Publications

1. Wang Z, Brand R, Adolf-Bryfogle J, Grewal J, Qi Y, Combs SA, Golovach N, Alford R, Rangwala H, Clark PM. EGGNet, a Generalizable Geometric Deep Learning Framework for Protein Complex Pose Scoring.. ACS omega, 2024.
2. Ghezzi C, Chen BY, Damoiseaux R, Clark PM. Pacritinib inhibits glucose consumption in squamous cell lung cancer cells by targeting FLT3.. Scientific reports, 2023.
3. Greig JA, Breton C, Ashley SN, Martins KM, Gorsuch C, Chorazeczewski JK, Furmanak T, Smith MK, Zhu Y, Bell P, Shoop W, Li H, Smith J, Tomberlin G, Clark P, Mitchell TW, Buza EL, Yan H, Jantz D, Wilson JM. Treating Transthyretin Amyloidosis via Adeno-Associated Virus Vector Delivery of Meganucleases.. Human gene therapy, 2022.
4. Ghezzi C, Perez S, Ryan K, Wong A, Chen BY, Damoiseaux R, Clark PM. Early Reduction of Glucose Consumption Is a Biomarker of Kinase Inhibitor Efficacy Which Can Be Reversed with GLUT1 Overexpression in Lung Cancer Cells.. Molecular imaging and biology, 2022.
5. Chen BY, Salas JR, Trias AO, Perez Rodriguez A, Tsang JE, Guemes M, Le TM, Galic Z, Shepard HM, Steinman L, Nathanson DA, Czernin J, Witte ON, Radu CG, Schultz KA, Clark PM. Targeting deoxycytidine kinase improves symptoms in mouse models of multiple sclerosis.. Immunology, 2022.
6. Wang Z, Combs SA, Brand R, Calvo MR, Xu P, Price G, Golovach N, Salawu EO, Wise CJ, Ponnapalli SP, Clark PM. LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction.. Scientific reports, 2022.
7. Salas JR, Clark PM. Signaling Pathways That Drive 18F-FDG Accumulation in Cancer.. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2022.
8. Fajardo VM, Feng I, Chen BY, Perez-Ramirez CA, Shi B, Clark P, Tian R, Lien CL, Pellegrini M, Christofk H, Nakano H, Nakano A. GLUT1 overexpression enhances glucose metabolism and promotes neonatal heart regeneration.. Scientific reports, 2021.
9. Breton C, Clark PM, Wang L, Greig JA, Wilson JM. Correction to: ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing.. BMC genomics, 2020.
10. Jayaraman P, Mosbruger T, Hu T, Tairis NG, Wu C, Clark PM, D'Arcy M, Ferriola D, Mackiewicz K, Gai X, Monos D, Sarmady M. AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies.. Bioinformatics (Oxford, England), 2020.
11. Tsang JE, Urner LM, Kim G, Chow K, Baufeld L, Faull K, Cloughesy TF, Clark PM, Jung ME, Nathanson DA. Development of a Potent Brain-Penetrant EGFR Tyrosine Kinase Inhibitor against Malignant Brain Tumors.. ACS medicinal chemistry letters, 2020.
12. Breton C, Clark PM, Wang L, Greig JA, Wilson JM. ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing.. BMC genomics, 2020.
13. Lisova K, Chen BY, Wang J, Fong KM, Clark PM, van Dam RM. Rapid, efficient, and economical synthesis of PET tracers in a droplet microreactor: application to O-(2-[18F]fluoroethyl)-L-tyrosine ([18F]FET).. EJNMMI radiopharmacy and chemistry, 2019.
14. Wang L, Smith BA, Balanis NG, Tsai BL, Nguyen K, Cheng MW, Obusan MB, Esedebe FN, Patel SJ, Zhang H, Clark PM, Sisk AE, Said JW, Huang J, Graeber TG, Witte ON, Chin AI, Park JW. A genetically defined disease model reveals that urothelial cells can initiate divergent bladder cancer phenotypes.. Proceedings of the National Academy of Sciences of the United States of America, 2019.
15. Ghezzi C, Wong A, Chen BY, Ribalet B, Damoiseaux R, Clark PM. A high-throughput screen identifies that CDK7 activates glucose consumption in lung cancer cells.. Nature communications, 2019.
16. Chen BY, Ghezzi C, Villegas B, Quon A, Radu CG, Witte ON, Clark PM. 18F-FAC PET Visualizes Brain-Infiltrating Leukocytes in a Mouse Model of Multiple Sclerosis.. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2019.
17. Hordeaux J, Yuan Y, Clark PM, Wang Q, Martino RA, Sims JJ, Bell P, Raymond A, Stanford WL, Wilson JM. The GPI-Linked Protein LY6A Drives AAV-PHP.B Transport across the Blood-Brain Barrier.. Molecular therapy : the journal of the American Society of Gene Therapy, 2019.
18. Shin BC, Cepeda C, Estrada-Sánchez AM, Levine MS, Hodaei L, Dai Y, Jung J, Ganguly A, Clark P, Devaskar SU. Neural Deletion of Glucose Transporter Isoform 3 Creates Distinct Postnatal and Adult Neurobehavioral Phenotypes.. The Journal of neuroscience : the official journal of the Society for Neuroscience, 2018.
19. Shieh M, Chitnis N, Clark P, Johnson FB, Kamoun M, Monos D. Computational assessment of miRNA binding to low and high expression HLA-DPB1 allelic sequences.. Human immunology, 2018.
20. Wang L, Smith J, Breton C, Clark P, Zhang J, Ying L, Che Y, Lape J, Bell P, Calcedo R, Buza EL, Saveliev A, Bartsevich VV, He Z, White J, Li M, Jantz D, Wilson JM. Meganuclease targeting of PCSK9 in macaque liver leads to stable reduction in serum cholesterol.. Nature biotechnology, 2018.
21. Salas JR, Chen BY, Wong A, Cheng D, Van Arnam JS, Witte ON, Clark PM. 18F-FAC PET Selectively Images Liver-Infiltrating CD4 and CD8 T Cells in a Mouse Model of Autoimmune Hepatitis.. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2018.
22. Salas JR, Chen BY, Wong A, Duarte S, Angarita SAK, Lipshutz GS, Witte ON, Clark PM. Noninvasive Imaging of Drug-Induced Liver Injury with 18F-DFA PET.. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2018.
23. Nakano H, Minami I, Braas D, Pappoe H, Wu X, Sagadevan A, Vergnes L, Fu K, Morselli M, Dunham C, Ding X, Stieg AZ, Gimzewski JK, Pellegrini M, Clark PM, Reue K, Lusis AJ, Ribalet B, Kurdistani SK, Christofk H, Nakatsuji N, Nakano A. Glucose inhibits cardiac muscle maturation through nucleotide biosynthesis.. eLife, 2017.
24. Mai WX, Gosa L, Daniels VW, Ta L, Tsang JE, Higgins B, Gilmore WB, Bayley NA, Harati MD, Lee JT, Yong WH, Kornblum HI, Bensinger SJ, Mischel PS, Rao PN, Clark PM, Cloughesy TF, Letai A, Nathanson DA. Cytoplasmic p53 couples oncogene-driven glucose metabolism to apoptosis and is a therapeutic target in glioblastoma.. Nature medicine, 2017.
25. Rigoutsos I, Lee SK, Nam SY, Anfossi S, Pasculli B, Pichler M, Jing Y, Rodriguez-Aguayo C, Telonis AG, Rossi S, Ivan C, Catela Ivkovic T, Fabris L, Clark PM, Ling H, Shimizu M, Redis RS, Shah MY, Zhang X, Okugawa Y, Jung EJ, Tsirigos A, Huang L, Ferdin J, Gafà R, Spizzo R, Nicoloso MS, Paranjape AN, Shariati M, Tiron A, Yeh JJ, Teruel-Montoya R, Xiao L, Melo SA, Menter D, Jiang ZQ, Flores ER, Negrini M, Goel A, Bar-Eli M, Mani SA, Liu CG, Lopez-Berestein G, Berindan-Neagoe I, Esteller M, Kopetz S, Lanza G, Calin GA. N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration.. Genome biology, 2017.
26. Chitnis N, Clark PM, Kamoun M, Stolle C, Brad Johnson F, Monos DS. An Expanded Role for HLA Genes: HLA-B Encodes a microRNA that Regulates IgA and Other Immune Response Transcripts.. Frontiers in immunology, 2017.
27. Clark PM, Ebiana VA, Gosa L, Cloughesy TF, Nathanson DA. Harnessing Preclinical Molecular Imaging to Inform Advances in Personalized Cancer Medicine.. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2017.
28. Dai Y, Zhao Y, Tomi M, Shin BC, Thamotharan S, Mazarati A, Sankar R, Wang EA, Cepeda C, Levine MS, Zhang J, Frew A, Alger JR, Clark PM, Sondhi M, Kositamongkol S, Leibovitch L, Devaskar SU. Sex-Specific Life Course Changes in the Neuro-Metabolic Phenotype of Glut3 Null Heterozygous Mice: Ketogenic Diet Ameliorates Electroencephalographic Seizures and Improves Sociability.. Endocrinology, 2017.
29. Clark PM, Duke JL, Ferriola D, Bravo-Egana V, Vago T, Hassan A, Papazoglou A, Monos D. Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization.. Clinical chemistry, 2016.
30. Mogilyansky E, Clark P, Quann K, Zhou H, Londin E, Jing Y, Rigoutsos I. Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b.. Frontiers in genetics, 2016.
31. Dapprich J, Ferriola D, Mackiewicz K, Clark PM, Rappaport E, D'Arcy M, Sasson A, Gai X, Schug J, Kaestner KH, Monos D. The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity.. BMC genomics, 2016.
32. Warrick JI, Raman JD, Kaag M, Bruggeman T, Cates J, Clark P, DeGraff DJ. Enhancer of zeste homolog 2 (EZH2) expression in bladder cancer.. Urologic oncology, 2016.
33. Clark PM, Mai WX, Cloughesy TF, Nathanson DA. Emerging Approaches for Targeting Metabolic Vulnerabilities in Malignant Glioma.. Current neurology and neuroscience reports, 2016.
34. Faltermeier CM, Drake JM, Clark PM, Smith BA, Zong Y, Volpe C, Mathis C, Morrissey C, Castor B, Huang J, Witte ON. Functional screen identifies kinases driving prostate cancer visceral and bone metastasis.. Proceedings of the National Academy of Sciences of the United States of America, 2015.
35. Evdokimov NM, Clark PM, Flores G, Chai T, Faull KF, Phelps ME, Witte ON, Jung ME. Development of 2-Deoxy-2-[(18)F]fluororibose for Positron Emission Tomography Imaging Liver Function in Vivo.. Journal of medicinal chemistry, 2015.
36. Londin E, Loher P, Telonis AG, Quann K, Clark P, Jing Y, Hatzimichael E, Kirino Y, Honda S, Lally M, Ramratnam B, Comstock CE, Knudsen KE, Gomella L, Spaeth GL, Hark L, Katz LJ, Witkiewicz A, Rostami A, Jimenez SA, Hollingsworth MA, Yeh JJ, Shaw CA, McKenzie SE, Bray P, Nelson PT, Zupo S, Van Roosbroeck K, Keating MJ, Calin GA, Yeo C, Jimbo M, Cozzitorto J, Brody JR, Delgrosso K, Mattick JS, Fortina P, Rigoutsos I. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.. Proceedings of the National Academy of Sciences of the United States of America, 2015.
37. Park JY, Clark P, Londin E, Sponziello M, Kricka LJ, Fortina P. Clinical exome performance for reporting secondary genetic findings.. Clinical chemistry, 2014.
38. Park JY, Kricka LJ, Clark P, Londin E, Fortina P. Clinical genomics: when whole genome sequencing is like a whole-body CT scan.. Clinical chemistry, 2014.
39. Clark PM, Loher P, Quann K, Brody J, Londin ER, Rigoutsos I. Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types.. Scientific reports, 2014.
40. Clark PM, Flores G, Evdokimov NM, McCracken MN, Chai T, Nair-Gill E, O'Mahony F, Beaven SW, Faull KF, Phelps ME, Jung ME, Witte ON. Positron emission tomography probe demonstrates a striking concentration of ribose salvage in the liver.. Proceedings of the National Academy of Sciences of the United States of America, 2014.
41. Londin ER, Clark P, Sponziello M, Kricka LJ, Fortina P, Park JY. Performance of exome sequencing for pharmacogenomics.. Personalized medicine, 2014.
42. Ramakrishnan P, Clark PM, Mason DE, Peters EC, Hsieh-Wilson LC, Baltimore D. Activation of the transcriptional function of the NF-κB protein c-Rel by O-GlcNAc glycosylation.. Science signaling, 2013.
43. Clark PM, Rexach JE, Hsieh-Wilson LC. Visualization of O-GlcNAc glycosylation stoichiometry and dynamics using resolvable poly(ethylene glycol) mass tags.. Current protocols in chemical biology, 2013.
44. Yi W, Clark PM, Mason DE, Keenan MC, Hill C, Goddard WA, Peters EC, Driggers EM, Hsieh-Wilson LC. Phosphofructokinase 1 glycosylation regulates cell growth and metabolism.. Science (New York, N.Y.), 2012.
45. Xia Z, Clark P, Huynh T, Loher P, Zhao Y, Chen HW, Ren P, Rigoutsos I, Zhou R. Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.. Scientific reports, 2012.
46. Dillon B, Naidoo B, Knight H, Clark P. NICE guidance on erlotinib for first-line treatment of EGFR-TK mutation-positive advanced or metastatic non-small-cell lung cancer.. The Lancet. Oncology, 2012.
47. Clark PM, Dawany N, Dampier W, Byers SW, Pestell RG, Tozeren A. Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases.. Inflammatory bowel diseases, 2012.
48. Rexach JE, Clark PM, Mason DE, Neve RL, Peters EC, Hsieh-Wilson LC. Dynamic O-GlcNAc modification regulates CREB-mediated gene expression and memory formation.. Nature chemical biology, 2012.
49. Rinaldi F, George E, Clark P. NICE guidance on erlotinib for the maintenance treatment of non-small-cell lung cancer.. The Lancet. Oncology, 2011.
50. Rogers CJ, Clark PM, Tully SE, Abrol R, Garcia KC, Goddard WA, Hsieh-Wilson LC. Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches.. Proceedings of the National Academy of Sciences of the United States of America, 2011.
51. Fitzpatrick JC, Clark PM, Capaldi FM. Effect of decellularization protocol on the mechanical behavior of porcine descending aorta.. International journal of biomaterials, 2010.
52. Elledge HM, Kazmierczak P, Clark P, Joseph JS, Kolatkar A, Kuhn P, Müller U. Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
53. Lund L, Jacobsen J, Clark P, Borre M, Nørgaard M, Northern Danish Cancer Quality Assessment Group. Impact of comorbidity on survival of invasive bladder cancer patients, 1996-2007: a Danish population-based cohort study.. Urology, 2009.
54. Clark PM, Dweck JF, Mason DE, Hart CR, Buck SB, Peters EC, Agnew BJ, Hsieh-Wilson LC. Direct in-gel fluorescence detection and cellular imaging of O-GlcNAc-modified proteins.. Journal of the American Chemical Society, 2008.
55. Rexach JE, Clark PM, Hsieh-Wilson LC. Chemical approaches to understanding O-GlcNAc glycosylation in the brain.. Nature chemical biology, 2008.
56. Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics.. Nature chemical biology, 2007.
57. Gama CI, Tully SE, Sotogaku N, Clark PM, Rawat M, Vaidehi N, Goddard WA, Nishi A, Hsieh-Wilson LC. Sulfation patterns of glycosaminoglycans encode molecular recognition and activity.. Nature chemical biology, 2006.
58. Stein JP, Clark P, Miranda G, Cai J, Groshen S, Skinner DG. Urethral tumor recurrence following cystectomy and urinary diversion: clinical and pathological characteristics in 768 male patients.. The Journal of urology, 2005.