Job Details

Senior Research Investigator - Cremins Lab - Penn Engineering
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Position Number: 5727608
Location: Philadelphia, PA
Position Type: Health - Communication Disorders

Senior Research Investigator - Cremins Lab - Penn Engineering

University Overview

The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that provide opportunities for undergraduate, graduate and continuing education, all influenced by Penn's distinctive interdisciplinary approach to scholarship and learning. As an employer Penn has been ranked nationally on many occasions with the most recent award from Forbes who named Penn one of America's Best Large Employers in 2023.

Penn offers a unique working environment within the city of Philadelphia. The University is situated on a beautiful urban campus, with easy access to a range of educational, cultural, and recreational activities. With its historical significance and landmarks, lively cultural offerings, and wide variety of atmospheres, Philadelphia is the perfect place to call home for work and play.

The University offers a competitive benefits package that includes excellent healthcare and tuition benefits for employees and their families, generous retirement benefits, a wide variety of professional development opportunities, supportive work and family benefits, a wealth of health and wellness programs and resources, and much more.

Posted Job Title
Senior Research Investigator - Cremins Lab - Penn Engineering

Job Profile Title
Research Investigator, Senior

Job Description Summary
The Cremins lab works at the spatial biology-technology interface to understand chromatin-to-synapse communication during neural circuit activation in the mammalian brain. We aim to understand how chromatin works through long-range physical folding mechanisms to encode neuronal specification and long-term synaptic plasticity in healthy and diseased neural circuits. We pursue a multi-disciplinary approach integrating data across biological scales in the brain, including molecular Chromosome-Conformation-Capture sequencing technologies, single-cell imaging, optogenetics, genome engineering, induced pluripotent stem cell differentiation to neurons/organoids, and in vitro and in vivo electrophysiological measurements.

Our long-term scientific goal is to dissect the fundamental mechanisms by which chromatin architecture causally governs genome function and, ultimately, long-term synaptic plasticity and neural circuit features in healthy mammalian brains as well as during the onset and progression of neurodegenerative and neurodevelopmental disease states.

Our long-term mentorship goal is to develop a diverse cohort of next-generation scientific thinkers and leaders cross-trained in molecular and computational approaches. We seek to create a positive, high-energy environment with open and honest communication to empower individuals to discover and refine their purpose and grow into the best versions of themselves.

The Senior Research Investigator (SRI) in the Cremins Lab will work with a dynamic team to conduct research in the area of sequencing and analysis of complex multimodal genomics data. Collaborate with the team to design, optimize, and standardize experimental and analysis pipelines to accelerate high-quality publications. Develop new code and statistical methods to analyze genomics and spatial transcriptomics datasets to map the neural connectome. They will also be responsible for maintaining and organizing lab records, training junior scientists on technical assays, preparing and reviewing manuscripts, and helping with grant applications.
Successful candidates will possess strong data processing skills in the UNIX/Linux environment and familiarity with high-performance computing clusters. They will have experience in learning diverse data types generated by various platforms and technologies, including genomics, proteomics, imaging, and spatial transcriptomics data.
This role is ideal for you if you enjoy the excitement of a bleeding-edge scientific laboratory and welcome the challenge of serving as a steady consistent organizational and genomics scientist role in a fast-paced environment. Those who will thrive in the role are dedicated to collaboration and keen on playing an active role in maintaining excellent protocols, a clean, organized, and safe laboratory, and eager to lead themselves and others toward maintaining a warm, positive, and inclusive lab climate. Organized individuals with a can-do attitude, a passion for building unity and community within a larger laboratory, a knack for independent problem-solving and getting things done, and the ability to independently and positively create molecular and cellular data with attention to detail would excel in this role.

Job Description

Job Responsibilities

Scientific

Supervise and conduct Illumina linkering, library preparation for all genomics experiments, quantification, library pooling, and placing sequencing runs for the lab
Generate novel genomics and connectome datasets to understand structure-function relationships of neuronal genomes.
Process and analyze imaging and sequencing data (image registration, segmentation, feature detection, clustering, anchoring to single cell datasets)
Manuscript and grant preparation and review

Collaborate fluidly with other computational experts to conduct efficient analyses leading to discovery in mammalian neuron genome structure-function data. In parallel, train to understand the innerworkings of loop, TAD, subTAD, and trans interaction code for genome folding in single-cell 3D genome data sets
Develop new algorithms for analysis of RNA FISH, DNA FISH, and neural connectome in situ sequencing technologies
Train on the Cremins lab's code and statistical analysis BE504 course and then role out principles to the younger laboratory trainees
Guide lab members to write and edit methods sections and figures for research papers where the analysis is used in the manuscript.

Teaching and Daily leadership tasks

Oversee and write established SOPs for new and existing molecular sequencing technologies
Oversee and write established SOPs for new and existing computational algorithms
Train new lab members on sequencing technologies and computational algorithms
As the opportunity allows in the SRIs expertise areas, serve as the primary mentor for 1 technician in the Cremins laboratory

Administrative

Interview top Cremins lab job candidates after curating applications and initial screening to find the top 5 candidates for interview

Scientific Writing

Edit, format, and facilitate stylistic and grammatical edits for lab's annual grant progress reports
Coordinae team members to arrange scientific content to meet grant progress report deadlines
Organize, edit, and catalyze the writeup and creation of lab protocols
Edit and provide feedback on postdoc and student proposal, grant submission, and manuscript drafts
Assist PI in filling out of paperwork including but not limited to dbGAP and ENCODE data portal approvals; grant and University-related paperwork; yearly RRPR reports for the lab's grants - including coordinating with the subTeam members to get the content assembled

Many new writing opportunities for grants, papers, and scientific marketing materials are available if this is a passion and interest of the selected candidate
Potential to learn NIH R21 and R01 grant writing from the PI and partner with the PI to submit grant applications

Qualifications

PhD in cell biology or neuroscience and 5-7 years of postdoctoral experience is required.
Experience in cell culture, 3D genome architecture, multi-omics, spatial transcriptomics, mouse genetics, and behavioral and circuit neuroscience
Experience with Illumina library preparation and handling NextSeq1000/2000 and Novaseq instruments is required
Experience in histology and fluorescence microscopy is essential
Experience in Python/R programming language, Linux environment, and cluster computing
Experience in statistical analysis
Ability to work independently and apply critical thinking and sound judgment
Excellent organizational and time management skills
Ability to work with a multi-disciplinary team
The position requires excellent communication and interpersonal skills, independent thinking, and a desire to work in a complex and high-energy environment.

Job Location - City, State
Philadelphia, Pennsylvania

Department / School
School of Engineering and Applied Science

Pay Range
$43,888.00 - $90,000.00 Annual Rate
Salary offers are made based on the candidate's qualifications, experience, skills, and education as they directly relate to the requirements of the position, as well as internal and market factors and grade profile.

Affirmative Action Statement
Penn adheres to a policy that prohibits discrimination on the basis of race, color, sex, sexual orientation, gender identity, religion, creed, national or ethnic origin, citizenship status, age, disability, veteran status, or any other legally protected class.

Special Requirements
Background check required after a conditional job offer is made. Consideration of the background check will be tailored to the requirements of the job.

University Benefits

Health, Life, and Flexible Spending Accounts: Penn offers comprehensive medical, prescription, behavioral health, dental, vision, and life insurance benefits to protect you and your family's health and welfare. You can also use flexible spending accounts to pay for eligible health care and dependent care expenses with pre-tax dollars.
Tuition: Take advantage of Penn's exceptional tuition benefits. You, your spouse, and your dependent children can get tuition assistance here at Penn. Your dependent children are also eligible for tuition assistance at other institutions.
Retirement: Penn offers generous retirement plans to help you save for your future. Penn's Basic, Matching, and Supplemental retirement plans allow you to save for retirement on a pre-tax or Roth basis. Choose from a wide variety of investment options through TIAA and Vanguard.
Time Away from Work: Penn provides you with a substantial amount of time away from work during the course of the year. This allows you to relax, take vacations, attend to personal affairs, recover from illness or injury, spend time with family-whatever your personal needs may be.
Long-Term Care Insurance: In partnership with Genworth Financial, Penn offers faculty and staff (and your eligible family members) long-term care insurance to help you cover some of the costs of long-term care services received at home, in the community or in a nursing facility. If you apply when you're newly hired, you won't have to provide proof of good health or be subject to underwriting requirements. Eligible family members must always provide proof of good health and are subject to underwriting.
Wellness and Work-life Resources: Penn is committed to supporting our faculty and staff as they balance the competing demands of work and personal life. That's why we offer a wide variety of programs and resources to help you care for your health, your family, and your work-life balance.
Professional and Personal Development: Penn provides an array of resources to help you advance yourself personally and professionally.
University Resources: As a member of the Penn community, you have access to a wide range of University resources as well as cultural and recreational activities. Take advantage of the University's libraries and athletic facilities, or visit our arboretum and art galleries. There's always something going on at Penn, whether it's a new exhibit at the Penn Museum, the latest music or theater presentation at the Annenberg Center, or the Penn Relays at Franklin Field to name just a few examples. As a member of the Penn community, you're right in the middle of the excitement-and you and your family can enjoy many of these activities for free.
Discounts and Special Services: From arts and entertainment to transportation and mortgages, you'll find great deals for University faculty and staff. Not only do Penn arts and cultural centers and museums offer free and discounted admission and memberships to faculty and staff. You can also enjoy substantial savings on other goods and services such as new cars from Ford and General Motors, cellular phone service plans, movie tickets, and admission to theme parks.
Flexible Work Hours: Flexible work options offer creative approaches for completing work while promoting balance between work and personal commitments. These approaches involve use of non-traditional work hours, locations, and/or job structures.
Penn Home Ownership Services: Penn offers a forgivable loan for eligible employees interested in buying a home or currently residing in West Philadelphia, which can be used for closing costs or home improvements.
Adoption Assistance: Penn will reimburse eligible employees on qualified expenses in connection with the legal adoption of an eligible child, such as travel or court fees, for up to two adoptions in your household.

To learn more, please visit: https://www.hr.upenn.edu/PennHR/benefits-pay

To apply, visit https://wd1.myworkdaysite.com/en-US/recruiting/upenn/careers-at-penn/job/SEAS-Bioengineering/Senior-Research-Investigator---Cremins-Lab---Penn-Engineering_JR00098675