Every day, we collaborate at the forefront of fundamental and translational science in pursuit of groundbreaking treatment strategies for cancer, Parkinson’s and other diseases. Through shared values and an entrepreneurial spirit, we spark innovation to multiply the impact of discovery and answer critical questions about our world.
As a reflection of this commitment, we are pleased to join the Coalition for Next Generation Life Sciences, a collaborative effort to enhance transparency by publishing outcomes data for graduate students and postdoctoral fellows. Metrics include:
- Admissions and matriculation data of Ph.D. students
- Median time-to-degree and completion data for Ph.D. programs
- Demographics of Ph.D. students and postdoctoral scholars by gender, underrepresented minority status and citizenship status
- Median time in postdoctoral status at the institution
- Career outcomes for Ph.D. and postdoctoral alumni, classified by job sector and career type using a common taxonomy Source: Coalition for Next Generation Life Sciences
Learn more about the Coalition by visiting nglscoalition.org.
For questions about VAI graduate student data, please contact Christy Mayo at [email protected]. For questions about VAI postdoctoral fellow data, please contact Dr. Erica Gobrogge at [email protected].
Graduate Student Statistics
Current Graduate Students
Numbers current as of Sept. 1, 2024
By Gender
Data represents current student population
Total students: 59
Self-Identified Underrepresented Populations in Science-based on NIH Definition
Data does not include international students
Total students: 37
Citizenship
Data represents current student population
Total students: 59
Admissions
Fall 2024 Cohort
Applicant Pool
Time to Degree(TTD)
By Year of Graduation (in Three Year Aggregates)
By Demographic Categories
Retention, Attrition & Complete Outcomes
Outcomes in Multi-Year Aggregates of Entering Cohorts
Please hover over the chart to see the data.
Aggregate Outcomes by Gender*
Please hover over the chart to see the data.
*Through 2017 entering cohort, as of August 2024
Ph.D. Career Outcomes by Career Type*
Please hover over the chart to see the data.
*Through 2017 entering cohort, as of August 2024
Ph.D. Career Outcomes by Job Sector*
Please hover over the chart to see the data.
*Through 2017 entering cohort, as of August 2024
Postdoctoral Fellow Statistics
Please hover over each chart to see data.
Van Andel Institute Definition of a Postdoctoral Fellow/Fellowship
The fellowship is a limited time after receipt of a doctoral degree for mentored and advanced training through research under the supervision of a principal investigator (mentor). The postdoctoral fellow, in mutual agreement with their mentor, undertakes an individual research project and service, teaching and professional development activities that together will provide the experience and knowledge essential for career advancement and establishing an independent career.
By Gender
As of Jan. 1 of each year.
Citizenship Status
As of Jan. 1 of each year.
Race/Ethnicity for USC/PR
As of Jan. 1 of each year. Data does not include international postdocs.
Time as a Postdoctoral Fellow
Median Time in Postdoc Training by Gender
Median Time in Postdoc Training by Nationality
Postdoctoral Fellows’ Career Outcomes Based on Last Known Position
Sector
Includes all VAI posdocs (n=221) who have completed training as of Feb. 28, 2024 (UCOT v2017).
Career Type
Includes all VAI posdocs (n=221) who have completed training as of Feb. 28, 2024 (UCOT v2017).
Job Function
Includes all VAI posdocs (n=221) who have completed training as of Feb. 28, 2024 (UCOT v2017).
Van Andel Institute Graduate School graduates have moved on to successful careers in academia and industry, including:
- Calvin College
- Duke University
- Johns Hopkins University
- Liberty University
- Mayo Clinic
- Mercy Health Saint Mary’s
- Michigan State University
- Michigan State University College of Human Medicine
- Morgridge Institute for Research
- Motive Medical Intelligence
- NorthStar Michigan Cooperative
- NxGen MDX
- Personal Genome Diagnostics (PGDx)
- The State University of New Jersey
- University of Central Florida
- University of Colorado Boulder
- University of Illinois-Chicago
- University of Michigan
- University of North Carolina
- University of Wisconsin-Madison
- Wake Forest School of Medicine
- Zoetis
On average, Van Andel Institute Graduate School students’ time to degree is 5.3 years.
| Cohort | Retention | Persistence | Ph.D. Graduation | M.S. Graduates | Withdrew | Retained | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Year | N | N | % | N | % | N | % | N | N | N |
| 2007 | 3 | 3 | 100% | 2 | 67% | 2 | 67% | 0 | 1 | 0 |
| 2008 | 3 | 2 | 67% | 2 | 67% | 1 | 33% | 1 | 1 | 0 |
| 2009 | 3 | 3 | 100% | 3 | 100% | 2 | 67% | 1 | 0 | 0 |
| 2010 | 4 | 4 | 100% | 3 | 75% | 3 | 75% | 0 | 1 | 0 |
| 2011 | 5 | 5 | 100% | 3 | 60% | 3 | 60% | 0 | 2 | 0 |
| 2012 | 5 | 5 | 100% | 4 | 80% | 4 | 80% | 0 | 1 | 0 |
| 2013 | 5 | 4 | 80% | 4 | 80% | 4 | 80% | 0 | 1 | 0 |
| 2014 | 5 | 4 | 80% | 4 | 80% | 4 | 80% | 0 | 1 | 0 |
| 2015 | 4 | 4 | 100% | 4 | 100% | 3 | 75% | 1 | 0 | 0 |
| 2016 | 6 | 6 | 100% | 5 | 83% | 4 | 67% | 1 | 1 | 0 |
| 2017 | 7 | 7 | 100% | 7 | 100% | 7 | 100% | 0 | 0 | 0 |
| 2018 | 6 | 6 | 100% | 6 | 100% | 2 | 33% | 0 | 0 | 4 |
| 2019 | 10 | 10 | 100% | 9 | 100% | 1 | 10% | 0 | 1 | 8 |
| 2020 | 7 | 7 | 100% | 7 | 100% | 0 | 0 | 0 | 7 | |
| 2021 | 13 | 13 | 100% | 12 | 92% | 0 | 0 | 1 | 12 | |
| 2022 | 9 | 9 | 100% | 9 | 100% | 0 | 0 | 0 | 9 | |
| cum | 95 | 92 | 97% | 84 | 88% | 40 | 4 | 11 | 40 | |
Peer-reviewed publications
Below is a list of publications students have published while enrolled in the Van Andel Institute Graduate School.
2024
Massari CM, Dues DJ, Bergsma A, Sipple K, Frye M, Williams ET, Moore DJ. 2024. Neuropathology in an α-synuclein preformed fibril mouse model occurs independent of the Parkinson’s disease-linked lysosomal ATP13A2 protein. Neurobiol Dis 202:106701.
Sokol KH, Lee CJ, Rogers TJ, Waldhart A, Ellis AE, Madireddy S, Daniels SR, House RJ, Ye X, Olsenavich M, Johnson A, Furness BR, Sheldon RD, Lien EC. 2024. Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking. Cell Chem Biol.
Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib W, Heo L, Laird PW, Berman B, Triche Jr TJ, Shen H. 2024. BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nuc Acids Res 52(6):e32.
Booms A, Pierce SE, van der Schans EJC, Coetzee GA. 2024. Parkinson’s disease risk enhancers in microglia. iScience 27(2):108921.
Lubben N, Byrnildsen JK, Webb CM, Li HL, Leyns CEG, Changolkar L, Zhang B, Meymand ES, O’Reilly M, Madaj Z, DeWeerd D, Fell MJ, Lee VYM, Bassett DS, Henderson MX. 2024. LRRK2 kinase inhibition reverses G2019s mutation-dependent effects on tau pathology progression. Transl Neurodegener 13(1):13.
House RJ, Eapen JP, Shen H, Graveel C, Steensma MR. 2024. Ceas: An R package for Seahorse data analysis and visualization. Bioinformatics, btae503.
Guak H, Weiland M, Vander Ark A, Zhai L, Lau K, Corrado M, Davidson P, Asiedu E, Mabvakure B, Compton S, DeCamp L, Scullion CA, Jones RG, Nowinski S, Krawczyk C. 2024. Transcriptional programming mediated by the histone demethylase KDM5C regulate dendritic cell population heterogeneity and function. Cell Rep 43(8):114506.
House RJ*, Soper-Hopper MT*, Vincent MP, Ellis AE, Capan CD, Madaj ZB, Wolfrum E, Isaguirre CN, Castello CD, Johnson AB, Escobar Galvis ML, Williams KS, Lee H, Sheldon RD. 2024. A diverse proteome is present and enzymatically active in metabolite extracts. Nat Comm 15:5796.
*Co-first authors
Ma EH, Dahabieh MS, DeCamp LM, Kaymak I, Kitchen-Goosen SM, Oswald BM, Longo J, Roy DG, Verway MJ, Johnson RM, Samborska B, Duimstra LR, Scullion LR, Steadman M, Vos M, Roddy TP, Krawczyk CM, Williams KS, Sheldon RD, Jones RG. 2024. 13C metabolite tracing reveals glutamine and acetate as critical in vivo fuels for CD8 T. Sci Adv 10(22).
Arumugam M, Tovar EA, Essenburg CJ, Dischinger PS, Beddows I, Wolfrum E, Madaj ZB, Turner L, Feenstra K, Gallik KL, Cohen L, Nichols M, Sheridan RTC, Esquibel CR, Mouneimne G, Graveel CR, Steensma MR. 2024. Nf1 deficiency modulates stromal environment in the pretumorigenic rat mammary gland. Front Cell Dev Biol 12.
Cooper JF, Nguyen K, Gates D, Wolfrum E, Capan C, Lee H, Williams D, Okoye C, Wojtovich AP, Burton NO. Preprint. Oocyte mitochondria link maternal environment to offspring phenotype. Res Sq.
Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib W, Heo L, Laird PW, Berman B, Triche T, Shen H. 2024. BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nuc Acids Res 52(6):e32.
Nguyen N, Carpenter KA, Ensing J, Gilliland C, Rudisel EJ, Mu EM, Thurlow KE, Triche Jr. TJ, Grainger S. 2024. EGFR-dependent endocytosis of Wnt9a and Fzd9b promotes β-catenin signaling during hematopoietic stem cell development in zebrafish. Sci Sig 17(832).
Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. 2024. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. Sci Adv 10(13).
Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. 2024. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 15:2642.
Grit JL, Turner L, Essenburg CJ, Gallik KL, Dischinger PS, Shurlow ND, Pate MJ, Graveel CR, Steensma MR. 2024. Ex-vivo patient-derived explant model for neurofibromatosis type 1-related cutaneous neurofibromas. J Invest Dermatol 21:S0022-202X(24)00117-9.
Abla O, Ries RE, Triche Jr TJ, Gerbing RB, Hirsch B, Raimondi S, Cooper TM, Farrar JE, Buteyn N, Harmon LM, Wen H, Deshpande AJ, Kolb EA, Gamis AS, Aplenc R, Alonzo T, Meshinchi S. 2024. Structural variants involving MLLT10 fusion are associated with adverse outcomes in pediatric acute myeloid leukemia. Blood Adv.
House RJ, Tovar EA, Redlon LN, Essenburg CJ, Dischinger PS, Ellis AE, Beddows I, Sheldon RD, Lien EC, Graveel CR, Steensma MR. 2024. NF1 deficiency drives metabolic reprogramming in ER+ breast cancer. Mol Metab 80:101876.
Beddows I, Fan H, Heinze K, Johnson BK, Leonova A, Senz J, Djirackor S, Cho KR, Pearce CL, Huntsman DG, Angelesio MS, Shen H. 2024. Cell state of origin impacts development of distinct endometriosis-related ovarian carcinoma histotypes. Can Res 84(1):26–38.
2023
Dues DJ, Ma Y, Nguyen APT, Offerman AV, Beddows I, Moore DJ. 2023. Formation of templated inclusions in a forebrain a-synuclein mouse model is independent of LRRK2. Neurobiol Dis 188:106338.
George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf, Y. 2023. Epigenomic reprogramming in iAs-mediated carcinogenesis. Adv Pharmacol 96:319–365.
Wedan RJ, Longenecker JZ, Nowinski SM. 2023. Mitochondrial fatty acid synthesis is an emergent central regulator of mammalian oxidative metabolism. Cell Metab 26(1):36–47.
Dues DJ, Tran Nguyen AP, Becker K, Ma J, Moore DJ. 2023. Hippocampal subfield vulnerability to α-synuclein pathology precedes neurodegeneration and cognitive dysfunction. npj Parkinsons Dis 9(125).
Diegel CR, Kramer I, Moes C, Foxa GE, McDonald MJ, Madaj ZB, Guth S, Liu J, Harris JL, Kneissel M, Williams BO. 2023. Inhibiting WNT secretion reduces high bone mass caused by Sost loss-of-function or gain-of-function in Lrp5. Bone Res 11(1):47.
Chen L, Daniels S, Dvorak R, Chu H-Y. 2023. Reduced thalamic excitation to motor cortical pyramidal tract neurons in parkinsonism. Sci Adv 9(34).
Luda KM, Longo J, Kitchen-Goosen SM, Duimstra LR, Ma EH, Watson MJ, Oswald BM, Fu Z, Madaj Z, Kupai A, Dickson BM, DeCamp LM, Dahabieh MS, Compton SE, Teis R, Kaymak I, Lau KH, Kelly DP, Puchalska P, Williams KS, Krawczyk CM, Lévesque D, Boisvert FM, Sheldon RD, Rothbart SB, Crawford PA, Jones RG. 2023. Ketolysis drives CD8+ T cell effector function through effects on histone acetylation. Immunity.
Floramo JS, Molchanov V, Liu H, Liu Y, Craig SEL, Yang T. 2023. An integrated view of stressors as causative agents in OA pathogenesis. Biomolecules 13(5):721.
Compton SE, Kitchen-Goosen SM, DeCamp LM, Lau KH, Mabvakure, Vos M, Williams KS, Wong KK, Shi X, Rothbart SB, Krawczyk CK, Jones RG. 2023. LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation. Mol Cell.
Compton SE, Kitchen-Goosen SM, DeCamp LM, Lau KH, Mabvakure, Vos M, Williams KS, Wong KK, Shi X, Rothbart SB, Krawczyk CK, Jones RG. 2023. LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation. Mol Cell.
Peelaerts W, Mercado G, George S, Villumsen M, Kasen A, Aguileta, Linstow C, Sutter AB, Kuhn E, Stetzik L, Sheridan R, Bergkvist L, Meyerdirk L, Lindqvist A, Escobar Galvis ML, Van den Haute C, Hultgren SJ, Baekelandt V, Pospisilik JA, Brudek T, Aznar S, Steiner JA, Henderson MX, Brundin L, Ivanova MI, Hannan TJ, Brundin P. 2023. Urinary tract infections trigger synucleinopathy via the innate immune response. Acta Neuropathol 6.
Bertrums EJM, Smith JL, Harmon L, Ries RE, Want YCJ, Alonzo TA, Menssen AJ, Chisholm KM, Leonti AR, Tarlock K, Ostronoff F, Pogosova-Agadjanyan EL, Kaspers GJL, Hasle H, Dworzak M, Walter C, Muhlegger N, Moreiro C, Pardo L, Hirsch B, Raimondi S, Cooper TM, Aplenc R, Gamis AS, Kolb EA, Farrar JE, Stirewalt D, Ma X, Shaw TI, Furlan SN, Eidenschink Brodersen L, Loken MR, van den Heuvel-Eibrink MM, Zwaan M, Triche Jr TJ, Goemans BF, Meshinchi S. 2023. Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica.
*Liu H, Liu Y, Jin SG, Johnson J, Xuan H, Lu D, Li J, Zhai L, Li X, Zhao Y, Liu M, Craig SEL, Floramo JS, Molchanov V, Li J, Li J-D, Krawczyk CM, Shi X, Pfeifer GP, Yang T. 2023. TRIM28 secures skeletal stem cell fate during skeletogenesis by silencing neural gene expression and repressing GREM1/AKT/mTOR signaling axis. Cell Rep 14(1):112012.
Berryhill CA, Hanquier JN, Doud EH, Cordeiro-Spinetti E, Dickson BM, Rothbart SB, Mosley AL, Cornett EM. 2023. Global lysine methylome profiling using systematically characterized affinity reagents. Sci Rep13(1):377.
2022
Kupai A, Nakahara H, Voss KM, Hirano MS, Rodriguez A, Lackey DL, Murayama JF, Mathieson CJ, Shan B, Horton EC, Curtis GH, Huang J, Hille MB. 2022. Phosphorylation of serine residues S252, S268/S269, and S879 in p120 catenin activates migration of presomitic mesoderm in gastrulating zebrafish embryos. Dev Dynam 51(12):1952–1967.
Liu H, Craig SEL, Molchanov V, Floramo JS, Zhao Y, Yang T. 2022. SUMOylation in skeletal development, homeostasis, and disease. Cells 11(17):2710.
Bagchi A, Beddows I, Cornelius A, Robinson GW, Jewell SD. 2022. Rare cases of medulloblastoma with hypermutation. Cancer Rep 5(5):31521.
Chen L, Nagaraja C, Daniels S, Fisk ZA, Dvorak R, Meyerdirk L, Steiner JA, Escobar Galvis ML, Henderson MX, Rousseaux MWC, Brundin P, Chu HY. 2022. Synaptic location is a determinant of the detrimental effects of α-synuclein pathology to glutamatergic transmission in the basolateral amygdala. eLife 11:e78055.
Kasen A, Houck C, Burmeister AR, Sha Q, Brundin L, Brundin P. 2022. Upregulation of α-synuclein following immune activation: Possible trigger of Parkinson’s disease. Neurobiol Dis 166:105654.
*Liu H, Craig SEL, Molchanov V, Floramo JS, Zhao Y, Yang T. 2022. SUMOylation in skeletal development, homeostasis, and disease. Cells11(17):2710.
Wilson SL, Shen SY, Harmon L, Burgener JM, Triche Jr T, Bratman SV, De Carvalho DD, Hoffman MM. 2022. Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls. Cell Rep Methods 2(9):100294.
Maupin KA, Diegel CR, Stevens PD, Dick D, VAI Vivarium and Transgenics Core, Williams BO. 2022. Mutation of the galectin-3 glycan-binding domain (Lgals3-R200S) enhances cortical bone expansion in male mice and trabecular bone mass in female mice. FEBS Open Bio 12(10):1717–1728.
Endicott JL, Nolte PA, Shen H, Laird PW. 2022. Cell division drives DNA methylation loss in late-replicating domains in primary human cells. Nat Comm 13:6659.
Yang CH*, Fagnocchi L*, Apostle S, Wegert V, Casani-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Brás J, Thomasen M, Grunnert LG, Vaag AA, Gillberg L, Grundberg, E, Conesa A, Körner A, PERMUTE, Pospisilik JA. 2022. Independent phenotypic plasticity axes define distinct obesity subtypes. Nat Metab.
*Co-first authorship
**Highlighted in News & Views
***Graduate students Andrea Parham and Mitch McDonald are part of PERMUTE
. 2022. Molecular characterization of Portuguese patients with hereditary cerebellar ataxia. Cells 11(6):981.
Genome-wide association of polygenic risk extremes for Alzheimer’s disease in the UK Biobank. Sci Rep 12(1):8404.
Kaymak I, Luda KM, Duimstra LR, Ma EH, Longo J, Dahabieh MS, Faubert B, Oswald BM, Watson MJ, Kitchen-Goosen SM, DeCamp LM, Compton SE, Fu Z, DeBerardinis RJ, Williams KS, Sheldon RD, Jones RG. 2022. Carbon source availability drives nutrient utilization in CD8+ T cells. Cell Metab.
Prahl J, Pierce SE, Schans EJC, Coetzee G, Tyson T. 2022. The Parkinson’s disease variant rs356182 regulates neuronal differentiation independently from alpha-synuclein. Hum Mol Genet.
Goralski T, Ram J. 2022. Extracellular calcium receptor as a target for glutathione and Its derivatives. Intl J Mol Sci 23(2):717.
Prahl J, Coetzee G. 2022. Genetic elements at the alpha-synuclein locus. Front Neurosci.
Meng Y, Wang G, He H, Lau KH, Hurt A, Bixler BJ, Parham A, Jin SG, Zu X, Vasquez KM, Pfeifer GP, Szabó PE. 2022. Z-DNA is remodelled by ZBTB43 in prospermatagonia to safeguard the germline and epigenome. Nat Cell Biol.
Flores G, Grohar PJ. 2022. One oncogene, several vulerabilities: EWS/FL1 targeted therapies for Ewing sarcoma. J Bone Oncol 31:100404.
Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei M, Vander Scaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. 2022. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2(7):100144.
Prahl J, Pierce SE, Coetzee GA, Tyson T. 2022. Alpha-synuclein negatively controls cell proliferation in dopaminergic neurons. Mol Cell Neurosci 119:103702.
2021
Flores G, Grohar PJ. 2021. One oncogene, several vulnerabilities: EWS/FLI targeted therapies for Ewing sarcoma. J Bone Oncol 31:100404.
Traa A, Machiela E, Rudich PD, Soo SK, Senchuk MM, Van Raamsdonk JM. 2021. Identification of novel therapeutic targets for polyglutamine diseases that target mitochondrial fragmentation. Int J Mol Sci 22(24):13447.
Machiela E, Rudich PD, Traa A, Anglas U, Soo SK, Senchuk MM, Van Raamsdonk J. 2021. Targeting mitochondrial network disorganization is protective in C. elegans models of Huntington’s disease. Aging Dis12(7):1753–1772.
Vaughan RM, Kupai A, Rothbart SB. 2021. Chromatin regulation through ubiquitin and ubiquitin-like histone modifications. Trends Biochem Sci 46(4): 258–269.
de Oliveira LMA, Cordeiro-Spinetti E, Neves FPG, Sujii PS, Ribeiro RL, de Lyra SS, . . . Bonatelli ML. 2021. Going online in pandemic time: a DivulgaMicro workshop experience. J Microbiol Biol Educ 22(1):22.1.79.
Sargent D, Cunningham LA, Dues DJ, Ma Y, Kordich JJ, Mercado G, Brundin P, Cowell RM, Moore DJ. 2021. Neuronal VPS35 deletion induces spinal cord motor neuron degeneration and early post-natal lethality. Brain Commun 3(3).
Booms A, Coetzee G. 2021. Functions of intracellular alpha-synuclein in microglia: Implications for Parkinson’s disease risk. Front Cell Neurosci.
Bagchi A, Beddows I, Cornelius A, Robinson GW, Jewell SD. 2021. Rare cases of medulloblastoma with hypermutation. Cancer Rep e1521.
Dehghani N, Guven G, Kun-Rodrigues C, Gouveia C, Foster K, Hanagasi H, Lohmann E, Samanci B, Gurvit H, Bilgic B, Brás J, Guerreiro R. 2021. A comprehensive analysis of copy number variation in a Turkish dementia cohort. Hum Genom 15:48.
Liu Y, Molchanov V, Yang T. 2021. Enzymatic machinery of ubiquitin and ubiquitin-like modification systems in chondrocyte homeostasis and osteoarthritis. Curr Rheumatol Rep 23:62.
Ruan Z*, Haley E*, Orozco I*, Sabat M, Myers R, Roth R, Du J#, Lü W#. 2021. Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition. Nat Struct Mol Biol.
Dehghani N, Brás J, Guerreiro R. 2021. How understudied populations have contributed to our understanding of Alzheimer’s disease genetics. Brain.
. 2021. Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor. EMBO Mol Med 13(2):e12640.
Bagchi A, Madaj Z, Engel KB, Guan P, Rohrer DC, Valley DR, Wolfrum E, Feenstra K, Roche N, Hostetter G, Moore HM, Jewell SD. 2021. Impact of preanalytical factors on the measurement of tumor tissue biomarkers using immunohistochemistry. J Histochem Cytochem 69(5)297–320.
Grit JL, Johnson BK, Dischinger PS, Essenburg CJ, Adams M, Campbell S, Pollard K, Pratilas CA, Triche TJ Jr., Graveel CR, Steensma MR. 2021. Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling. Epi Chromatin 14(7).
2020
Dickson BM, Tiedemann RL, Chomiak AA, Cornett EM, Vaughan RM, Rothbart SB. 2020. A physical basis for quantitative ChIP-sequencing. J Biol Chem 295(47):15826–15837.
*Selected as an Editor’s Pick and featured on the cover
Nollet EA, Cardo-Vila M, Ganguly SS, Tran JD, Schulz VV, Cress A, Corey E, Miranti CK. 2020. Androgen receptor-induced integrin α6β1 and Bnip3 promote survival and resistance to PI3K inhibitors in castration-resistant prostate cancer. Oncogene 39(31): 5390–5404.
Machiela E, Liontis T, Dues DJ, Rudich PD, Traa A, Wyman L, Kaufman C, Cooper JF, Lew L, Nadarajan S, Senchuk MM, Van Raamsdonk JM. 2020. Disruption of mitochondrial dynamics increases stress resistance through activation of multiple stress response pathways. FASEB J 34(6):8475–8492.
. 2020. KCNN2 mutation in autosomal-dominant tremulous myoclonus-dystonia. Eur J Neurol 27(8):1471–1477.
Vaughan RM, Kupai A, Rothbart SB. 2020. Chromatin regulation through ubiquitin and ubiquitin-like histone modifications. Trends Biochem Sci.
Tovar EA, Sheridan R, Essenburg CJ, Dischinger PS, Arumugam M, Callaghan ME, Graveel CR*, Steensma MR*. 2020. Dissecting the rat mammary gland: Isolation, characterization and culture of purified mammary epithelial cells and fibroblasts. Bio-protocol 10(22).
*Equal contributions
Vaughan RM, Kupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. 2020. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 13(1):44.
Dues DJ, Moore DJ. 2020. LRRK2 and protein aggregation in Parkinson’s disease: Insights from animal models. Front Neurosci 14:719
Cunningham LA, Moore DJ. 2020. Endosomal sorting pathways in the pathogenesis of Parkinson’s disease. Prog Brain Res 252:271–306.
Grit JL, Pridgeon MG, Essenburg CJ, Wolfrum E, Madaj ZB, Turner L, Wulfkuhle J, Petricoin EF 3rd, Graveel CR, Steensma MR. 2020. Kinome profiling of NF1-related MPNSTs in response to kinase inhibition and doxorubicin reveals therapeutic vulnerabilities. Genes (Basel) 11(3):331
Maupin KA, Dick D, Lee J, Williams BO. 2020. Loss of Lgals3 protects against gonadectomy-induced cortical bone loss in mice. Calcif Tissue Int 106(3):283–229
Diegel CR, Hann S, Ayturk UM, Hu JCW, Lim KE, Droscha CJ, Madaj ZB, Foxa GE, Izaguirre I; VAI Vivarium and Transgenics Core, Robling AG, Warman ML, Williams BO. 2020. Independent validation of experimental results requires timely and unrestricted access to animal models and reagents. PLoS Genet 16(6):e1008940
Kupai A, Vaughan RM, Dickson BM, Rothbart SB. 2020. A degenerate peptide library approach to reveal sequence determinants of methyllysine-driven protein interactions. Front Cell Dev Biol 8:241.
Pierce SE, Booms A, Prahl J, van der Schans EJC, Tyson T, Coetzee GA. 2020. Post-GWAS knowledge gap: the how, where and when. npj Parkinsons 6:23.
Zhuang Y, Liu H, Zhou XE, Verma RK, de Waal PW, Jang W, Xu TH, Wang L, Meng X, Zhao G, Kang Y, Melcher K, Fan H, Lambert NA, Xu HE, Zheng C. 2020. Structure of formylpeptide receptor 2-G i complex reveals insights into ligand recognition and signaling (https://www.nature.com/articles/s41467-020-14728-9) . Nat Commun 11(1):1-12.
Ma S, Shen Q, Zhao LH, Mao C, Zhou XE, Shen DD, de Waal PW, Bi P, Li C, Jiang Y, Wang MW, Sexton PM, Wootten D, Melcher K, Zhang Y, Xu HE. 2020. Molecular basis for hormone recognition and activation of corticotropin-releasing factor receptors (https://www.sciencedirect.com/science/article/abs/pii/S1097276520300137) . Mol Cell 77(3):669–680.
Gedminas JM, Chasse MH, McBrairty M, Beddows I, Kitchen-Goosen SM, Grohar PJ. 2020. Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor.
Oncogenesis 9(4):41.
Diegel CR, Hann S, Ayturk UM, Hu JCW, Lim K, Droscha CJ, Madaj ZB, Foxa GE, Izaguirre I, VAI Vivarium and Transgenics Core, Paracha N, Pidhaynyy B, Dowd TL, Robling AG, Warman ML, Williams BO. 2020. An osteocalcin-deficient mouse strain without endocrine abnormalities. PLOS Genet.
de Waal PW, Shi J, You E, Wang X, Melcher K, Jiang Y, Xu HE, Dickson BM. 2020. Molecular mechanisms of fentanyl mediated β-arrestin biased signaling. PLOS Comp Biol.
Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZB, Beddows I, Dikalov S, Adams M, Klumpp-Thomas CA, Kitchen-Goosen SM, Martin SE, Caplen NJ, Helman LJ, Grohar PJ. 2020. CDK9 blockade exploits context-dependent transcriptional changes to improve activity and limit toxicity of mithramycin for Ewing sarcoma. Mol Cancer Ther.
2019
Dutka P, Mukherjee S, Gao X, Kang Y, de Waal PW, Wang L, Zhuang Y. 2019. Development of “plug and play” fiducial marks for structural studies of GPCR signaling complexes by single-particle cryo-EM (https://www.sciencedirect.com/science/article/abs/pii/S0969212619303454) . Structure 27(12):1862–1874.
Yin W, Li Z, Jin M, Yin YL, de Waal PW, Pal K, Yin Y, Gao X, He Y, Gao J, Wang X, Zhang Y, Zhou H, Melcher K, Jiang Y, Cong Y, Zhou XE, Yu X, Xu HE. 2019. A complex structure of arrestin-2 bound to a G protein-coupled receptor (https://www.nature.com/articles/s41422-019-0256-2) . Cell Res 29(12):971–983.
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Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2019. Resistance to stress can be experimentally dissociated from longevity. J Gerontol A Biol Sci Med Sci 74(8):1206–1214.
Toth RK, Tran JD, Muldong MT, Nollet EA, Schulz VV, Jensen CC, Hazlehurst LA, Corey E, Durden D, Jamieson C, Miranti CK, Warfel NA. 2019. Hypoxia-induced PIM kinase and laminin-activated integrin α6 mediate resistance to PI3K inhibitors in bone-metastatic CRPC. Am J Clin Exp Urol 7(4):297–312.
Bergsma A, Ganguly SS, Wiegand ME, Dick D, Williams BO, Miranti CK. 2019. Regulation of cytoskeleton and adhesion signaling in osteoclasts by tetraspanin CD82. Bone Rep 10:100196.
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Vaughan RM, Rothbart SB*, Dickson BM*. 2019. The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for maintaining DNA methylation. J Biol Chem.
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Booms A, Coetzee GA, Pierce SE. 2019. MCF-7 as a model for functional analysis of breast cancer risk variants. Cancer Epidemiol Biomarkers Prev.
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Keaton SA, Madaj ZB, Heilman P, Smart L, Grit J, Gibbons R, Postolache TT, Roaten K, Achtyes ED, Brundin L. 2019. An inflammatory profile linked to increased suicide risk. J Affect Disord 247:57–65.
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Zhao LH*, Ma S*, Sutkeviciute I*, Shen DD*, Zhou XE, de Waal PW, Li CH, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanbe T, Gradella TJ, Melcher K, Wang MW#, Vilardaga JP#, Xu HE#, Zhang Y#. 2019. Structure and dynamics of the active human parathyroid hormone receptor-1. Science.
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Chen X, Kordich JK, Williams ET, Levine N, Cole-Strauss A, Marshall L, Labrie V, Ma J, Lipton JW, Moore DJ. 2019. Parkinson’s disease-linked D620N VPS35 knockin mice manifest tau neuropathology and dopaminergic neurodegeneration. Proc Natl Acad Sci U S A.
2018
Cooper JF, Spielbauer KK, Senchuk MM, Nadarajan S, Colaiacovo MP, Van Raamsdonk JM. 2018. α-synuclein expression from a single copy transgene increases sensitivity to stress and accelerates neuronal loss in genetic models of Parkinson’s disease. Exp Neurol 310:58–69.
Burgenske DM, Monsma D, MacKeigan JP. 2018. Patient-derived xenograft models of colorectal cancer: procedures for engraftment and propagation. Methods Mol Biol 1765:307–314.
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Martin KR, Celano SL, Solitro AR, Gunaydin H, Scott M, O’Hagan RC, Shumway SD, Fuller P, MacKeigan JP. 2018. A potent and selective ULK1 inhibitor suppresses autophagy and sensitizes cancer cells to nutrient stress. iScience 8:74–84.
Bergsma A, Ganguly SS, Dick D, Williams BO, Miranti CK. 2018. Global deletion of tetraspanin CD82 attenuates bone growth and enhances bone marrow adipogenesis. Bone 113:105–113.
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Gu X, Bridges MD, Yan Y, de Waal PW, Zhou XE, Suino-Powell KM, Xu HE, Hubbell WL, Melcher K. 2018. Conformational heterogeneity of the allosteric drug and metabolite (ADaM) site in AMP-activated protein kinase (AMPK). J Biol Chem293(44):16994–17007.
Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. 2018. A DNA methylation reader complex that enhances gene transcription. Science 362(6419):1182–1186.
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Valkenburg KC, De Marzo AM, Williams BO. 2017. Deletion of tumor suppressors adenomatous polyposis coli and Smad4 in murine luminal epithelial cells causes invasive prostate cancer and loss of androgen receptor expression. Oncotarget 8(46):80265-80277.
Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD. Nature.
Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenberg AJ. 2018. Examining the roles of H3K4 methylation states with systematically characterized antibodies. Mol Cell.
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Krajnak K, Dahl R. 2018. A new target for Alzheimer’s disease: a small molecule SERCA activator is neuroprotective in vitro and improves memory and cognition in APP/PS1 mice. Bioorg Med Chem Lett 28(9):1591–1594.
Krajnak K, Dahl R. 2018. Small molecule SUMOylation activators are novel neuroprotective agents. Bioorg Med Chem Lett 28(3): 405–409.
Yang S, Wu T, Xu TH, de Waal PW, He Y, Pu M, Chen Y, DeBruine ZJ, Zhang B, Zaidi SA, Popov P, Guo Y, Han GW, Lu Y, Suino-Powell K, Song S, Harikumar KG, Miller LJ, Katritch V, Xu HE, Shui W, Stevens RC, Melcher K, Zhao S, Xu F. 2018. Crystal structure of the Frizzled 4 receptor in a ligand-free state. Nature.
Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. 2018. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance. Nuc Acids Res.
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Yin W, Zhou XE, Yang D, de Waal PW, Want M, Dai A, Cai X, Haung CY, Liu P, Wang X, Yin Y, Liu B, Zhou Y, Wang J, Liu H, Caffrey M, Melcher K, Xu Y, Wang MW, Xu HE, Jiang Y. 2018. Crystal structure of the human 5-HT1B serotonin receptor bound to an inverse agonist. Cell Disc 4(12).
Williams ET, Glauser L, Tsika E, Jiang H, Islam S, Moore DJ. 2018. Parkin mediates the ubiquitination of VPS35 and modulates retromer-dependent endosomal sorting. Hum Mol Genet.
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Williams ET, Moore DJ. 2018. Deciphering the role of VPS35 in Parkinson’s disease. J Neurosci Res 96(8):1339–1340.
Senchuk MM, Dues DJ, Schaar CE, Johnson BK, Madaj ZB, Bowman MJ, Winn ME, Van Raamsdonk JM. 2018. Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans. PLoS Genet 14(3): e1007268.
Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. 2018. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1. Proc Natl Acad Sci U S A
Kang Y*, Kuybeda O*, de Waal PW*, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE. 2018. Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature.
2017
Cooper JF, Machiela M, Dues DJ, Spielbauer KK, Senchuk MM, Van Raamsdonk JM. 2017. Activation of the mitochondrial unfolded protein response promotes longevity and dopamine neuron survival in Parkinson’s disease models. Sci Rep 7:16441.
DeBruine ZJ, Xu HE, Melcher K. 2017. Assembly and architecture of the Wnt/β-catenin signalosome at the membrane. Br J Pharmacol 174(24):4564–4574.
Dunn EM, Billquist EJ, VanderStoep AL, Bax PG, Westrate LM, McLellan LK, Peterson SC, MacKeigan JP, Putzke AP. 2017. Dual roles of Fer kinase are required for proper hematopoiesis and vascular endothelium organization during zebrafish development. Biology (Basel) 6(4):40.
Merrill NM, Schipper JL, Karnes JB, Kauffman AL, Martin KR, MacKeigan JP. 2017. PI3K-C2α knockdown decreases autophagy and maturation of endocytic vesicles. PLoS One 12(9):e0184909.
Bryleva EY, Keaton SA, Grit J, Madaj Z, Sauro-Nagendra A, Smart L, Halstead S, Achtyes E, Brundin L. 2017. The acute-phase mediator serum amyloid A is associated with symptoms of depression and fatigue. Acta Psychiatr Scand 135(5):409–418.
DeBruine ZJ, Ke J, Harikumar KG, Gu X, Borowsky P, Williams BO, Xu W, Miller LJ, Xu HE, Melcher K. 2017. Wnt5a promotes frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerization. Genes Dev 31(9):916–926.
Chassé MH, Muthurajan UM, Clark NJ, Kramer MA, Chakravarthy S, Irving T, Luger K. 2017. Biochemical and biophysical methods for analysis of poly(ADP-ribose) polymerase 1 and its interactions with chromatin. Methods Mol Biol 1608:231–253.
Valkenburg KC, DeMarzo AM, Williams BO. 2017. Deletion of tumor suppressors adenomatous polyposis coli and Smad4 in murine luminal epithelial cells causes invasive prostate cancer and loss of androgen receptor expression. Oncotarget 8(46):80265–80277.
Droscha CJ, Diegel CR, Ethen NJ, Burgers TA, McDonald MJ, Maupin KA, Naidu AS, Wang PF, Teh BT, Williams BO. 2017. Osteoblast-specific deletion of Hprt2/Cdc73 results in high bone mass and increased bone turnover. Bone 98:68–78.
Gu X, Yan Y, Novick SJ, Kovach A, Goswami D, Ke J, Tan MHE, Wang L, Li X, de Waal PW, Webb MR, Griffin PR, Xu HE, Melcher K. 2017. Deconvoluting AMP-dependent kinase (AMPK) adenine nucleotide binding and sensing. J Biol Chem 292(30):12653–12666.
Thellman NM, Botting C, Madaj Z, Triezenberg SJ. 2017. An immortalized human dorsal root ganglia cell line provides a novel context to study herpes simplex virus Type-1 latency and reactivation. J Virology 91(12): 00080-17.
Thellman NM, Triezenberg SJ. 2017. Herpes simplex virus establishment, maintenance, and reactivation: in vitro modeling of latency. Pathogens 6(3):28.
Tyson T, Senchuk M, Cooper JF, George S, Van Raamsdonk JM, Brundin P. 2017. Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synuclein. Sci Rep7:7506.
Williams ET, Chen X, Moore DJ. 2017. VPS35, the retromer complex and Parkinson’s disease. J Parkinsons Dis 7(2):219–233.
Yin Y, de Waal PW, He Y, Zhao LH, Yang D, Cai X, Jiang Y, Melcher K, Wang MW, Xu HE. 2017. Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein–coupled receptors. J Biol Chem 292(24):9865–9881.
Zhou XE, He Y, de Waal PW, Gao X, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein–coupled receptors. Cell 170(3):457–469.e13.
Golani LK, Wallace-Povirk A, Deis SM, Wong J, Ke J, Gu X, Raghavan S, Wilson MR, Li X, Polin L, de Waal PW, White K, Kushner J, O’Connor C, Hou Z, Xu HE, Melcher K, Dann 3rd CE, Matherly LH, Gangjee A. 2016. Tumor targeting with novel 6-substituted pyrrolo [2,3-d] pyrimidine antifolates with heteroatom bridge substitutions via cellular uptake by folate receptor α and the proton-coupled folate transporter and inhibition of de novo purine nucleotide biosynthesis. J Med Chem 59(17):7856–7876.
Ghosh A, Tyson T, George S, Hildebrandt EN, Steiner JA, Madaj Z, Schulz E, Machiela E, McDonald WG, Escobar Galvis ML, Kordower JH, Van Raamsdonk JM, Colca JR, Brundin P. 2016. Mitochondrial pyruvate carrier regulates autophagy, inflammation, and neurodegeneration in experimental models of Parkinson’s disease. Sci Transl Med 368: 368ra174.
Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatic regulator BRD4. J Chem Phys 145(15):154113.
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*Editor’s pick, cover article and F1000 Prime article
2024
Massari CM, Dues DJ, Bergsma A, Sipple K, Frye M, Williams ET, Moore DJ. 2024. Neuropathology in an α-synuclein preformed fibril mouse model occurs independent of the Parkinson’s disease-linked lysosomal ATP13A2 protein. Neurobiol Dis 202:106701.
Sokol KH, Lee CJ, Rogers TJ, Waldhart A, Ellis AE, Madireddy S, Daniels SR, House RJ, Ye X, Olsenavich M, Johnson A, Furness BR, Sheldon RD, Lien EC. 2024. Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking. Cell Chem Biol.
Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib W, Heo L, Laird PW, Berman B, Triche Jr TJ, Shen H. 2024. BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nuc Acids Res 52(6):e32.
Booms A, Pierce SE, van der Schans EJC, Coetzee GA. 2024. Parkinson’s disease risk enhancers in microglia. iScience 27(2):108921.
Lubben N, Byrnildsen JK, Webb CM, Li HL, Leyns CEG, Changolkar L, Zhang B, Meymand ES, O’Reilly M, Madaj Z, DeWeerd D, Fell MJ, Lee VYM, Bassett DS, Henderson MX. 2024. LRRK2 kinase inhibition reverses G2019s mutation-dependent effects on tau pathology progression. Transl Neurodegener 13(1):13.
House RJ, Eapen JP, Shen H, Graveel C, Steensma MR. 2024. Ceas: An R package for Seahorse data analysis and visualization. Bioinformatics, btae503.
Guak H, Weiland M, Vander Ark A, Zhai L, Lau K, Corrado M, Davidson P, Asiedu E, Mabvakure B, Compton S, DeCamp L, Scullion CA, Jones RG, Nowinski S, Krawczyk C. 2024. Transcriptional programming mediated by the histone demethylase KDM5C regulate dendritic cell population heterogeneity and function. Cell Rep 43(8):114506.
House RJ*, Soper-Hopper MT*, Vincent MP, Ellis AE, Capan CD, Madaj ZB, Wolfrum E, Isaguirre CN, Castello CD, Johnson AB, Escobar Galvis ML, Williams KS, Lee H, Sheldon RD. 2024. A diverse proteome is present and enzymatically active in metabolite extracts. Nat Comm 15:5796.
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Ma EH, Dahabieh MS, DeCamp LM, Kaymak I, Kitchen-Goosen SM, Oswald BM, Longo J, Roy DG, Verway MJ, Johnson RM, Samborska B, Duimstra LR, Scullion LR, Steadman M, Vos M, Roddy TP, Krawczyk CM, Williams KS, Sheldon RD, Jones RG. 2024. 13C metabolite tracing reveals glutamine and acetate as critical in vivo fuels for CD8 T. Sci Adv 10(22).
Arumugam M, Tovar EA, Essenburg CJ, Dischinger PS, Beddows I, Wolfrum E, Madaj ZB, Turner L, Feenstra K, Gallik KL, Cohen L, Nichols M, Sheridan RTC, Esquibel CR, Mouneimne G, Graveel CR, Steensma MR. 2024. Nf1 deficiency modulates stromal environment in the pretumorigenic rat mammary gland. Front Cell Dev Biol 12.
Cooper JF, Nguyen K, Gates D, Wolfrum E, Capan C, Lee H, Williams D, Okoye C, Wojtovich AP, Burton NO. Preprint. Oocyte mitochondria link maternal environment to offspring phenotype. Res Sq.
Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib W, Heo L, Laird PW, Berman B, Triche T, Shen H. 2024. BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nuc Acids Res 52(6):e32.
Nguyen N, Carpenter KA, Ensing J, Gilliland C, Rudisel EJ, Mu EM, Thurlow KE, Triche Jr. TJ, Grainger S. 2024. EGFR-dependent endocytosis of Wnt9a and Fzd9b promotes β-catenin signaling during hematopoietic stem cell development in zebrafish. Sci Sig 17(832).
Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. 2024. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. Sci Adv 10(13).
Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. 2024. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 15:2642.
Grit JL, Turner L, Essenburg CJ, Gallik KL, Dischinger PS, Shurlow ND, Pate MJ, Graveel CR, Steensma MR. 2024. Ex-vivo patient-derived explant model for neurofibromatosis type 1-related cutaneous neurofibromas. J Invest Dermatol 21:S0022-202X(24)00117-9.
Abla O, Ries RE, Triche Jr TJ, Gerbing RB, Hirsch B, Raimondi S, Cooper TM, Farrar JE, Buteyn N, Harmon LM, Wen H, Deshpande AJ, Kolb EA, Gamis AS, Aplenc R, Alonzo T, Meshinchi S. 2024. Structural variants involving MLLT10 fusion are associated with adverse outcomes in pediatric acute myeloid leukemia. Blood Adv.
House RJ, Tovar EA, Redlon LN, Essenburg CJ, Dischinger PS, Ellis AE, Beddows I, Sheldon RD, Lien EC, Graveel CR, Steensma MR. 2024. NF1 deficiency drives metabolic reprogramming in ER+ breast cancer. Mol Metab 80:101876.
Beddows I, Fan H, Heinze K, Johnson BK, Leonova A, Senz J, Djirackor S, Cho KR, Pearce CL, Huntsman DG, Angelesio MS, Shen H. 2024. Cell state of origin impacts development of distinct endometriosis-related ovarian carcinoma histotypes. Can Res 84(1):26–38.
2023
Dues DJ, Ma Y, Nguyen APT, Offerman AV, Beddows I, Moore DJ. 2023. Formation of templated inclusions in a forebrain a-synuclein mouse model is independent of LRRK2. Neurobiol Dis 188:106338.
George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf, Y. 2023. Epigenomic reprogramming in iAs-mediated carcinogenesis. Adv Pharmacol 96:319–365.
Wedan RJ, Longenecker JZ, Nowinski SM. 2023. Mitochondrial fatty acid synthesis is an emergent central regulator of mammalian oxidative metabolism. Cell Metab 26(1):36–47.
Dues DJ, Tran Nguyen AP, Becker K, Ma J, Moore DJ. 2023. Hippocampal subfield vulnerability to α-synuclein pathology precedes neurodegeneration and cognitive dysfunction. npj Parkinsons Dis 9(125).
Diegel CR, Kramer I, Moes C, Foxa GE, McDonald MJ, Madaj ZB, Guth S, Liu J, Harris JL, Kneissel M, Williams BO. 2023. Inhibiting WNT secretion reduces high bone mass caused by Sost loss-of-function or gain-of-function in Lrp5. Bone Res 11(1):47.
Chen L, Daniels S, Dvorak R, Chu H-Y. 2023. Reduced thalamic excitation to motor cortical pyramidal tract neurons in parkinsonism. Sci Adv 9(34).
Luda KM, Longo J, Kitchen-Goosen SM, Duimstra LR, Ma EH, Watson MJ, Oswald BM, Fu Z, Madaj Z, Kupai A, Dickson BM, DeCamp LM, Dahabieh MS, Compton SE, Teis R, Kaymak I, Lau KH, Kelly DP, Puchalska P, Williams KS, Krawczyk CM, Lévesque D, Boisvert FM, Sheldon RD, Rothbart SB, Crawford PA, Jones RG. 2023. Ketolysis drives CD8+ T cell effector function through effects on histone acetylation. Immunity.
Floramo JS, Molchanov V, Liu H, Liu Y, Craig SEL, Yang T. 2023. An integrated view of stressors as causative agents in OA pathogenesis. Biomolecules 13(5):721.
Compton SE, Kitchen-Goosen SM, DeCamp LM, Lau KH, Mabvakure, Vos M, Williams KS, Wong KK, Shi X, Rothbart SB, Krawczyk CK, Jones RG. 2023. LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation. Mol Cell.
Compton SE, Kitchen-Goosen SM, DeCamp LM, Lau KH, Mabvakure, Vos M, Williams KS, Wong KK, Shi X, Rothbart SB, Krawczyk CK, Jones RG. 2023. LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation. Mol Cell.
Peelaerts W, Mercado G, George S, Villumsen M, Kasen A, Aguileta, Linstow C, Sutter AB, Kuhn E, Stetzik L, Sheridan R, Bergkvist L, Meyerdirk L, Lindqvist A, Escobar Galvis ML, Van den Haute C, Hultgren SJ, Baekelandt V, Pospisilik JA, Brudek T, Aznar S, Steiner JA, Henderson MX, Brundin L, Ivanova MI, Hannan TJ, Brundin P. 2023. Urinary tract infections trigger synucleinopathy via the innate immune response. Acta Neuropathol 6.
Bertrums EJM, Smith JL, Harmon L, Ries RE, Want YCJ, Alonzo TA, Menssen AJ, Chisholm KM, Leonti AR, Tarlock K, Ostronoff F, Pogosova-Agadjanyan EL, Kaspers GJL, Hasle H, Dworzak M, Walter C, Muhlegger N, Moreiro C, Pardo L, Hirsch B, Raimondi S, Cooper TM, Aplenc R, Gamis AS, Kolb EA, Farrar JE, Stirewalt D, Ma X, Shaw TI, Furlan SN, Eidenschink Brodersen L, Loken MR, van den Heuvel-Eibrink MM, Zwaan M, Triche Jr TJ, Goemans BF, Meshinchi S. 2023. Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica.
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Kupai A, Nakahara H, Voss KM, Hirano MS, Rodriguez A, Lackey DL, Murayama JF, Mathieson CJ, Shan B, Horton EC, Curtis GH, Huang J, Hille MB. 2022. Phosphorylation of serine residues S252, S268/S269, and S879 in p120 catenin activates migration of presomitic mesoderm in gastrulating zebrafish embryos. Dev Dynam 51(12):1952–1967.
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Maupin KA, Diegel CR, Stevens PD, Dick D, VAI Vivarium and Transgenics Core, Williams BO. 2022. Mutation of the galectin-3 glycan-binding domain (Lgals3-R200S) enhances cortical bone expansion in male mice and trabecular bone mass in female mice. FEBS Open Bio 12(10):1717–1728.
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2019
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Booms A, Coetzee GA, Pierce SE. 2019. MCF-7 as a model for functional analysis of breast cancer risk variants. Cancer Epidemiol Biomarkers Prev.
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Chen X, Kordich JK, Williams ET, Levine N, Cole-Strauss A, Marshall L, Labrie V, Ma J, Lipton JW, Moore DJ. 2019. Parkinson’s disease-linked D620N VPS35 knockin mice manifest tau neuropathology and dopaminergic neurodegeneration. Proc Natl Acad Sci U S A.
2018
Cooper JF, Spielbauer KK, Senchuk MM, Nadarajan S, Colaiacovo MP, Van Raamsdonk JM. 2018. α-synuclein expression from a single copy transgene increases sensitivity to stress and accelerates neuronal loss in genetic models of Parkinson’s disease. Exp Neurol 310:58–69.
Burgenske DM, Monsma D, MacKeigan JP. 2018. Patient-derived xenograft models of colorectal cancer: procedures for engraftment and propagation. Methods Mol Biol 1765:307–314.
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Maupin K, Weaver K, Bergsma A, Christie C, Zhong ZA, Yang T, Williams BO. 2018. Enhanced cortical bone expansion in Lgals3-deficient mice during aging. Bone Res 6:7.
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Krajnak K, Dahl R. 2018. A new target for Alzheimer’s disease: a small molecule SERCA activator is neuroprotective in vitro and improves memory and cognition in APP/PS1 mice. Bioorg Med Chem Lett 28(9):1591–1594.
Krajnak K, Dahl R. 2018. Small molecule SUMOylation activators are novel neuroprotective agents. Bioorg Med Chem Lett 28(3): 405–409.
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Williams ET, Glauser L, Tsika E, Jiang H, Islam S, Moore DJ. 2018. Parkin mediates the ubiquitination of VPS35 and modulates retromer-dependent endosomal sorting. Hum Mol Genet.
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Williams ET, Moore DJ. 2018. Deciphering the role of VPS35 in Parkinson’s disease. J Neurosci Res 96(8):1339–1340.
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2017
Cooper JF, Machiela M, Dues DJ, Spielbauer KK, Senchuk MM, Van Raamsdonk JM. 2017. Activation of the mitochondrial unfolded protein response promotes longevity and dopamine neuron survival in Parkinson’s disease models. Sci Rep 7:16441.
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Tyson T, Senchuk M, Cooper JF, George S, Van Raamsdonk JM, Brundin P. 2017. Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synuclein. Sci Rep7:7506.
Williams ET, Chen X, Moore DJ. 2017. VPS35, the retromer complex and Parkinson’s disease. J Parkinsons Dis 7(2):219–233.
Yin Y, de Waal PW, He Y, Zhao LH, Yang D, Cai X, Jiang Y, Melcher K, Wang MW, Xu HE. 2017. Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein–coupled receptors. J Biol Chem 292(24):9865–9881.
Zhou XE, He Y, de Waal PW, Gao X, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein–coupled receptors. Cell 170(3):457–469.e13.
Golani LK, Wallace-Povirk A, Deis SM, Wong J, Ke J, Gu X, Raghavan S, Wilson MR, Li X, Polin L, de Waal PW, White K, Kushner J, O’Connor C, Hou Z, Xu HE, Melcher K, Dann 3rd CE, Matherly LH, Gangjee A. 2016. Tumor targeting with novel 6-substituted pyrrolo [2,3-d] pyrimidine antifolates with heteroatom bridge substitutions via cellular uptake by folate receptor α and the proton-coupled folate transporter and inhibition of de novo purine nucleotide biosynthesis. J Med Chem 59(17):7856–7876.
Ghosh A, Tyson T, George S, Hildebrandt EN, Steiner JA, Madaj Z, Schulz E, Machiela E, McDonald WG, Escobar Galvis ML, Kordower JH, Van Raamsdonk JM, Colca JR, Brundin P. 2016. Mitochondrial pyruvate carrier regulates autophagy, inflammation, and neurodegeneration in experimental models of Parkinson’s disease. Sci Transl Med 368: 368ra174.
Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatic regulator BRD4. J Chem Phys 145(15):154113.
Zhou XE*, He Y*, de Waal PW*, Gao X*, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein-coupled receptors. Cell 170(3):457–469.e13.
*Co-first authors
**Cover of Cell
Gu X, Yan Y, Novick SJ, Kovich A, Goswami D, Ke Y, Tan MHE, Wang L, Li X, de Waal PW, Webb MR, Griffin PR, Xu HE, Melcher K. 2017. Deconvoluting AMP-dependent kinas (AMPK) adenine nucleotide binding and sensing.
J Bio Chem.
Yin Y, de Waal PW, He Y, Zhao LH, Yang D, Cai X, Jiang Y, Melcher K, Wang MW, Xu HE. 2017. Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein –coupled receptors. J Biol Chem.
*Editor’s pick, cover article and F1000 Prime article
Non peer-reviewed publications
2015
Cooper, Jason, Kevin Maupin, and Nathan Merrill. 2015. Origins of Cancer Symposium 2015: posttranslational modifications and cancer. Genes & Cancer 6(7–8): 303–306.
2014
Howard, Andrew M., Eric A. Nollet, and Nikki M. Thellman. 2014. Origins of Cancer Symposium report: beyond the tumor cell. Genes & Cancer 5(11–12): 375–377.
Miranti, Cindy K., Alexis Bergsma, and Annemiek B. van Spriel. 2014. Tetraspanins as master organizers of the plasma membrane. In Cell Membrane Nanodomains: From Biochemistry to Nanoscopy, Alessandra Cambi and Diane S. Lidke, eds. Boca Raton, FL: CRC Press, pp. 59–86.
2013
Nollet, Eric A., and Cindy K. Miranti. 2013. Integrin and matrix regulation of autophagy and mitophagy. In Autophagy, Yannick Bailly, ed. New York: InTech, pp. 465–485.
Burgenske, Dani M., and Kenneth C. Valkenburg. 2013. Origins of Cancer Symposium report. Genes & Cancer 4(11–12): 457–459.
2012
Westrate, Laura, and Jeffrey P. MacKeigan. 2012. PINK1. In Encyclopedia of Signaling Molecules, Sangdun Choi, ed. New York: Springer, p. 1429.
Niemi, Natalie M., and Jeffrey P. MacKeigan. 2012. MK-STYX. In Encyclopedia of Signaling Molecules, S. Choi, ed. New York: Springer, pp. 1089–1093.
2010
Klomp, Jeff A., Bin T. Teh, and Kyle A. Furge. 2010. An integrated oncogenomic approach: from genes to pathway analysis. In An Omics Perspective on Cancer Research, William C.S. Cho, ed. New York: Springer, p. 31.
2009
Wolters, Natalie M., and Jeffrey P. MacKeigan. 2009. Applications of RNA interference in drug discovery. In A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery, T. Chen, ed. London: Taylor and Francis, pp. 157–168.