Increased support for computationalbiology, mapping and analysis of complex traits, and comprehensive phenotyping are key elements of theLaboratory's five-year strategic plan for research, completed and approved in November 2004. The plan alsoplaces a major focus on using a multi-disciplinary approach that integrates in silico and in vivo methodologiesto study mammalian biology and disease at the systems level. The space, infrastructure, and other functionsrequired for the planned growth of Jackson's research program are synonymous with those needed forsuccessful operation of the CGD.Center Advisory Board The Center Advisory Board, drawn from experts outside the proposed Center, will review the Center'sprogress and activities annually at a two-day meeting at The Jackson Laboratory. Minutes from thesemeetings will be included in each progress report to NIGMS. The four to six members will be chosen on thebasis of their expertise and stature in the international scientific community. Because the use of amultidisciplinary in silico - in vivo approach to study biology at the systems level is the emerging focus overallat Jackson as well as the focus of the proposed Center, we will choose members who broadly reflect the areasof our systems biology research. These will include experts in the use of computational approaches to studybiological and genetic mechanisms; in genome organization and evolution; and in complex trait analysis andmapping. Drs. Churchill, Woychik, and Kenneth Paigen will attend each Board meeting. The Board will select pilot projects for funding (see Research Development and Training Core) afterreviewing all applications. Pilot project recipients from the previous year will submit written reports before theannual Advisory Board meeting and will meet with the Advisors during their visit. Progress toward significantpublications and submission of NIGMS grants or other grants related to systems biology or genome structurewill be monitored, and the award and review process adjusted if needed to increase success of the program.The Board will recommend candidates for recruitment to The Jackson Laboratory and the CGD, particularlythose promising young investigators in systems biology research who would mesh well with existing ScientificStaff and benefit from the genetic and phenotyping resources offered by the CGD. The Advisors will alsomake these recommendations to Dr. Woychik and will review the progress of current CGD Investigators. Inparticular, the board will be responsible for reviewing the progress of Ms. Svenson (Project 4 co-Leader) andmaking recommendations regarding her advancement to Project Leader. Each project and core supported by the Center will be reviewed annually by the Board. Review willinclude written evaluation. The Board will look at usage statistics, overall management of the cores and qualityof work, fee structures and costs, and overall value to CGD members. The Board will recommend newmethodologies to be included in the relevant cores. From other Advisory Board meetings at Jackson, we havefound that both the Advisors and the core support personnel enjoy and benefit from direct interactions, eitherthrough tours of the relevant facilities, or poster sessions in which core personnel describe their work. Theseposter sessions are lively events held in a central location that are also effective in drawing Jackson ScientificStaff members' interest to new capabilities within the core services.Each annual Advisory Board meeting will feature a presentation by one Advisor to the entire JacksonLaboratory research and resource community, followed by a reception. Through this rotating series of209Churchill, Gary A.presentations and social interactions, the entire Jackson faculty will become engaged with the researchperspectives in systems biology represented on the Board.Research Coordination A full-time Ph.D.-level Project Manager, to be hired, will work with Dr. Churchill and the core leaders todevelop and implement procedures and policies that enable efficient coordination among core activities andensure that the cores meet the research needs of the six Center projects. The Project Manager will providethis function for all core components with the exception of the pilot projects (see Research Training andDevelopment Core), which will be under the direct supervision of the Center PI, Dr. Churchill. Regularmeetings of core users will provide another mechanism to ensure research coordination among cores.Investigators using the Animal or Molecular Biology cores will meet at least monthly to coordinate collection ofbiological and DNA samples and review progress of phenotyping screens, genotyping, gene expressionexperiments, and mapping projects. Investigators using the Computation Core will meet at least monthly tocoordinate use of the Core services and resources.Core Management Center members will have access to all of The Jackson Laboratory's central Scientific Services, whichare described in the Resources and Environment (R&E) section. The Molecular Biology and ComputationCores proposed for our Center are elements of these Scientific Services. Ms. Valerie Scott, Senior Director ofScientific Services, is responsible for their overall management. She reports to Mr. Chuck Hewett, ChiefOperating Officer of the Laboratory, and is advised by the Director of the Laboratory, the Director of Research& Discovery, and the Scientific Advisory Committee, which comprises six Scientific Staff members. A technicalexpert acts as the Service Manager in each Scientific Service; they are responsible for day-to-day operationsmanagement including Service staff supervision, developing and managing budgets, and bringing newtechnologies into the Service. The Scientific Services are supported (in relatively even proportions) byinstitutional funds, user fees, and several external funding sources, including the Cancer Center Support Grant,National Heart, Lung and Blood Institute, and the National Center for Research Resources. A major goal ofthe Core facilities is to provide access to quality services at reasonable prices. Toward that end, The JacksonLaboratory commits institutional funds to ongoing operator training, equipment maintenance, and servicecontracts for major instrumentation without passing that cost on to users. Fees are reviewed by the ScientificAdvisory Committee, Services Faculty Advisors, and the Chief Financial Officer before being implemented atthe start of the fiscal year in June.Research Administration The Jackson Laboratory has an efficient research administrative structure that will support the CGD infiscal management and compliance matters. The Office of Sponsored Programs is a centralized administrativedepartment that provides assistance in obtaining sponsored research funds, managing sponsored researchactivity, and offering administrative support services. The Grants Office coordinates the grant applicationprocess and provides administrative oversight of federally mandated internal compliance committees.Sponsored Research Programs prepares and tracks all application and award budgets; reviews andapproves all re-budgeting requests according to sponsor requirements; and negotiates and tracks allsubcontract and consortium agreements with collaborating institutions. Research Administrative SupportServices provides administrative and secretarial support to the Scientific Staff and associated researchassociates/scientists, laboratory personnel, and postdoctoral fellows. It is also responsible for coordination andadministration of the seminar speaker and visiting investigator programs. Ms. Louise Lopez will provide thissupport for Dr. Churchill for administering the CGD. The Scientific Program Development group assistsnewinvestigators in obtaining competitive research funding and identifies relevant federal and private sources offunds. They advise scientific staff members on grantsmanship strategies as needed. Grant proposals andmanuscripts are edited upon request, with emphasis on new Scientific Staff and those investigators for whomEnglish is a second language.210Churchill, Gary A.Core 2- Research Development andTraining Core Dr. Richard P. Woychik, Core Leader211
| Wang, Jeremy R; Holt, James; McMillan, Leonard et al. (2018) FMLRC: Hybrid long read error correction using an FM-index. BMC Bioinformatics 19:50 |
| Ju, Chelsea J-T; Zhao, Zhuangtian; Wang, Wei (2017) Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates. IEEE/ACM Trans Comput Biol Bioinform 14:522-533 |
| Simecek, Petr; Forejt, Jiri; Williams, Robert W et al. (2017) High-Resolution Maps of Mouse Reference Populations. G3 (Bethesda) 7:3427-3434 |
| Tyler, Anna L; Ji, Bo; Gatti, Daniel M et al. (2017) Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice. Genetics 206:621-639 |
| Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L et al. (2017) Structural Variation Shapes the Landscape of Recombination in Mouse. Genetics 206:603-619 |
| Parvanov, Emil D; Tian, Hui; Billings, Timothy et al. (2017) PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis. Mol Biol Cell 28:488-499 |
| Morgan, Andrew P; Didion, John P; Doran, Anthony G et al. (2016) Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers. G3 (Bethesda) 6:4211-4216 |
| Chesler, Elissa J; Gatti, Daniel M; Morgan, Andrew P et al. (2016) Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection. G3 (Bethesda) 6:3893-3902 |
| Gu, Tongjun; Gatti, Daniel M; Srivastava, Anuj et al. (2016) Genetic Architectures of Quantitative Variation in RNA Editing Pathways. Genetics 202:787-98 |
| Korstanje, Ron; Deutsch, Konstantin; Bolanos-Palmieri, Patricia et al. (2016) Loss of Kynurenine 3-Mono-oxygenase Causes Proteinuria. J Am Soc Nephrol 27:3271-3277 |
Showing the most recent 10 out of 128 publications
