Publications

  1. Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G. BIMA V3: an aligner customized for mate pair library sequencing. Bioinformatics. 2014 Feb 26.
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  2. Ansell SM, Hodge LS, Secreto FJ, Manske M, Braggio E, Price-Troska T, Ziesmer S, Li Y, Johnson SH, Hart SN, Kocher JP, Vasmatzis G, Chanan-Kahn A, Gertz M, Fonseca R, Dogan A, Cerhan JR, Novak AJ. Activation of TAK1 by MYD88 L265P drives malignant B-cell Growth in non-Hodgkin lymphoma. Blood Cancer J. 2014; 4:e183. Epub 2014 Feb 14.
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  3. Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, Eberhardt NL, Neuhauser C, Vasmatzis G, Grebe SK. A simple method for gene phasing using mate pair sequencing. BMC Med Genet. 2014; 15:19. Epub 2014 Feb 06.
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  4. Gao G, Johnson SH, Kasperbauer JL, Eckloff BW, Tombers NM, Vasmatzis G, Smith DI. Mate pair sequencing of oropharyngeal squamous cell carcinomas reveals that HPV integration occurs much less frequently than in cervical cancer. J Clin Virol. 2014 Mar; 59(3):195-200. Epub 2013 Dec 28.
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  5. Gomez CR, Kosari F, Munz JM, Schreiber CA, Knutson GJ, Ida CM, El Khattouti A, Karnes RJ, Cheville JC, Vasmatzis G, Vuk-Pavlovic S. Prognostic value of discs large homolog 7 transcript levels in prostate cancer. PLoS One. 2013; 8(12):e82833. Epub 2013 Dec 09.
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  6. Kosari F, Ida CM, Aubry MC, Yang L, Kovtun IV, Klein JL, Li Y, Erdogan S, Tomaszek SC, Murphy SJ, Bolette LC, Kolbert CP, Yang P, Wigle DA, Vasmatzis G. ASCL1 and RET expression defines a clinically relevant subgroup of lung adenocarcinoma characterized by neuroendocrine differentiation. Oncogene. 2013 Sep 16. [Epub ahead of print]
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  7. Feldman AL, Vasmatzis G, Asmann YW, Davila J, Middha S, Eckloff BW, Johnson SH, Porcher JC, Ansell SM, Caride A. Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma. Genes Chromosomes Cancer. 2013 Nov; 52(11):1097-102. Epub 2013 Sep 02.
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  8. Murphy SJ, Hart SN, Lima JF, Kipp BR, Klebig M, Winters JL, Szabo C, Zhang L, Eckloff BW, Petersen GM, Scherer SE, Gibbs RA, McWilliams RR, Vasmatzis G, Couch FJ. Genetic alterations associated with progression from pancreatic intraepithelial neoplasia to invasive pancreatic tumor. Gastroenterology. 2013 Nov; 145(5):1098-1109.e1. Epub 2013 Aug 02.
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  9. Lasho T, Johnson SH, Smith DI, Crispino JD, Pardanani A, Vasmatzis G, Tefferi A. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing. Am J Hematol. 2013 Sep; 88(9):741-6. Epub 2013 Aug 01.
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  10. Kovtun IV, Cheville JC, Murphy SJ, Johnson SH, Zarei S, Kosari F, Sukov WR, Karnes RJ, Vasmatzis G. Lineage relationship of Gleason patterns in Gleason score 7 prostate cancer. Cancer Res. 2013 Jun 1; 73(11):3275-84. Epub 2013 May 21.
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  11. Shim J, Humphreys GI, Venkatesan BM, Munz JM, Zou X, Sathe C, Schulten K, Kosari F, Nardulli AM, Vasmatzis G, Bashir R. Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep. 2013; 3:1389.
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  12. Zhang Y, Foreman O, Wigle DA, Kosari F, Vasmatzis G, Salisbury JL, van Deursen J, Galardy PJ. USP44 regulates centrosome positioning to prevent aneuploidy and suppress tumorigenesis. J Clin Invest. 2012 Dec 3; 122(12):4362-74. Epub 2012 Nov 26.
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  13. Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, Feldman AL, Eckloff BW, Karnes RJ, Vasmatzis G. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer. DNA Res. 2012 Oct; 19(5):395-406. Epub 2012 Sep 18.
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  14. Vasmatzis G, Johnson SH, Knudson RA, Ketterling RP, Braggio E, Fonseca R, Viswanatha DS, Law ME, Kip NS, Ozsan N, Grebe SK, Frederick LA, Eckloff BW, Thompson EA, Kadin ME, Milosevic D, Porcher JC, Asmann YW, Smith DI, Kovtun IV, Ansell SM, Dogan A, Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas. Blood. 2012 Sep 13; 120(11):2280-9. Epub 2012 Aug 01.
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  15. Kosari F, Cheville JC, Ida CM, Karnes RJ, Leontovich AA, Sebo TJ, Erdogan S, Rodriguez E, Murphy SJ, Vasmatzis G. Shared gene expression alterations in prostate cancer and histologically benign prostate from patients with prostate cancer. Am J Pathol. 2012 Jul; 181(1):34-42. Epub 2012 May 26.
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  16. Karnes RJ, Cheville JC, Ida CM, Sebo TJ, Nair AA, Tang H, Munz JM, Kosari F, Vasmatzis G. The ability of biomarkers to predict systemic progression in men with high-risk prostate cancer treated surgically is dependent on ERG status. Cancer Res. 2010 Nov 15; 70(22):8994-9002. Epub 2010 Nov 09.
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  17. Feldman AL, Dogan A, Smith DI, Law ME, Ansell SM, Johnson SH, Porcher JC, Ozsan N, Wieben ED, Eckloff BW, Vasmatzis G. Discovery of recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas by massively parallel genomic sequencing. Blood. 2011 Jan 20; 117(3):915-9. Epub 2010 Oct 28.
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  18. Li Y, Sheu CC, Ye Y, de Andrade M, Wang L, Chang SC, Aubry MC, Aakre JA, Allen MS, Chen F, Cunningham JM, Deschamps C, Jiang R, Lin J, Marks RS, Pankratz VS, Su L, Li Y, Sun Z, Tang H, Vasmatzis G, Harris CC, Spitz MR, Jen J, Wang R, Zhang ZF, Christiani Genetic variants and risk of lung cancer in never smokers: a genome-wide association study. Lancet Oncol. 2010 Apr; 11(4):321-30. Epub 2010 Mar 19.
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  19. Shin S, Kim TD, Jin F, van Deursen JM, Dehm SM, Tindall DJ, Grande JP, Munz JM, Vasmatzis G, Janknecht R. Induction of prostatic intraepithelial neoplasia and modulation of androgen receptor by ETS variant 1/ETS-related protein 81. Cancer Res. 2009 Oct 15; 69(20):8102-10. Epub 2009 Sep 29
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  20. Boland JM, Erdogan S, Vasmatzis G, Yang P, Tillmans LS, Johnson MR, Wang X, Peterson LM, Halling KC, Oliveira AM, Aubry MC, Yi ES. Anaplastic lymphoma kinase immunoreactivity correlates with ALK gene rearrangement and transcriptional up-regulation in non-small cell lung carcinomas. Hum Pathol. 2009 Aug; 40(8):1152-8. Epub 2009 Apr 22.
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  21. Savci-Heijink CD, Kosari F, Aubry MC, Caron BL, Sun Z, Yang P, Vasmatzis G. The role of desmoglein-3 in the diagnosis of squamous cell carcinoma of the lung. Am J Pathol. 2009 May; 174(5):1629-37. Epub 2009 Mar 26.
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  22. Klee EW, Erdogan S, Tillmans L, Kosari F, Sun Z, Wigle DA, Yang P, Aubry MC, Vasmatzis G. Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-sampling. BMC Med Genomics. 2009; 2:13. Epub 2009 Mar 09.
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  23. Cheville JC, Karnes RJ, Therneau TM, Kosari F, Munz JM, Tillmans L, Basal E, Rangel LJ, Bergstralh E, Kovtun IV, Savci-Heijink CD, Klee EW, Vasmatzis G. Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy. J Clin Oncol. 2008 Aug 20; 26(24):3930-6.
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  24. Kosari F, Munz JM, Savci-Heijink CD, Spiro C, Klee EW, Kube DM, Tillmans L, Slezak J, Karnes RJ, Cheville JC, Vasmatzis G. Identification of prognostic biomarkers for prostate cancer. Clin Cancer Res. 2008 Mar 15; 14(6):1734-43.
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  25. Vasmatzis G, Klee EW, Kube DM, Therneau TM, Kosari F. Quantitating tissue specificity of human genes to facilitate biomarker discovery. Bioinformatics. 2007 Jun 1; 23(11):1348-55. Epub 2007 Mar 23.
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  26. Kube DM, Savci-Heijink CD, Lamblin AF, Kosari F, Vasmatzis G, Cheville JC, Connelly DP, Klee GG. Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer. BMC Mol Biol. 2007; 8:25. Epub 2007 Mar 21.
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  27. Klee EW, Finlay JA, McDonald C, Attewell JR, Hebrink D, Dyer R, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. Bioinformatics methods for prioritizing serum biomarker candidates. Clin Chem. 2006 Nov; 52(11):2162-4.
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  28. Finlay JA, Klee EW, McDonald C, Attewell JR, Hebrink D, Dyer R, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. A systematic method for selection of promising serum protein biomarkers to improve prostate cancer (PCa1) detection. Clin Chem. 2006 Nov; 52(11):2159-62.
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  29. Chang H, Venkatesan BM, Iqbal SM, Andreadakis G, Kosari F, Vasmatzis G, Peroulis D, Bashir R. DNA counterion current and saturation examined by a MEMS-based solid state nanopore sensor. Biomed Microdevices. 2006 Sep; 8(3):263-9.
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  30. Parker AS, Kosari F, Lohse CM, Houston Thompson R, Kwon ED, Murphy L, Riehle DL, Blute ML, Leibovich BC, Vasmatzis G, Cheville JC. High expression levels of survivin protein independently predict a poor outcome for patients who undergo surgery for clear cell renal cell carcinoma. Cancer. 2006 Jul 1; 107(1):37-45.
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  31. Murillo H, Schmidt LJ, Karter M, Hafner KA, Kondo Y, Ballman KV, Vasmatzis G, Jenkins RB, Tindall DJ. Prostate cancer cells use genetic and epigenetic mechanisms for progression to androgen independence. Genes Chromosomes Cancer. 2006 Jul; 45(7):702-16.
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  32. Wang X, Zheng L, Zeng Z, Zhou G, Chien J, Qian C, Vasmatzis G, Shridhar V, Chen L, Liu W. DIXDC1 isoform, l-DIXDC1, is a novel filamentous actin-binding protein. Biochem Biophys Res Commun. 2006 Aug 18; 347(1):22-30. Epub 2006 Jun 19.
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  33. Kosari F, Parker AS, Kube DM, Lohse CM, Leibovich BC, Blute ML, Cheville JC, Vasmatzis G. Clear cell renal cell carcinoma: Gene expression analyses identify a potential signature for tumor aggressiveness. Clin Cancer Res. 2005 Jul 15; 11(14):5128-39.
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  34. Sun Z, Yang P, Aubry MC, Kosari F, Endo C, Molina J, Vasmatzis G. Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung? Mol Cancer. 2004 Dec 03; 3(1):35.
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  35. Yang P, Sun Z, Aubry MC, Kosari F, Bamlet W, Endo C, Molina JR, Vasmatzis G. Study design considerations in clinical outcome research of lung cancer using microarray analysis. Lung Cancer. 2004 Nov; 46(2):215-26.
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  36. Chang H, Kosari F, Andreadakis G, Alam MA, Vasmatzis G, Bashir R. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano lett. 2004 Aug; 4(8):1551-6.
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  37. Bergen HR 3rd, Vasmatzis G, Cliby WA, Johnson KL, Oberg AL, Muddiman DC. Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry. Dis Markers. 2003-2004; 19(4-5):239-49.
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  38. Kosari F, Asmann YW, Cheville JC, Vasmatzis G. Cysteine-rich secretory protein-3: A potential biomarker for prostate cancer. Cancer Epidemiol Biomarkers Prev. 2002 Nov; 11(11):1419-26.
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  39. Chang H, Ikram A, Kosari F, Vasmatzis G, Bhunia A, Bashir R. Electrical characterization of micro-organisms using microfabricated devices. Journal of Vacuum Science & Technology B. 2002 Sep-Oct; 20(5):2058-64.
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  40. Chang H, Ikram A, Geng T, Kosari F, Vasmatzis G, Bhunia A, Bashir R. Electrical characterization of microorganisms using microfabricated devices. J VAC SCI TECHNOL B. 2002 SEP-OCT; 20(5):2058-64.
  41. Asmann YW, Kosari F, Wang K, Cheville JC, Vasmatzis G. Identification of differentially expressed genes in normal and malignant prostate by electronic profiling of expressed sequence tags. Cancer Res. 2002 Jun 1; 62(11):3308-14.
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  42. Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S. Gal repressosome contains an antiparallel DNA loop. Nat Struct Biol. 2001 May; 8(5):432-6.
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  43. Yerushalmi N, Keppler-Hafkemeyer A, Vasmatzis G, Liu XF, Olsson P, Bera TK, Duray P, Lee B, Pastan I. ERGL, a novel gene related to ERGIC-53 that is highly expressed in normal and neoplastic prostate and several other tissues. Gene. 2001 Mar; 265(1-2):55-60.
  44. Geanacopoulos M, Vasmatzis G, Zhurkin V, Adhya S. Structure-based genetic analysis of Gal repressosome: GalR tetramer and the DNA loop it forms. Nat Struct Biol. 2001 May; 8(5):432-6.
  45. Onda M, Kreitman RJ, Vasmatzis G, Lee B, Pastan I. Reduction of the nonspecific toxicity of immunotoxin anti-Tac(Fv)-PE38 (LMB-2) by mutations in the Fv which lower the isoelectric point. Blood (Pt I Suppl 1), 1999; 94(10):1246.
  46. Liu XF, Essand M, Vasmatzis G, Lee B, Pastan I. Identification of three new alternate human kallikrein 2 transcripts: Evidence of long transcript and alternative splicing. Biochem Biophys Res Commun. 1999; 264(3):833-9.
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  47. Essand M, Vasmatzis G, Brinkmann U, Lee B, Pastan I. High expression of a specific T-cell receptor gamma transcript in epithelial cells of the prostate. Proc Natl Acad Sci USA. 1999; 96(16):9287-92.
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  48. Vasmatzis G, Brinkmann U, Lee B, Pastan I. Novel genes in the PAGE and GAGE family of tumor antigens found by homology walking in the EST database. Cancer Res. 1999; 59(7):1445-8.
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  49. Pastan L, Vasmatzis G, Essand M, Olsson P, Liu XF, Iavarone C, Ailey B, Duray P, Bera T, Lee B. Discovery of new targets for prostate cancer immunotherapy by EST database analysis. Clin Cancer Res Suppl S. 1999 Nov; 5:3869S-3869.
  50. Geanacopoulos M, Vasmatzis G, Lewis DEA, Roy S, Lee B, Adhya S. GalR mutants diffective in repressosome formation. Genes & Development. 1999; 13:1251-62.
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  51. Almog O, Benhar I, Vasmatzis G, Tordova M, Lee B, Pastan I, Gilliland GL. Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: conformational influence of an engineered disulfide bond. Proteins. 1998 May 1; 31(2):128-38.
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  52. Nambiar MP, Vasmatzis G, Lee BK, FitzGerald DJ, Pastan IH. Production of stable scFv by mutation of the unusual amino acids at the framework region. FASEB J. 1998 Apr 24; 12(8 Suppl S):683.
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  53. Vasmatzis G, Essand M, Brinkmann U, Lee B, Pastan I. Discovery of three new genes specifically expressed in human prostate by expressed sequence tag database analysis. Proc Natl Acad Sci USA. 1998; 95(1):300-4.
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  54. Brinkmann U, Vasmatzis G, Lee B, Yerushalmi N, Essand M, Pastan I. PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus. Proc Natl Acad Sci USA. 1998; 95(18):10757-62.
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  55. Chowdhury PS, Vasmatzis G, Beers R, Lee B, Pastan I. Improvement of the stability and yield of scFv immunotoxins by molecular modeling and protein engineering. FASEB J. 1998; 12(8):681 Suppl S.
  56. Chowdhury PS, Vasmatzis G, Beers R, Lee B, Pastan I. Improvement of the stability and yield of K1 scFv immunotoxin by computer design and protein engineering. J Mol Biol. 1998; 281(5):917-28.
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  57. Lee B, Vasmatzis G. Stabilization of protein structure. Curr Opin Biotechnol. 1997; 8(4):423-8.
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  58. Brinkmann U, Carlo AD, Vasmatzis G, Kurochkina N, Beers R, Lee B, Pastan I. Stabilization of a recombinant Fv fragment by base-loop interconnection and v(h)-v(l) permutation. J Mol Biol. 1997; 268(1):107-17.
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  59. Zhang C, Vasmatzis G, Cornette J, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol. 1997; 267(3):707-26.
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  60. Vasmatzis G, Zhang C, Cornette J, DeLisi C. Computational of side chain specificity for pockets in class I MHC molecules. Mol Immunol. 1996; 33(16):1231-9.
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  61. Vasmatzis G, Cornette J, Sezerman U, DeLisi C. TcR recognition of the MHC-peptide dimer: Structural properties of a ternary complex. J Mol Biol. 1996; 261(1):72-89.
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  62. Vasmatzis G, Brower RC, DeLisi C. Predicting immunoglobulin-like hypervariable loops. Biopolymers. 1994; 34:1669-80.
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  63. Brower RC, Vasmatzis G, Siverman M, DeLisi C. Peptide conformations on a lattice by exhaustive search and simulated annealing. Biopolymers. 1993; 33:329-34.
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