker School of Molecular Engineering and Argonne National Laboratory.  There will be opportunities to work at both labs, interact with scientists in biology and engineering and access extensive cleanroom-based nanofabrication, device characterization and single cell genomics facilities.  Anyone with training in interdisciplinary sciences is welcome to apply. Please contact onibasu at uchicago.edu with a brief statement of research interest, CV, and two references with their email addresses if interested.

 

Post-doc or graduate student: Host Pathogen Interactions

We are recruiting goal-oriented, creative, collaborative and highly motivated graduate students or post-docs to use multi-omics assays and high-resolution imaging to study microbiome and cellular interactions in the context of complex disorders such as inflammatory bowel disease. We perform single-cell genomic, epigenetic, transcriptomic, and proteomic assays to study the role of gut microbiome in shaping the immune system. We use high throughput single-cell technologies, such as 10X Genomics scRNA-seq and scATAC-seq, Drop-seq, DroNc-seq, and mDrop-seq to dissect the role of microbiota in modulating immune cells to address important questions in immune disorders. Experiences in large-scale dataset analysis through the use of programming languages would be a plus.

We also develop and apply cutting-edge imaging and microfluidic technologies to observe the interactions between the microbiota and the host, by direct visualization of molecular and cellular interactions at single-cell and tissue level. We use human biopsies, surgical samples, organoids and microfluidic based simple cellular models for research with goals for advancing fundamental sciences as well as clinical applications. We are also exploring spatial transcriptomics assays (RNAscope, NanoString GeoMx) Applicants with relevant experiences in immunology, microbiology, genetics, cell biology, molecular biology, bioengineering or relevant fields are encouraged to join our team. Experience with sequencing, flow cytometry, microfluidics and multiplexed imaging are preferred but not required.

If you are interested, please write to Oni Basu (onibasu at uchicago.edu) with a brief statement of research interest, CV, and two references with their email addresses.

 

Research scientist or post-doc: Modeling to assess risk and treat venous thrombosis in patients under hemodialysis

We are looking for a motivated research scientist or post-doc with interest and/or training in bioengineering to join a multi-disciplinary team in the Department of Medicine with expertise in applied Physics, systems Biology, nephrology, interventional cardiology, radiology, hematology, and vascular surgery.

Patients with End-Stage Renal Disease (ESRD) who undergo regular hemodialysis suffer from frequent complications like thrombosis and stenosis. These failures may require hospitalization, radiologic intervention and/or surgery and can even be life-threatening. The complex interplay of vein geometry, hemodynamics, secreted endothelial factors and soluble blood factors contribute to the access thrombosis and stenosis. We are constructing personalized models of the vein sections in ESRD patients who are likely to thrombose or stenose. Our model will capture the biophysical and biochemical properties of access thrombosis in ESRD to predict a patient’s likelihood to develop disease and test different prevention or treatment options in vitro.

The candidate should have experience in a multiple, if not all, of these common laboratory techniques: 3D printing, device fabrication, microfluidics, cell culture, optical imaging, and image processing. The candidate will also perform chemical and clinical assays for which training will be provided. This work will be performed under the co-supervision of Oni Basu and Prof. Mary Hammes in Nephrology. If interested, please contact Oni Basu (onibasu at uchicago.edu) with a brief statement of research interest, CV, and two references with their email addresses.

 

Lab Manager

We are looking for a motivated, research focused individual to join our lab as the Lab Manager. This is an exciting opportunity to work on high throughput single cell genomics experiments. We are looking for a candidate who has significant experience with pipetting, PCR, running gels, constructing Next-Generation Sequencing libraries, handling RNA, and is eager to learn other techniques. Optical microscopy experience is a plus. Experience in single cell genomics is desired. Responsibilities will include the following non-laboratory duties: assisting with developing or amending research protocols, assisting with equipment scheduling and maintenance, placing lab orders, tracking inventory, supervising research technicians, collaborating with other labs/ researchers, and providing general administrative support. Responsibilities may include the following laboratory duties: help setting up and performing experiments (10x Genomics and Drop-seq), interacting with students and other laboratory staff under the direction of the principal investigator, overall lab management and maintenance. Bachelor’s degree in a field relevant to the research and a minimum of four years of relevant research experience are required. If interested, please contact Oni Basu (onibasu at uchicago.edu) with a CV and a reference.