Bioinformatics Core Lab Manager

Department/Unit:
Molecular & Cellular Physiology

Work Shift:
Day (United States of America)

Salary Range:
$77,075.00 - $119,466.00

Perform rigorous, reproducible analysis of bulk and single-cell genomic datasets, working directly with research teams to translate biological questions into appropriate computational analyses and publication- and grant-ready results and furthering Albany Medical College shared core facility research operations for bioinformatics core, including conducting laboratory tests, and experiments. Independently manage daily core facility operations a while consulting frequently with Core Director and core facility users regarding service delivery, technical capabilities, infrastructure needs, and utilization. This position is appointed to a single core facility but is structured to be applicable across multiple core types (e.g., imaging, flow cytometry, bioinformatics). Ability to move beyond the generation of standard bioinformatics outputs and interpret genomic results in the context of the underlying biological question. Manage multiple concurrent bioinformatics projects, prioritize analyses according to project timelines, communicate project status clearly, and maintain appropriate documentation of completed analyses.

Core Facility Operations and Management

- Design, support, and troubleshoot core-based computational and analyticalworkflows and methodologies in support of core facility users; assist users in obtaining high-quality data for publication and grant submissions; compile, analyze, document core-generated data, usage metrics, quality control records, and performance indicators, as appropriate.

- Prepare and/or assist investigators with  methods descriptions related to coresoftware, dataplatforms, computational analyses, or analytical workflows for inclusion in manuscripts and grants.

- Review software documentation, methods manuals, vendor documentation, and scientific literature for information on developing, optimizing, and troubleshooting of core technologies, workflows, analytical methods, and SOPs (Standard Operating Procedure) documents.

- Confer regularly with the Core Director and core facility users to review service needs, technical capabilities, and future directions of the core. Assist in designing core services and protocols and modify existing procedures to meet user and institutional needs as required.

- Design and troubleshoot routine and complex technical workflows, analyses, software,, or instrumentation-related issues to support diverse research applications within the core.

- Maintain and advance technical expertise through hands-on experience, professional workshops, and specialized training, including bioinformatics, genomics, biostatistics, programming, data analiysis, or modality-specific courses as relevant to the core.

- Supervise the work of core facility staff and trainees, as applicable. Participate in hiring, onboarding, and training new personnel. Provide input and recommendations regarding personnel and user performance to the Core Director or departmental leadership as needed.

- Train, certify, and support investigators, staff, and trainees in the safe and effective use of core instrumentation software, data platforms, and computational resources, including follow-up with newly trained users to ensure proper usage.

- Monitor the satisfactory operation of shared core software, data platforms, computing systems, and other technical resources. Supervise daily use of core resources by assisting users, enforcing operating procedures, and ensuring work areas are cleaned, sanitized, and maintained according to institutional standards. Troubleshoot routine and complex software, workflow, or system-related problems, and coordinate technical support as needed.

- Schedule software maintenance, system updates targeted technical support and service visits or consultations with vendor and information technology staff.

- Coordinate the use of shared software, data platforms, computing resources and core services across departments and research groups.

- Maintain and manage online scheduling and project-management systems, track  core services and computational resource usage, , and report violations of operating procedures to the Core Director or advisory committees, as applicable.

- Ensure availability of resources necessary for core operations(e.g.,software licenses, data storage, computing capacity, secure data-transfer solutions, and other technical resources).

- Be familiar with regulatory requirements as applicable to the core facility operations and ensure users comply with those standards.

- Oversee core facility compliance and ensure adherence to applicable local, state, federal and institutional requirements related to data security, confidentiality, privacy, information technology, and the appropriate use of storage of research data.

- Coordinate with AMC Information Services, Information Security, Facilities, Environmental Health & Safety, Facilities, and other institutional departments to resolve any core related concerns or incidents and assist in setting up, relocating expanding, or decommissioning of core spaces and technology resources.

- Serve as a liaison between the AMC Purchasing Department and department administration to troubleshoot procurement, service contract, software licensing, data storage, computing resource and supply chain issues impacting core operations.

- Perform other duties related to the work described herein.

Bioinformatics Core Responsibilities

- Perform end-to-end bulk RNA-seq analysis, including quality control, alignment or quantification, differential expression, pathway enrichment, visualization, and biological interpretation.

- Analyze single-cell RNA-seq and spatial datasets, including quality control, normalization, integration, dimensionality reduction, clustering, cell-type annotation, differential expression, compositional analysis, and pathway-level interpretation.

- Perform ATAC-seq, CUT&Tag, and CUT&RUN analyses, including peak calling, differential accessibility or binding, genomic annotation, motif analysis, and integration with transcriptional datasets.

- Integrate datasets across experimental conditions, tissues, time points, species, and genomic modalities to identify biologically meaningful pathways, cell states, and regulatory mechanisms.

- Generate publication-quality figures, including UMAPs, heatmaps, dot plots, volcano plots, enrichment plots, genome-track visualizations, and integrated multiomic figures.

- Develop and maintain reproducible R, Python, and Linux analysis workflows and standardized core pipelines.

- Participate in meetings with investigators to present results and explain computational findings to researchers with different levels of bioinformatics experience.

- Contribute bioinformatics methods, figures, preliminary analyses, and technical language for manuscripts, abstracts, presentations, and grant applications.

- Evaluate and assist with the implementation of new computational methods and genomic technologies as the Bioinformatics Core expands.

Qualifications

- A bachelor’s degree in biology, biochemistry, molecular biology, biomedical engineering or a related scientific field is required.
- Master's degree or PhD in bioinformatics, computational biology, genomics, biostatistics, molecular biology, or a related discipline preferred.
- Requires three (3) or more years of increasingly responsible experience in a laboratory or core facility operations.
- Five (5) or more years of increasingly responsible experience conducting in a research laboratory or shared research core environment laboratory research including operational or technical leadership with managerial experience is also preferred.
- Experience supporting shared instrumentation, multi-user environments, or core facility operations - preferred
- Modality-specific expertise (e.g., fluorescence microscopy, live-cell imaging, flow cytometry, computational analysis)
- Reads and interprets documents such as safety rules and procedures manuals.
- Uses effective written and verbal communication skills to work cooperatively with customers and employees.
- Listens well, takes direction and engages in interactive dialogues with others.
- Seeks the input of others to achieve consensus.
- Comprehends, remembers and carries out instructions. The individual communications any questions to a Supervisor as the need arises.
- Thoroughly, accurately and legibly documents test results and quality control.
- Communicates effectively with staff, and other departments.
- Effectively communicates implications and/or applications experiments.
- Add, subtract, multiply and divide in all units of measure, using whole numbers, common fractions, and decimals.
- Do statistical analysis, prepare graphical displays and perform calculations to prepare conclusions.

Equivalent combination of relevant education and experience may be substituted as appropriate.

Physical Demands

- Standing - Constantly
- Walking - Constantly
- Sitting - Rarely
- Lifting - Frequently
- Carrying - Frequently
- Pushing - Occasionally
- Pulling - Occasionally
- Climbing - Occasionally
- Balancing - Occasionally
- Stooping - Frequently
- Kneeling - Frequently
- Crouching - Frequently
- Crawling - Occasionally
- Reaching - Frequently
- Handling - Frequently
- Grasping - Frequently
- Feeling - Constantly
- Talking - Constantly
- Hearing - Constantly
- Repetitive Motions - Constantly
- Eye/Hand/Foot Coordination - Constantly

Working Conditions

- Extreme cold - Rarely
- Extreme heat - Rarely
- Humidity - Rarely
- Wet - Rarely
- Noise - Constantly
- Hazards - Frequently
- Temperature Change - Rarely
- Atmospheric Conditions - Rarely
- Vibration - Rarely

Thank you for your interest in Albany Med Health System!​

Albany Med Health System is an equal opportunity employer.

This role may require access to information considered sensitive to Albany Med Health System, its patients, affiliates, and partners, including but not limited to HIPAA Protected Health Information and other information regulated by Federal and New York State statutes. Workforce members are expected to ensure that:

Access to information is based on a “need to know” and is the minimum necessary to properly perform assigned duties. Use or disclosure shall not exceed the minimum amount of information needed to accomplish an intended purpose. Reasonable efforts, consistent with Albany Med Health System policies and standards, shall be made to ensure that information is adequately protected from unauthorized access and modification.