PUBLICATIONS

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  1. Zhang J, Cai Y, Xiao T, Lu J, Peng H, Sterling SM, Walsh RM, Rits-Volloch S, Sliz P, Chen B. Structural impact on SARS-CoV-2 spike protein by D614G substitution. bioRxiv. 2020 Oct 13. View abstract
  2. Brat GA, Weber GM, Gehlenborg N, Avillach P, Palmer NP, Chiovato L, Cimino J, Waitman LR, Omenn GS, Malovini A, Moore JH, Beaulieu-Jones BK, Tibollo V, Murphy SN, Yi SL, Keller MS, Bellazzi R, Hanauer DA, Serret-Larmande A, Gutierrez-Sacristan A, Holmes JJ, Bell DS, Mandl KD, Follett RW, Klann JG, Murad DA, Scudeller L, Bucalo M, Kirchoff K, Craig J, Obeid J, Jouhet V, Griffier R, Cossin S, Moal B, Patel LP, Bellasi A, Prokosch HU, Kraska D, Sliz P, Tan ALM, Ngiam KY, Zambelli A, Mowery DL, Schiver E, Devkota B, Bradford RL, Daniar M, Daniel C, Benoit V, Bey R, Paris N, Serre P, Orlova N, Dubiel J, Hilka M, Jannot AS, Breant S, Leblanc J, Griffon N, Burgun A, Bernaux M, Sandrin A, Salamanca E, Cormont S, Ganslandt T, Gradinger T, Champ J, Boeker M, Martel P, Esteve L, Gramfort A, Grisel O, Leprovost D, Moreau T, Varoquaux G, Vie JJ, Wassermann D, Mensch A, Caucheteux C, Haverkamp C, Lemaitre G, Bosari S, Krantz ID, South A, Cai T, Kohane IS. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. NPJ Digit Med. 2020; 3:109. View abstract
  3. Greenfield DA, Schmidt HR, Skiba MA, Mandler MD, Anderson JR, Sliz P, Kruse AC. Virtual Screening for Ligand Discovery at the s1 Receptor. ACS Med Chem Lett. 2020 Aug 13; 11(8):1555-1561. View abstract
  4. Rockowitz S, LeCompte N, Carmack M, Quitadamo A, Wang L, Park M, Knight D, Sexton E, Smith L, Sheidley B, Field M, Holm IA, Brownstein CA, Agrawal PB, Kornetsky S, Poduri A, Snapper SB, Beggs AH, Yu TW, Williams DA, Sliz P. Children's rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genom Med. 2020; 5:29. View abstract
  5. Liu Q, Shvarts T, Sliz P, Gregory RI. RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. Nucleic Acids Res. 2020 07 02; 48(W1):W218-W229. View abstract
  6. Yu C, Wang L, Rowe RG, Han A, Ji W, McMahon C, Baier AS, Huang YC, Marion W, Pearson DS, Kruse AC, Daley GQ, Wu H, Sliz P. A nanobody targeting the LIN28:let-7 interaction fragment of TUT4 blocks uridylation of let-7. Proc Natl Acad Sci U S A. 2020 03 03; 117(9):4653-4663. View abstract
  7. Eubanks AL, Perkins MM, Sylvester K, Ganley JG, Posfai D, Sanschargrin PC, Hong J, Sliz P, Derbyshire ER. In silico Screening and Evaluation of Plasmodium falciparum Protein Kinase 5 (PK5) Inhibitors. ChemMedChem. 2018 12 06; 13(23):2479-2483. View abstract
  8. Choe J, Lin S, Zhang W, Liu Q, Wang L, Ramirez-Moya J, Du P, Kim W, Tang S, Sliz P, Santisteban P, George RE, Richards WG, Wong KK, Locker N, Slack FJ, Gregory RI. mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature. 2018 09; 561(7724):556-560. View abstract
  9. Wang L, Rowe RG, Jaimes A, Yu C, Nam Y, Pearson DS, Zhang J, Xie X, Marion W, Heffron GJ, Daley GQ, Sliz P. Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep. 2018 06 05; 23(10):3091-3101. View abstract
  10. Bourgeois FT, Avillach P, Kong SW, Heinz MM, Tran TA, Chakrabarty R, Bickel J, Sliz P, Borglund EM, Kornetsky S, Mandl KD. Development of the Precision Link Biobank at Boston Children's Hospital: Challenges and Opportunities. J Pers Med. 2017 Dec 15; 7(4). View abstract
  11. Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P. Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biol. 2017 12 02; 14(12):1756-1765. View abstract
  12. Wang L, Yang Q, Jaimes A, Wang T, Strobelt H, Chen J, Sliz P. MightyScreen: An Open-Source Visualization Application for Screening Data Analysis. SLAS Discov. 2018 02; 23(2):218-223. View abstract
  13. Wang L, Nam Y, Lee AK, Yu C, Roth K, Chen C, Ransey EM, Sliz P. LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation. Cell Rep. 2017 03 14; 18(11):2664-2675. View abstract
  14. Kulczyk AW, Moeller A, Meyer P, Sliz P, Richardson CC. Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis. Proc Natl Acad Sci U S A. 2017 03 07; 114(10):E1848-E1856. View abstract
  15. Durzynska I, Xu X, Adelmant G, Ficarro SB, Marto JA, Sliz P, Uljon S, Blacklow SC. STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1. Structure. 2017 02 07; 25(2):287-294. View abstract
  16. Bailey E, Cui Y, Casey A, Stoler JM, Ai X, Ma D, Handin R, Sliz P, Vargas SO, El-Chemaly SY. Pulmonary Vasculopathy Associated with FIGF Gene Mutation. Am J Pathol. 2017 Jan; 187(1):25-32. View abstract
  17. McKinney B, Meyer PA, Crosas M, Sliz P. Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets. Ann N Y Acad Sci. 2017 01; 1387(1):95-104. View abstract
  18. Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. 2016 07 07; 19(1):66-80. View abstract
  19. Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 07; 7:10882. View abstract
  20. Lelyveld VS, Björkbom A, Ransey EM, Sliz P, Szostak JW. Pinpointing RNA-Protein Cross-Links with Site-Specific Stable Isotope-Labeled Oligonucleotides. J Am Chem Soc. 2015 Dec 16; 137(49):15378-81. View abstract
  21. Du P, Wang L, Sliz P, Gregory RI. A Biogenesis Step Upstream of Microprocessor Controls miR-17~92 Expression. Cell. 2015 Aug 13; 162(4):885-99. View abstract
  22. Socias SM, Morin A, Timony MA, Sliz P. AppCiter: A Web Application for Increasing Rates and Accuracy of Scientific Software Citation. Structure. 2015 May 05; 23(5):807-808. View abstract
  23. Balch C, Arias-Pulido H, Banerjee S, Lancaster AK, Clark KB, Perilstein M, Hawkins B, Rhodes J, Sliz P, Wilkins J, Chittenden TW. Science and technology consortia in U.S. biomedical research: a paradigm shift in response to unsustainable academic growth. Bioessays. 2015 Feb; 37(2):119-22. View abstract
  24. Thornton JE, Du P, Jing L, Sjekloca L, Lin S, Grossi E, Sliz P, Zon LI, Gregory RI. Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4). Nucleic Acids Res. 2014 Oct; 42(18):11777-91. View abstract
  25. Derbyshire ER, Zuzarte-Luís V, Magalhães AD, Kato N, Sanschagrin PC, Wang J, Zhou W, Miduturu CV, Mazitschek R, Sliz P, Mota MM, Gray NS, Clardy J. Chemical interrogation of the malaria kinome. Chembiochem. 2014 Sep 05; 15(13):1920-30. View abstract
  26. Morin A, Sliz P. Structural biology computing: Lessons for the biomedical research sciences. Biopolymers. 2013 Nov; 99(11):809-16. View abstract
  27. Morin A, Eisenbraun B, Key J, Sanschagrin PC, Timony MA, Ottaviano M, Sliz P. Collaboration gets the most out of software. Elife. 2013 Sep 10; 2:e01456. View abstract
  28. Sliz P, Morin A. Optimizing peer review of software code. Science. 2013 Jul 19; 341(6143):236-7. View abstract
  29. Morin A, Urban J, Sliz P. A quick guide to software licensing for the scientist-programmer. PLoS Comput Biol. 2012; 8(7):e1002598. View abstract
  30. Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P. Research priorities. Shining light into black boxes. Science. 2012 Apr 13; 336(6078):159-60. View abstract
  31. Stokes-Rees I, Levesque I, Murphy FV, Yang W, Deacon A, Sliz P. Adapting federated cyberinfrastructure for shared data collection facilities in structural biology. J Synchrotron Radiat. 2012 May; 19(Pt 3):462-7. View abstract
  32. O'Donovan DJ, Stokes-Rees I, Nam Y, Blacklow SC, Schröder GF, Brunger AT, Sliz P. A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallogr D Biol Crystallogr. 2012 Mar; 68(Pt 3):261-7. View abstract
  33. Choi SH, Wales TE, Nam Y, O'Donovan DJ, Sliz P, Engen JR, Blacklow SC. Conformational locking upon cooperative assembly of notch transcription complexes. Structure. 2012 Feb 08; 20(2):340-9. View abstract
  34. Jiang J, Lazarus MB, Pasquina L, Sliz P, Walker S. A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase. Nat Chem Biol. 2011 Nov 13; 8(1):72-7. View abstract
  35. Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P. Molecular basis for interaction of let-7 microRNAs with Lin28. Cell. 2011 Nov 23; 147(5):1080-91. View abstract
  36. Lazarus MB, Nam Y, Jiang J, Sliz P, Walker S. Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature. 2011 Jan 27; 469(7331):564-7. View abstract
  37. Stokes-Rees I, Sliz P. Protein structure determination by exhaustive search of Protein Data Bank derived databases. Proc Natl Acad Sci U S A. 2010 Dec 14; 107(50):21476-81. View abstract
  38. Fuse S, Tsukamoto H, Yuan Y, Wang TS, Zhang Y, Bolla M, Walker S, Sliz P, Kahne D. Functional and structural analysis of a key region of the cell wall inhibitor moenomycin. ACS Chem Biol. 2010 Jul 16; 5(7):701-11. View abstract
  39. Patel V, Booker M, Kramer M, Ross L, Celatka CA, Kennedy LM, Dvorin JD, Duraisingh MT, Sliz P, Wirth DF, Clardy J. Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biol Chem. 2008 Dec 12; 283(50):35078-85. View abstract
  40. Yuan Y, Fuse S, Ostash B, Sliz P, Kahne D, Walker S. Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design. ACS Chem Biol. 2008 Jul 18; 3(7):429-36. View abstract
  41. Piskounova E, Viswanathan SR, Janas M, LaPierre RJ, Daley GQ, Sliz P, Gregory RI. Determinants of microRNA processing inhibition by the developmentally regulated RNA-binding protein Lin28. J Biol Chem. 2008 Aug 01; 283(31):21310-4. View abstract
  42. Kim S, Malinverni JC, Sliz P, Silhavy TJ, Harrison SC, Kahne D. Structure and function of an essential component of the outer membrane protein assembly machine. Science. 2007 Aug 17; 317(5840):961-4. View abstract
  43. Yuan Y, Barrett D, Zhang Y, Kahne D, Sliz P, Walker S. Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis. Proc Natl Acad Sci U S A. 2007 Mar 27; 104(13):5348-53. View abstract
  44. Nam Y, Sliz P, Pear WS, Aster JC, Blacklow SC. Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci U S A. 2007 Feb 13; 104(7):2103-8. View abstract
  45. Azam M, Nardi V, Shakespeare WC, Metcalf CA, Bohacek RS, Wang Y, Sundaramoorthi R, Sliz P, Veach DR, Bornmann WG, Clarkson B, Dalgarno DC, Sawyer TK, Daley GQ. Activity of dual SRC-ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance. Proc Natl Acad Sci U S A. 2006 Jun 13; 103(24):9244-9. View abstract
  46. Nam Y, Sliz P, Song L, Aster JC, Blacklow SC. Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes. Cell. 2006 Mar 10; 124(5):973-83. View abstract
  47. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature. 2005 Dec 01; 438(7068):633-8. View abstract
  48. Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, Kirchhausen T, Walz T. Molecular model for a complete clathrin lattice from electron cryomicroscopy. Nature. 2004 Dec 02; 432(7017):573-9. View abstract
  49. Gonen T, Sliz P, Kistler J, Cheng Y, Walz T. Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature. 2004 May 13; 429(6988):193-7. View abstract
  50. Jin L, Sliz P, Chen L, Macián F, Rao A, Hogan PG, Harrison SC. An asymmetric NFAT1 dimer on a pseudo-palindromic kappa B-like DNA site. Nat Struct Biol. 2003 Oct; 10(10):807-11. View abstract
  51. Sliz P, Harrison SC, Rosenbaum G. How does radiation damage in protein crystals depend on X-ray dose? Structure. 2003 Jan; 11(1):13-9. View abstract
  52. Sliz P, Michielin O, Cerottini JC, Luescher I, Romero P, Karplus M, Wiley DC. Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes. J Immunol. 2001 Sep 15; 167(6):3276-84. View abstract
  53. Piotr Sliz. Structure, Function and Interactions of Enzyme IIA from the Phosphoenolpyruvate:lactose Phosphotransferase. 2000. View abstract
  54. Sliz P, Engelmann R, Hengstenberg W, Pai EF. The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system. Structure. 1997 Jun 15; 5(6):775-88. View abstract
  55. Sliz P, Schörter KH, De Vos WM, Pai EF. Crystallization and preliminary structural studies of lactose-specific enzyme IIA from Lactococcus lactis. Acta Crystallogr D Biol Crystallogr. 1996 Nov 01; 52(Pt 6):1199-201. View abstract