Scientist- Abraham’s Lab

About the job

Join our Team!

The Abraham Laboratory in the Department of Computational Biology at St. Jude Children's Research Hospital is seeking an innovative and collaborative Scientist to investigate how gene regulation and nuclear organization shape mammalian cell identity and contribute to disease, including pediatric cancers.
This is an exciting bench-based role for a hands-on experimental scientist who is passionate about uncovering the mechanisms that control gene expression.

The successful candidate will study cis- and trans- regulatory mechanisms using cutting-edge molecular biology technologies and independently design and execute high-throughput functional genomics assays
Working at the intersection of molecular biology, functional genomics, and cancer biology, you will design and execute cutting-edge experiments that advance our understanding of how regulatory elements such as enhancers and super-enhancers drive normal development and disease.
As a key member of a highly collaborative multidisciplinary team, you will lead and contribute to research projects utilizing advanced genomic technologies, cell-based systems, and imaging approaches to answer fundamental biological questions with direct relevance to human health.
Ideal Candidate

The ideal candidate is a highly independent, hands-on scientist with strong troubleshooting skills and a collaborative mindset. This individual will serve as a key experimental partner within a shared-resource environment, working across multiple research projects focused on gene regulation and functional genomics.
Candidates are not required to have expertise in every area listed. We welcome individuals with experience in a combination of these techniques who are eager to expand their skill set and contribute across diverse research projects.

• Experience in some combination of the following areas is preferred:
• Molecular & Cellular Biology
• Molecular cloning
• Cell culture and tissue culture
• Viral transduction and cell line engineering
• Tissue processing and sample handling
• Functional Genomics & Omics Technologies
• Strong hands-on experience with at least one high-throughput sequencing-based assay such as: • ChIP-seq
• CUT&RUN
• ATAC-seq
• RNA-seq
• Hi-C or related genomic technologies

• Ability to independently troubleshoot and optimize genomics workflows
• Imaging & Cellular Phenotyping
• Immunofluorescence staining
• DNA and RNA FISH
• Confocal microscopy
• Cellular imaging-based assays
• Preferred / Nice-to-Have Experience
• Massively Parallel Reporter Assays (MPRA)
• High-throughput functional genomic screening
• Research involving transcriptional condensates, enhancer biology, or gene regulatory mechanisms
• Experience generating and analyzing large-scale genomic datasets

• Projects This Scientist May Support
• Depending on their expertise and project needs, the successful candidate may contribute to initiatives involving:
• MPRA-based functional genomics studies
• DNA and RNA imaging assays
• Transcriptional condensate biology
• Enhancer and super-enhancer regulation
• Genome-wide sequencing and functional genomics applications
• Large-scale dataset generation and characterization efforts
• This role is best suited for a scientist who enjoys being the go-to experimental expert, thrives in a highly collaborative environment, and has the technical confidence to independently drive complex research projects from concept to data generation.

• What You'll Do
• In this laboratory-based role, you will:
• Coordinate multiple research projects, carry out bench laboratory experiments utilizing various techniques, and determine whether additional or other tools, methods, or data are required
• Provide input regarding research protocols and experiments. Sets up protocols and assists in developing new laboratory techniques as required.
• Monitor the quality and integrity of recorded information and data.
• Identify, process, organize, interpret, review, and faithfully, comprehensively, and durably report relevant data.
• Draft sections of research manuscripts.
• Provide basic lab operation support to include equipment maintenance and purchasing. Monitor inventory levels and order lab supplies as needed.
• Collaborate on project and analysis design under the guidance of multiple invested PIs.
• Set personal task-level priorities across multiple interconnected projects.
• Adhere to field and lab standards for data generation and analysis.
• Perform other duties as assigned to meet the goals and objectives of the department and institution.
• Maintain regular and predictable attendance, especially in-person attendance at meetings and relevant presentations.
• Increase in independence and expertise over time.

• Special Skills, Knowledge, and Abilities:
• Ability to rapidly learn, optimize, and implement new or advanced techniques as required by the evolving research direction.
• Experience leading or substantially driving complex research projects.
• Can apply knowledge/skills within own area to deliver tasks with limited guidance
• Focus on setting high targets, following through actions, and achieving results. Ability to anticipate roadblocks and circumvent challenges.
• Very strong commitment to rigor and scientific integrity.
• Strong written and spoken English, presentation, and communication skills.
• Essential hands-on experience with: cell biology techniques such as cell culture, in-vitro cell assays, viral transduction, and tissue sample handling at least one applied high-throughput sequencing assay (e.g., ChIP-seq, CUT&RUN, ATAC-seq, Hi-C, RNA-seq, or related genomic technologies).
• Preferred experience with: generating stable cell lines using non-viral and viral-based delivery systems.
• high-throughput functional genomic screening such as MPRA, immunofluorescence staining, FISH and confocal microscopy. applicable regulations and lab protocols
• Optional but helpful experience with: Command line tools and experience running commercial pipelines using both cloud applications and computational clusters.

• Minimum Education and/or Training:
• Bachelor's degree in relevant scientific areas such as cancer biology, cell biology, molecular biology, developmental biology, biomedical sciences, or a related discipline is required.
• PhD, or equivalent doctoral degree strongly preferred.

• Scientist Minimum Experience:
• Eight (8) years of relevant work experience is required
• Six (6) years of relevant work experience is required with a Master's degree
• Three (3) years of relevant work experience is required with a PhD

This position is in Memphis, TN (100% on-site position), and relocation assistance is available.

Why Join the Abraham Lab?
The Abraham lab studies gene expression-regulation mechanisms. We are recruiting bench biologists to collaboratively develop approaches to find answers to biological questions about gene regulation in genome-wide datasets, usually from applied sequencing experiments like CUT&RUN, RNA-Seq (bulk, single-cell, and spatial), and HiChIP, as well as single-cell omic experiments. Our interests center on enhancers and super-enhancers. Specifically, we seek to understand how these regulatory elements establish gene expression programs in healthy cells, and how enhancers are altered by mutation, abused by mistargeting, and targetable with drugs in diseased cells. We characterize the specific core regulatory circuitries driving disease-relevant cells and seek to understand how mutations in the non-coding DNA of such cells can drive disease, including cancers, through gene misregulation. Our lab is actively involved in multidisciplinary collaboration across departments, primarily Molecular Oncology, to decipher gene regulatory networks in solid tumors and leukemias.

The successful candidate will become a fundamental component of a multidisciplinary, inter-institutional, bench/computational team assembled to study how gene expression regulation meaningfully differs between normal and pediatric cancer cells and might be productively targetable. The successful candidate will lead research projects within the laboratory with increasing independence in daily operation.

The Department of Computational Biology provides access to modern and frequently updated bench technologies and mentorship from faculty scientists with experience in data analysis, data management, and delivery of high-quality results for competitive projects. First-author, high-profile publications are required to share this element of discovery. Take the first step to joining our team by applying now!

Why St. Jude?
St. Jude Children's Research Hospital is internationally recognized for its world-class scientific environment, cutting-edge technologies, and commitment to advancing cures for catastrophic childhood diseases. Researchers benefit from exceptional institutional resources, a culture of collaboration, and strong support for professional growth and career development in both academic and industry career paths.
Whether your long-term goals are in academia, biotechnology, or pharmaceutical research, St. Jude provides the mentorship, infrastructure, and scientific community to help you succeed

Relevant Papers:

Hnisz D, Abraham BJ , Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10. PubMed PMID: 24119843
Lv J, Maher KA, Dong L, Valentine V, Staller S, Veluchamy A, Tian L, Kim Y, Ju B, Valentine M, Easton J, Pounds SB, Burden S, Abraham BJ . 3D-super-enhancers are condensate-associated cis-regulatory communities. Nucleic Acids Research. 2026 Feb 24;54(5):gkag191.doi: 10.1093/nar/gkag191. PMID: 41797539 PMCID: PMC12968393
Prutsch N, He S, Berezovskaya A, Durbin AD, Dharia NV, Maher KA, Matthews JD, Hare L, Turner SD, Stegmaier K, Kenner L, Merkel O, Look AT, Abraham BJ , Zimmerman MW. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma.
Cell Rep Med. 2024 Mar 19;5(3):101472. doi: 10.1016/j.xcrm.2024.101472. PMID: 38508140

Weichert-Leahey N, Zimmerman MW, Berezovskaya A, Look AT, Abraham BJ. Accurate Measurement of Cell Number-Normalized Differential Gene Expression in Cells Treated With Retinoic Acid. Bio Protoc. 2024 Nov 5;14(21):e5106. doi: 10.21769/BioProtoc.5106. eCollection 2024 Nov 5. PMID: 39525967; PMCID: PMC11543784

Zimmerman MW, Durbin AD, He S, Oppel F, Shi H, Tao T, Li Z, Berezovskaya A, Liu Y, Zhang J, Young RA, Abraham BJ , Look AT. Retinoic acid rewires the adrenergic core regulatory circuitry of childhood neuroblastoma. Science Advances. 2021 Oct 22; PMID: 34669465.

Compensation
In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $86,320 - $154,960 per year for the role of Scientist- Abraham’s Lab.
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