Timothy Tickle Email & Phone Number

Cambridge, Massachusetts, United States

• Build partnerships focusing on accelerating science through software engineering at the Data Sciences Platform.• Educate partners about the solutions and capabilities of the Data Sciences Platform through demonstrations and presentations.• Define solutions with corporate and government funding partners to serve scientific initiatives.• Represent the scientific community when evaluating market needs and program direction.• Identify funding leads and evaluate those leads in the context of our current project portfolio.• Author letters of interest, proposals and funding applications.• Coordinate with stakeholders and internal teams to define a statement of work as projects are funded and yearly thereafter to guide execution.• As a Principal Investigator, Investigator, or lead on funded initiatives, maintain oversight during the life of funded projects.• Review team work and demos to assure milestones are met as defined in the statement of work.• Risk manage milestones and delivery of work with stakeholders and internal teams.

Cambridge, Massachussets

Cambridge, Massachusetts

Act as a point of contact for internal and external communities, focused on growing expertise, infrastructure, products, and funding associated with single-cell genomics.• Act as the Broad site manager for the team developing the infrastructure and pipelines used in the Human Cell Atlas’ Data Coordination platform (HCA DCP).• Contribute to the development of HCA DCP design, standards, use cases, and SLAs.• Grow the HCA single-cell genomics analysis community by holding regular community outreach meetings, participating in holding annual analysis Jamborees, and coordinating the analysis working group governance with the HCA DCP.• Define and prioritize the development of functionality for the Single Cell Portal using an Agile, user-facing environment.• Approve Single Cell Portal releases through team demoes and user feedback.• Nurture the awareness and use of horizontally scalable analytics in the Regev Lab and the Klarman Cell Observatory.• Nucleate projects and interest groups to grow single-cell genomics expertise and technologies.• Participate and coordinate applications for funding development of methodology and software for single-cell genomics.

Cambridge, Massachusetts

Responsible for supporting a diverse and dynamic portfolio of data science and software engineering projects as needs require in the Aviv Regev Lab and the Klarman Cell Observatory.• Designed and steered the development of the Single Cell Portal, as well as, developing software for sequence and statistical analysis of single-cell RNA-Seq.• Developed computational methods and NGS pipelines for the downstream analysis of RNA-Seq (de novo and reference-based) clinical cancer studies including variant calling, fusion detection, lincRNA, and microbial community identification.• Translated internally developed code to software pipelines used internally or by the larger scientific community. This includes bringing methodology onto cloud-base frameworks for scalable analysis.• Consulted with Indiana University's super computing center on integrating and troubleshooting developed RNA-Seq pipelines.• Created interactive client side visualizations for exploring results of key pipelines.• Created and presented multiple workshops focused on single-cell RNA-Seq analysis and the programming language R.• Supported internal and external clients on all developed pipelines.• Created and maintained the scientific workflow framework for the development of pipelines.• Acted as a member of a team responsible for developing efficient lab practices around data storage. This includes creating software automating solutions as needed.• Member of the BroadE workshop planning committee and the Broad SoftEng Steering Committee.

Cambridge, Massachusetts

Consult on and lead microbial biomarker studies surrounding inflammatory bowel disease and type 1 diabetes.

Department Of Biostatistics, School Of Public Health

Responsible for the development and validation of methodology and infrastructure for translating metagenomics studies to human diseases.•Assist in and lead clinical study analysis in microbial biomarker associations with genetic, environmental, and host phenotypes.•Responsible for adhering to software development practices including versioning, regression/unit testing, lab coding standards, code reviews, supporting users, maintaining a web presence, and providing source code and Galaxy interfaces for public use.•Provide documentation, establish a web presence, and support software users.•Write scientific reports and create custom visualizations.•Mentor students, lab members, and visiting scientists on analysis and tool use.

Was responsible for all work associated with the ovarian exon tumor transcriptome study. Solely performed all wet-lab protocols and dry-lab analysis (excluding chip hybridizations performed at an off-site core facility).•Developed and performed wet lab protocols including: sample preparation and storage; tissue staining; pathology evaluation; cryosectioning; laser capture microdissection; immunohistochemistry; RNA extraction, and isolation; and cDNA generation, amplification, and preparation for Affymetrix GeneChip Human Exon 1.0 ST Arrays.•Managed ordering and storage of all associated reagents.•Participated in training other team members and interns in various wet lab protocols.•Formulated analysis and quality control protocols for exon data.•Developed software and database solutions to perform exon analysis.

Acted as the instructor of record; mentoring faculty Cynthia Gibas, PhD. Was solely responsible for designing and teaching the department's first undergraduate introductory bioinformatics class. Specific responsibilities included: •Selecting the subject matter and deriving a calendar and syllabus. •Designing and delivering all lectures, labs, and associated presentations. •Developing assessment activities including testing, review sessions, and homework. •Grading all labs, testing, and homework. •Guiding students on culminating projects. •Holding biweekly office hours and managing specific needs of students as they arose. •Evaluations available upon request.

ITCS 3050 (Intro to Bioinformatics), ITCS 6160 (Programming for Biologists), ITCS 2181(Computer Logic & Design), ITCS 3183 (Hardware Systems Design), ITCS 3181/5141(Computer Organization & Architecture) and ITCS 3650/3651 (Senior Projects). •Assisted professor in creating course content and developing course topics. •Taught classes on programming and how to use class related software. •Assisted students during lab sessions. •Held office hours to assist students with projects. •Tutored students weekly. •Assisted in writing and grading exams.

Co-taught the “Update on Microcomputer and Internet Technology” professional development course. • Created a complete day of instructional presentations spanning seven hours of content. • Assisted in setup, presenting the instructional sessions, and ran the lab. • Created class surveys, questionnaires, and handouts.

Acted as a Research Intern for Carolinas Medical Centers Blumenthal Cancer Research Center in collaboration between the University of North Carolina at Charlotte and Carolinas Medical Center. • Assisted the installation, use, and upkeep of bioinformatics software. • Gave presentations on bioinformatics algorithms and techniques useful for studies at the Molecular Biology Core Facility. • Performed analysis on microarray and other data for projects and publications. • Assisted in writing grants and publications.

Acted as and was given the full responsibility of a Netcentric Developer. • Developed netcentric services (web applications) from design documents. • Participated in code reviews, presentations, unit testing, performance testing, and troubleshooting. • Lead a focus group on the creation and maintenance of automated regression suites. • Was solely responsible for migrating the teams emailing web services to a new in-house web service. • Coordinated and tested associated web service environment settings with database administrators.

Act as first contact in assisting staff and faculty in resolving issues with computer use. Issues involved, but were not limited to, troubleshooting of applications, networking, and computing services; notifying administrators of server and network issues; and consulting users with computer use.

Postdoctoral Fellowship, Metagenomics

Responsible for the development and validation of methodology and infrastructure for translating metagenomics studies to human diseases..

Ph.D., Bioinformatics And Computational Biology

Dissertation: “Data Mining the Serous Ovarian Tumor Transcriptome”. Topic included: Ovarian tumor genetics, biomarker discovery.

Bs, Computer Science

Graduated Cum Laude. Research Project: Bioinformatics software development for ovarian tumor microarray analysis

Ba, History

Activities and Societies: Published 3 times in Wake Forest's literary journal "3 to 4 ounces".Graduated Cum Laude.