St. Jude Children's Research Hospital
Postdoctoral Research Associate - Computational Biology
St. Jude Children's Research Hospital, Memphis, Tennessee, us, 37544
Overview
The Abraham Lab is seeking a Postdoctoral Research Associate to study the roles of gene dysregulation and genome organization in pediatric cancers. This grant-funded position is part of an inter-institutional, interdisciplinary effort to deconvolve the roles of chromatin-modifying enzymes in genome-wide gene regulation. These enzymes represent emerging drug targets in pediatric solid tumors and collaboration with chemists and molecular oncologists will be key components of the work. Responsibilities
Lead computationally focused scientific research projects with increasing independence over time. Collaborate on project and analysis design guided by their PI. Develop new computational methods. Adhere to field and lab standards for data analysis. Identify, process, organize, interpret, review, and report relevant data. Direct data collection. Present research to colleagues within and outside the institution; draft a complex manuscript with minimal supervision, as required. Perform other duties as assigned to meet the goals and objectives of the department and institution. Maintains regular and predictable attendance. Minimum Education and/or Training
Ph.D. degree or equivalent in Bioinformatics, Molecular Biology, Biochemistry, Computer Science, or related field Special Skills, Knowledge, and Abilities
Required: Candidates must hold a doctoral degree (PhD, MD, or equivalent). Applicants with a PhD in a quantitative field (computational biology, bioinformatics, systems biology, genetics/genomics, statistics, mathematics, computer science, or related fields) are encouraged to apply. Strong candidates from a primarily wet-lab or clinical background who wish to develop sophisticated quantitative skills will also be considered. Successful candidates will have a track record of scientific productivity, e.g., a first author paper, or a demonstrable contribution to a large project. Experience in chromatin and expression analysis technologies is desired. The initial appointment will be for 1-2 years and can be renewed for up to a total of 5 years, depending on the candidate’s goals and qualifications. Preferred
Experience with applied high-throughput sequencing analysis methods, including but not limited to alignment, coverage quantification, differential coverage statistics, and multi-omic integration About the lab and St. Jude
St. Jude offers a work environment where you will impact the future care of pediatric cancer patients. As a Postdoctoral Research Associate, responsibilities include analyzing data generated from a variety of second- and third-generation sequencing applications that interrogate gene regulatory biology in health and disease. The Abraham lab studies gene expression-regulation mechanisms. We recruit computational biologists to collaboratively develop software approaches to analyze high-throughput sequencing data. We build analytical software pipelines to answer biological questions about gene regulation in genome-wide datasets, usually from sequencing experiments like CUT&RUN, RNA-Seq, and HiChIP, as well as single-cell omic experiments. Our interests center on enhancers and super-enhancers and how regulatory elements establish gene expression programs, how enhancers are altered by mutation, mistargeting, and drug targeting in diseased cells. We characterize core regulatory circuitries driving disease-relevant cells and study how mutations in non-coding DNA can drive disease, including cancers, through gene misregulation. The successful candidate will be a fundamental component of a multidisciplinary, inter-institutional team studying how gene expression regulation differs between normal and pediatric cancer cells and how it might be targeted. The candidate will lead research projects within the laboratory with increasing independence. Ideal candidates will have experience building, tailoring, and deploying analysis pipelines using tools such as bedtools, samtools, HiCPro, and Tuxedo tools, and experience managing large datasets. Strong communication and interpersonal skills are essential. Additional experience in understanding gene expression mechanisms and in building clear figures using R is preferred. The Department of Computational Biology provides access to high-performance computing clusters, a cloud computing environment, visualization tools, automated analytical pipelines, and mentorship from faculty scientists with experience in data analysis and management. First-author, high-profile publications are encouraged. Take the first step to joining our team by applying now. Publications / Relevant Papers
Adetunji MO, Abraham BJ. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics. 2022 Feb 23. Hnisz D, Abraham BJ, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013. Prutsch N, He S, et al. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma. Cell Rep Med. 2024. Shendy NAM, et al. Group 3 medulloblastoma transcriptional networks and EP300/CBP inhibition. Nat Commun. 2024. Weichert-Leahey N, Zimmerman MW, et al. Accurate Measurement of Cell Number-Normalized Differential Gene Expression. Bio Protoc. 2024. Zimmerman MW, et al. Retinoic acid rewires the adrenergic core regulatory circuitry of childhood neuroblastoma. Science Advances. 2021. St. Jude is an Equal Opportunity Employer. No Search Firms. St. Jude Children’s Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form will not be paid a fee without a valid written search agreement in place.
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The Abraham Lab is seeking a Postdoctoral Research Associate to study the roles of gene dysregulation and genome organization in pediatric cancers. This grant-funded position is part of an inter-institutional, interdisciplinary effort to deconvolve the roles of chromatin-modifying enzymes in genome-wide gene regulation. These enzymes represent emerging drug targets in pediatric solid tumors and collaboration with chemists and molecular oncologists will be key components of the work. Responsibilities
Lead computationally focused scientific research projects with increasing independence over time. Collaborate on project and analysis design guided by their PI. Develop new computational methods. Adhere to field and lab standards for data analysis. Identify, process, organize, interpret, review, and report relevant data. Direct data collection. Present research to colleagues within and outside the institution; draft a complex manuscript with minimal supervision, as required. Perform other duties as assigned to meet the goals and objectives of the department and institution. Maintains regular and predictable attendance. Minimum Education and/or Training
Ph.D. degree or equivalent in Bioinformatics, Molecular Biology, Biochemistry, Computer Science, or related field Special Skills, Knowledge, and Abilities
Required: Candidates must hold a doctoral degree (PhD, MD, or equivalent). Applicants with a PhD in a quantitative field (computational biology, bioinformatics, systems biology, genetics/genomics, statistics, mathematics, computer science, or related fields) are encouraged to apply. Strong candidates from a primarily wet-lab or clinical background who wish to develop sophisticated quantitative skills will also be considered. Successful candidates will have a track record of scientific productivity, e.g., a first author paper, or a demonstrable contribution to a large project. Experience in chromatin and expression analysis technologies is desired. The initial appointment will be for 1-2 years and can be renewed for up to a total of 5 years, depending on the candidate’s goals and qualifications. Preferred
Experience with applied high-throughput sequencing analysis methods, including but not limited to alignment, coverage quantification, differential coverage statistics, and multi-omic integration About the lab and St. Jude
St. Jude offers a work environment where you will impact the future care of pediatric cancer patients. As a Postdoctoral Research Associate, responsibilities include analyzing data generated from a variety of second- and third-generation sequencing applications that interrogate gene regulatory biology in health and disease. The Abraham lab studies gene expression-regulation mechanisms. We recruit computational biologists to collaboratively develop software approaches to analyze high-throughput sequencing data. We build analytical software pipelines to answer biological questions about gene regulation in genome-wide datasets, usually from sequencing experiments like CUT&RUN, RNA-Seq, and HiChIP, as well as single-cell omic experiments. Our interests center on enhancers and super-enhancers and how regulatory elements establish gene expression programs, how enhancers are altered by mutation, mistargeting, and drug targeting in diseased cells. We characterize core regulatory circuitries driving disease-relevant cells and study how mutations in non-coding DNA can drive disease, including cancers, through gene misregulation. The successful candidate will be a fundamental component of a multidisciplinary, inter-institutional team studying how gene expression regulation differs between normal and pediatric cancer cells and how it might be targeted. The candidate will lead research projects within the laboratory with increasing independence. Ideal candidates will have experience building, tailoring, and deploying analysis pipelines using tools such as bedtools, samtools, HiCPro, and Tuxedo tools, and experience managing large datasets. Strong communication and interpersonal skills are essential. Additional experience in understanding gene expression mechanisms and in building clear figures using R is preferred. The Department of Computational Biology provides access to high-performance computing clusters, a cloud computing environment, visualization tools, automated analytical pipelines, and mentorship from faculty scientists with experience in data analysis and management. First-author, high-profile publications are encouraged. Take the first step to joining our team by applying now. Publications / Relevant Papers
Adetunji MO, Abraham BJ. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics. 2022 Feb 23. Hnisz D, Abraham BJ, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013. Prutsch N, He S, et al. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma. Cell Rep Med. 2024. Shendy NAM, et al. Group 3 medulloblastoma transcriptional networks and EP300/CBP inhibition. Nat Commun. 2024. Weichert-Leahey N, Zimmerman MW, et al. Accurate Measurement of Cell Number-Normalized Differential Gene Expression. Bio Protoc. 2024. Zimmerman MW, et al. Retinoic acid rewires the adrenergic core regulatory circuitry of childhood neuroblastoma. Science Advances. 2021. St. Jude is an Equal Opportunity Employer. No Search Firms. St. Jude Children’s Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form will not be paid a fee without a valid written search agreement in place.
#J-18808-Ljbffr