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Piotr Sliz, Ph.D.

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Mentoring
Conformational Dynamics of Antibodies via In Silico Simulations
Summer, 05/23/14 - 08/25/14

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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 Jul 02; 48(W1):W218-W229. PMID: 32427338.
    Citations:    
  2. 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. PMID: 32060122.
    Citations:    
  3. 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. PMID: 30328274.
    Citations:    Fields:    
  4. 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. PMID: 30232453.
    Citations:    Fields:    
  5. 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. PMID: 29874593.
    Citations:    Fields:    
  6. 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). PMID: 29244735.
    Citations:    
  7. 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. PMID: 28945502.
    Citations: 1     Fields:    Translation:HumansCells
  8. 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. PMID: 28937848.
    Citations:    Fields:    
  9. 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. PMID: 28297670.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  10. 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. PMID: 28223502.
    Citations:    Fields:    Translation:Cells
  11. 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. PMID: 28089446.
    Citations: 1     Fields:    Translation:HumansCells
  12. 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. PMID: 27846380.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  13. 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. PMID: 27862010.
    Citations:    Fields:    Translation:HumansAnimalsCells
  14. 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. PMID: 27320042.
    Citations: 30     Fields:    Translation:HumansAnimalsCells
  15. 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. PMID: 26947396.
    Citations: 24     Fields:    
  16. 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. PMID: 26583201.
    Citations: 2     Fields:    Translation:Cells
  17. 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. PMID: 26255770.
    Citations: 19     Fields:    Translation:HumansAnimalsCells
  18. 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. PMID: 25955101.
    Citations: 2     Fields:    
  19. 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. PMID: 25387399.
    Citations: 3     Fields:    
  20. 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. PMID: 25223788.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  21. 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. PMID: 25111632.
    Citations: 5     Fields:    Translation:HumansAnimals
  22. Morin A, Sliz P. Structural biology computing: Lessons for the biomedical research sciences. Biopolymers. 2013 Nov; 99(11):809-16. PMID: 23828134.
    Citations: 1     Fields:    Translation:Humans
  23. 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. PMID: 24040512.
    Citations: 123     Fields:    Translation:Humans
  24. Sliz P, Morin A. Optimizing peer review of software code. Science. 2013 Jul 19; 341(6143):236-7. PMID: 23869002.
    Citations:    Fields:    Translation:Humans
  25. Morin A, Urban J, Sliz P. A quick guide to software licensing for the scientist-programmer. PLoS Comput Biol. 2012; 8(7):e1002598. PMID: 22844236.
    Citations: 7     Fields:    
  26. 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. PMID: 22499926.
    Citations: 18     Fields:    
  27. 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. PMID: 22514186.
    Citations: 2     Fields:    
  28. 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. PMID: 22349228.
    Citations: 5     Fields:    
  29. 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. PMID: 22325781.
    Citations: 23     Fields:    Translation:HumansCells
  30. 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. PMID: 22082911.
    Citations: 20     Fields:    Translation:HumansCells
  31. 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. PMID: 22078496.
    Citations: 118     Fields:    Translation:AnimalsCells
  32. 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. PMID: 21240259.
    Citations: 103     Fields:    Translation:HumansCells
  33. 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. PMID: 21098306.
    Citations: 15     Fields:    Translation:AnimalsCells
  34. 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. PMID: 20496948.
    Citations: 6     Fields:    Translation:Cells
  35. 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. PMID: 18842591.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  36. 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. PMID: 18642800.
    Citations: 15     Fields:    Translation:Cells
  37. 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. PMID: 18550544.
    Citations: 169     Fields:    Translation:HumansCells
  38. 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. PMID: 17702946.
    Citations: 142     Fields:    Translation:Cells
  39. 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. PMID: 17360321.
    Citations: 32     Fields:    Translation:AnimalsCells
  40. 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. PMID: 17284587.
    Citations: 57     Fields:    Translation:HumansCells
  41. 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. PMID: 16754879.
    Citations: 23     Fields:    Translation:HumansCells
  42. 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. PMID: 16530044.
    Citations: 154     Fields:    Translation:HumansAnimalsCells
  43. 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. PMID: 16319884.
    Citations: 209     Fields:    Translation:AnimalsCells
  44. 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. PMID: 15502812.
    Citations: 150     Fields:    Translation:AnimalsCells
  45. 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. PMID: 15141214.
    Citations: 115     Fields:    Translation:AnimalsCells
  46. 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. PMID: 12949491.
    Citations: 18     Fields:    Translation:HumansCells
  47. 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. PMID: 12517336.
    Citations: 17     Fields:    
  48. 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. PMID: 11544315.
    Citations: 21     Fields:    Translation:HumansCells
  49. Piotr Sliz. Structure, Function and Interactions of Enzyme IIA from the Phosphoenolpyruvate:lactose Phosphotransferase. 2000.
  50. 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. PMID: 9261069.
    Citations: 12     Fields:    Translation:Cells
  51. 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. PMID: 15299586.
    Citations:    Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.