1143 POST DOCTORAL FELLOW - GENOMICS OF GENE REGULATION

A postdoctoral fellow position is open in the Tan laboratory in the Department of Pediatrics at the Children’s Hospital of Philadelphia (CHOP). The project will use state-of-the-art genomics, molecular and cell biology approaches to investigate transcriptional regulation of the development of hematopoietic stem cells in mouse. The project provides an excellent training opportunity in regulatory genomics and developmental biology. The postdoctoral fellow will also have ample opportunities to collaborate with internationally recognized developmental biologists working on hematopoiesis at CHOP and the University of Pennsylvania.

The applicant should have a Ph.D. degree in biological sciences, such as genetics, molecular biology, and cell biology etc. The candidate should be proficient in mammalian cell culture and modern molecular and cell biology protocols. An established track record (as evidenced by publications in peer-viewed journals) in relevant field is required. Experience with next-gen sequencing technologies, genome editing, and enhancer assays is a significant plus.

CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities. CHOP is an interdisciplinary institution dedicated to conducting basic, clinical and translational research with a particular focus on conditions that affect children.

Requirements

The postdoctoral fellow (postdoc) will have a terminal degree PhD, MD, DVM, etc. and will, under the direction/guidance of a mentor (principal investigator), assume responsibility for a specific, on-going research project. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group.

Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results. Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

According to the CMS (Centers for Medicaid and Medicare Services) a copy of diploma or transcript is required as proof of academic achievement for all non-laboratory personnel performing non-waived POC testing.

EDUCATION AND EXPERIENCE:

  • PhD in biological sciences, such as genetics, molecular biology, cell biology, or related fields
  • Proficient in mammalian cell culture and modern molecular and cell biology protocols
  • An established track record (as evidenced by publications in peer-viewed journals) in relevant field is required
  • Experience with next-gen sequencing technologies, genome editing, and enhancer assays is preferred
  • Strong understanding of cancer molecular biology and genetics
  • Values research integrity and collaborative research
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently and with a strong work ethic
  • High level of motivation
  • Excellent communication/interpersonal skills
  • Ability to exercise discretion and judgment

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1191 POST DOCTORAL FELLOW - BIOMEDICAL AND HEALTH INFORMATICS

A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP), reporting to the Director of Bioinformatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities.

This position offers the opportunity to work in the very early-onset inflammatory bowel disease (VEO-IBD) research group at The Children's Hospital of Philadelphia (CHOP). The VEO-IBD Program is a multidisciplinary program that includes Judith Kelsen, MD pediatric gastroenterologist and program director, Marcella Devoto, PhD, genetic epidemiologist, Noor Dawany, PhD, lead bioinformatician, Kathleen Sullivan, MD, PhD, Chief of Immunology and Edward Behren, MD, Chief of Rheumatology. This translational program is studying the unique genomic contribution to the disease through NGS and functional analyses. In addition, the group is studying the relationship between the genomic architecture and subsequent immune dysregulation with the microbiome in this population. This research group is interdisciplinary and highly collaborative.

The desired candidate must have a terminal degree (PhD) in computational biology, computer science, statistics, or related field. The postdoctoral fellow will be involved in the analysis of next-generation sequencing data related to pediatric inflammatory bowel disease research in the Division of Gastroenterology, Hepatology and Nutrition. The candidate is expected to be able to develop new algorithms, make sense of the data and construct predictive models for precision medicine applications. The postdoctoral fellow will assume responsibility for a specific, on-going research project under the joint direction/guidance of Dr. Kelsen, Dr. Dawany, Dr. Devoto and Dr. Taylor, head of the Bioinformatics Group in the Department of Biomedical and Health Informatics. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results. The successful candidate is also expected to demonstrate basic scientific knowledge of cell biology, molecular biology, and/or immunology.

Postdocs will also be expected to acquire technical and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to develop new methods and protocols for research, and assist with the development of other research projects in the lab.

EDUCATION AND EXPERIENCE:

  • PhD in computational biology, computational science, statistics, or mathematics, engineering, genomics/genetics or related fields
  • UNIX/LINUX and high performance computing experience
  • Proficiency in R or similar commonly used statistical languages
  • Basic proficiency with Python, Perl, or other languages
  • Values research integrity and collaborative research
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently and with a strong work ethic
  • High level of motivation
  • Excellent communication/interpersonal skills
  • Ability to exercise discretion and judgment

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4504 POST DOCTORAL FELLOW - BIOINFORMATICS/ BIOSTATISTICS

A postdoctoral fellow position is open in the Tan research group in the Departments of Pediatrics and Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP). Dr. Tan is an associate professor of Pediatrics and Biomedical and Health Informatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities. CHOP is an interdisciplinary institution dedicated to conducting basic, clinical and translational research with a particular focus on conditions that affect children.

The Tan research group (http://www.healthcare.uiowa.edu/labs/tan/) is interdisciplinary and highly collaborative, utilizing both computational and experimental approaches to study gene regulation. We have pioneered multiple computational algorithms for regulatory genomics, epigenomics, and network biology. The candidate will work on developing computational algorithms for cancer regulatory genomics and epigenomics. Specific projects in these two laboratories will be defined by the candidate (and based on the candidates expertise) and with input from Dr. Tan and our close collaborators at the Center for Childhood Cancer Research CHOP and Abramson Cancer Center at the University of Pennsylvania.

The desired candidate must have a terminal degree (PhD) in computational biology, computer science, statistics, mathematics or related field with a strong understanding of biology. The postdoctoral fellow will be responsible for development of novel computational algorithms and integrative analysis of high-dimensional datasets, focused on generating insights into how mutations in regulatory DNA sequences contribute to oncogenesis. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the research group. Postdocs will be expected to participate in project planning, bioinformatics recording and interpretation/evaluation of data, and communication of results.

Postdoctoral fellows will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

The postdoctoral fellow (postdoc) will have a terminal degree PhD, MD, DVM, etc. and will, under the direction/guidance of a mentor (principal investigator), assume responsibility for a specific, on-going research project. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group.

Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results. Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

According to the CMS (Centers for Medicaid and Medicare Services) a copy of diploma or transcript is required as proof of academic achievement for all non-laboratory personnel performing non-waived POC testing.

EDUCATION AND EXPERIENCE:

  • PhD in computational biology, computational science, statistics, or mathematics, engineering, genomics/genetics or related fields
  • UNIX/LINUX and high performance computing experience
  • Exhibited knowledge of statistics and probability important to bioinformatics research
  • Proficiency in R or similar commonly used statistical languages
  • Basic proficiency with Python, Perl, or other languages
  • Strong understanding of cancer molecular biology and genetics
  • Exhibited knowledge of biological network analysis
  • Values research integrity and collaborative research
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently and with a strong work ethic
  • High level of motivation
  • Excellent communication/interpersonal skills
  • Ability to exercise discretion and judgment

SKILLS and ABILITIES

  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently
  • Ability to exercise discretion and judgment
  • Value for research integrity and collaborative research
  • High level of motivation
  • Good communication skills
  • Strong interpersonal skills

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5361 BIOINFORMATICS SCIENTIST II

Description: The Bioinformatics Scientist II will apply knowledge of bioinformatics algorithms and analysis platforms to consult with investigators on their projects and to serve as a collaborative investigator in academic output including assistance in experimental design and writing, including creation of scientifically rigorous visualizations, communications, and presentations of results. The Scientist will be working with a diverse, highly skilled, team-oriented laboratory and clinical oncology team in the Maris Lab at CHOP. The Candidate will process sequencing data both in local clusters as well as through cloud services. Candidates must be able to show proficiency in development of analysis systems, such as pipelines and automation for analysis of high-throughput data. Candidates will have an excellent understanding of the strengths and limitations of commonly used data generating platforms as they apply to experimental endpoints and will readily be able to set expectations and defend results through frequent and direct communication with collaborators.

JOB RESPONSIBILITIES
Pre-Analysis (20%): Contribute to the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support.

  • Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan
  • Contribute to the development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances
  • Advocate for specific collaboration requirements for continual advancement of shared pipeline and code resources
  • Provide collaboration-specific transparency for data processing and pre-analysis, including sample- and cohort-level status

(20%): Code and generally support code and applications on behalf of collaborative project and/or team.
Within the context of the collaboration or project, develop and apply best practices to code development:

  • Establish requirements with the project team
  • Review existing applications and code sources (both commercial and open source) and selection of best strategy for development or adoption
  • Advocate for chosen strategy to project team by showing value of approach
  • Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations
  • Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews

Data Analysis (20%): Analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data primarily under the direction of the collaborative project team

  • Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings
  • Incorporate more advanced applications and methods into analysis
  • Develop at least one “specialty” analytical or biomedical area that serves the collaborative team

Collaboration (20%): Establish role within collaborative project team as primary bioinformatics resource

  • Contribute to and influence project-level management by serving as bioinformatics point
  • Define and promote boundaries of support by assessing all stakeholders, including bioinformatics management, collaborator expectations, and funding levels and mechanisms
  • Regularly discuss satisfaction and expectations with collaborators; continually advocate for clear understanding of role
  • Develop new collaborations with high degree of supervision

Academic Output (20%): Develop presentations, grant sections, and manuscript sections with subsequent review by peers and mentors.

  • Regularly contribute to bioinformatics-focused manuscripts and publications
  • Regularly contribute to podium presentations and posters
  • Contribute to bioinformatics sections of grant and award proposals

EDUCATION AND EXPERIENCE

  • MS or Ph.D. In a biological, computational or related discipline.
  • At least three to five (3-5) years experience in applied bioinformatics, genomics and computational work.
  • Working experience with next generation sequencing data using common tools, including BWA, Novoalign, STAR, GATK, freebayes, samtools, Picard, SnpEff, bedtools, tabix, and other tools and resources, e.g. sequence retrieval, alignment and clustering techniques, expression profiling and protein related analysis, using major databases and data standards in the field.
  • Working knowledge and deep understanding of algorithms, data structures, and scientific programming, including workflow management packages.
  • Proficiency with the minimum programming languages of Python, Perl, and R.
  • Pipeline development, analysis, and troubleshooting experience with multi-omics data including whole genome and exome, RNA-Seq, targeted sequencing, ChIP-Seq, ATAC-Seq, SNP and methylation arrays.
  • Proficiency in Unix/Linux operating systems.
  • Ability to work efficiently on multiple projects.
  • Strong working knowledge of statistics including but not limited to hypothesis testing tools, power analysis, and the ability to aid researchers in experimental design.
  • Ability to communicate scientific and informatics concepts to a wide range of audiences.
  • Ability to work independently with minimal guidance while consistently exercising good judgment.
  • Ability to work in a academic team environment.
  • Excellent interpersonal skills to interact with both research and technical staff.
  • Familiarity with repositories of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases.

PREFERRED EDUCATION EXPERIENCE & CERT/LIC

  • Experience in high performance computing and cluster environments and cloud computing is highly desirable.
  • Knowledge and biological understanding of common library preparation technologies, including those from CGI, Illumina, and LifeTechnologies
  • Ability to independently research different analysis tools and parameters within each to come up with the most appropriate tool and workflow for answering relevant biological questions (e.g.: testing multiple algorithms for sensitivity and specificity)
  • Prior experience in oncology is very desirable but not required.
  • Strong working knowledge or training in advanced biomedical research.
  • Knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture.
  • Familiarity with broadly used machine learning algorithms

ADDITIONAL TECHNICAL REQUIREMENTS

  • Accountability and attention to timelines.
  • Excellent organization and communication skills with an emphasis on strong presentation skills.
  • Ability to work in a team environment.

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6709 BIOINFORMATICS SCIENTIST II

Description:
The Bioinformatics Scientist II position is an entry level position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of bioinformatics tools and methods to bench and clinical research problems in various biomedical domains. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. Activities occur with a moderate degree of supervision with some latitude for independent judgment, development of bioinformatics workflows and processes, and presentation of results. The Bioinformatics Scientist II will begin to apply best practices in collaborative science as a bioinformatics domain expert. Academic output, while not a primary focus of this position, is also expected with a moderate degree of supervision.

JOB RESPONSIBILITIES
Pre-Analysis (20%): Contribute to the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support.

  • Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan
  • Contribute to the development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances
  • Advocate for specific collaboration requirements for continual advancement of shared pipeline and code resources
  • Provide collaboration-specific transparency for data processing and pre-analysis, including sample- and cohort-level status

Coding (20%): Code and generally support code and applications on behalf of collaborative project and/or team.
Within the context of the collaboration or project, develop and apply best practices to code development:

  • Establish requirements with the project team
  • Review existing applications and code sources (both commercial and open source) and selection of best strategy for development or adoption
  • Advocate for chosen strategy to project team by showing value of approach
  • Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations
  • Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews

Data Analysis (20%): Analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data primarily under the direction of the collaborative project team

  • Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings
  • Incorporate more advanced applications and methods into analysis
  • Develop at least one “specialty” analytical or biomedical area that serves the collaborative team

Collaboration (20%): Establish role within collaborative project team as primary bioinformatics resource

  • Contribute to and influence project-level management by serving as bioinformatics point
  • Define and promote boundaries of support by assessing all stakeholders, including bioinformatics management, collaborator expectations, and funding levels and mechanisms
  • Regularly discuss satisfaction and expectations with collaborators; continually advocate for clear understanding of role
  • Develop new collaborations with high degree of supervision

Academic Output (20%): Develop presentations, grant sections, and manuscript sections with subsequent review by peers and mentors.

  • Regularly contribute to bioinformatics-focused manuscripts and publications
  • Regularly contribute to podium presentations and posters
  • Contribute to bioinformatics sections of grant and award proposals

EDUCATION AND EXPERIENCE

  • BS/MS/PhD in biological or computational discipline.
  • 3-7 years’ experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.
  • Strong UNIX/LINUX expertise required.
  • Proficiency in R or similar commonly used bioinformatics language required.
  • Experience with management and analysis of complex data types required.
  • Proficiency in various open source and commercial bioinformatics resources and software required.
  • Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.

PREFERRED EDUCATION EXPERIENCE & CERT/LIC

  • Experience with Python, Perl, or other languages preferred.
  • Experience with pipeline or workflow development frameworks preferred.
  • Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred.
  • Knowledge of the working mechanism of microarray, NGS, mass spectrometry, or other high-throughput technologies and awareness of their strengths and weaknesses, as well as applicability to a specific biological problem is preferred.
  • Ability to correctly select and perform statistical tests for most types of genomic data, and to properly interpret their results in the scenario of a specific study is preferred.

ADDITIONAL TECHNICAL REQUIREMENTS

  • Ability to interact with biologists and clinicians during a scientific discussion is required.
  • Accountability and attention to timelines.
  • Excellent organization and communication skills with an emphasis on strong presentation skills.
  • Ability to independently plan and execute analyses of moderate complexity required.
  • Ability to provide objective validation of results required.
  • Ability to work in a team environment.

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7253 INFORMATION ANALYST II

Description:
The Department of Biomedical and Health Informatics (DBHi) at The Children’s Hospital of Philadelphia (CHOP) is seeking an Information Analyst to extract and transform data from a variety of clinical and supporting non-clinical data sources to enable research initiatives. The amount and complexity of the data will demand careful attention to details of the underlying data model and may result in large schema changes or mapping. The candidate should possess strong SQL programming skills, basic performance tuning and must be able to communicate with the research teams to efficiently translate clinical data models into interpretable information for biomedical research activities.

  • Will generally extract and transform data from a variety of clinical and supporting non-clinical data sources to enable research and quality improvement initiatives leading to research across a rapidly evolving academic research enterprise.
  • Understands data validation, loading, and structures at an intermediate level.
  • Efficiently manipulates large-scale and complex data sets using a variety of formatting and/or analysis languages such as Perl, Python, and Java.
  • The amount and complexity of the data, especially those associated with genomic experiments, will demand careful attention to details of the underlying data model and may result in large schema changes or mapping.

JOB RESPONSIBILITIES

The responsibilities of an Information Analyst II – Research/DBHi encompass identical responsibilities as the Information Analyst I – Research/DBHi, but with a greater degree of complexity. An Information Analyst II – Research/DBHi also:

  • Defines strategy for each report, given knowledge of underlying schemas, integration requirements for disparate data sources (e.g., ETL), coding solutions, and 3rd party tool availability.
  • Transforms data models of high complexity into “research-ready” data models also of high complexity by employing code, knowledge of disparate schemas and SQL varieties, and large data set manipulation techniques.
  • Creates reports and provides product to customer along with clear, concise interpretation and caveats.
  • Clearly articulates problems, issues, and potential solutions to clients.
  • Makes oral presentations to colleagues, clients, and administration when requested.
  • Appropriately manages expectations of development time, functionality of resulting modules, and short-term vs. long-term achievements.
  • Stays current with clinical reporting capabilities across the industry, including developments at clinical data systems providers, other hospital and academic research centers, and general user forums.

REQUIRED LICENSES, CERTIFICATIONS, REGISTRATIONS
EPIC - Clarity Certification (90 days)

EDUCATION AND EXPERIENCE

  • Bachelor’s Degree in computer related field or commensurate experience
  • Preferred Education: Candidates with a degree in the life sciences, but who have pursued a career in informatics is highly desirable.
  • 2-5 years of data extraction / manipulation, preferably in a healthcare environment.
    • PREFERRED EDUCATION EXPERIENCE & CERT/LIC

      • 3+ years of programming and database experience with progressively more complex projects in a full-time, salaried industry or equivalent academic position.
      • Experience in healthcare and/or biomedical data management issues.
      • Experience in building databases in REDCap.

      ADDITIONAL TECHNICAL REQUIREMENTS

      • Must be able to efficiently translate clinical data modeled within a complex schema into interpretable information for biomedical research activities.
      • Situational awareness concerning data interpretation, quality, and integrity is essential.
      • Must exhibit good oral and written communication skills.
      • Working knowledge of SQL and one or more of the following: Perl, Python, Java, PostgreSQL, R and API programming.
      • Working knowledge of relational database application development, including stored procedures, SQL, data definition language, basic performance tuning and query optimization, and ETL techniques.

      INFORMATION SECURITY REQUIREMENTS

      • Understand and comply with all enterprise and IS departmental information security policies, procedures and standards.
      • Support the integration of information security in the development, design, and implementation of Hospital Technology Resources that process, transmit, or store CHOP information.
      • Support all compliance activities related to state, federal regulatory requirements, healthcare accreditation standards, and all other applicable regulations that govern the use and disclosure of patient, financial, or other confidential information.

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      MANDATORY REQUIREMENTS

      • Child Abuse Clearances
      • FBI Fingerprint Clearance
      • Drug Screening
      • Tobacco screening

      All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.

      The Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.