Publications

  1. Larson NB, Larson MC, Na J, Sosa CP, Wang C, Kocher JP, Rowsey R. Coverage profile correction of shallow-depth circulating cell-free DNA sequencing via multidistance learning. Pac Symp Biocomput. 2020; 25:599-610
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  2. Gupta S, Sosa CP, Kosari F, Folpe A, Bhinge KN, Yang L, Agahi A, Johnson SH, Frank I, Boorjian SA, Hansel DE, Al-Ahmadie HA, Reuter VE, Vasmatzis G, Jimenez RE, Herrera-Hernandez L, Cheville JC. A comparison of adult rhabdomyosarcoma and high-grade neuroendocrine carcinoma of the urinary bladder reveals novel PPP1R12A fusions in rhabdomyosarcoma. Hum Pathol. 2019 Jun; 88:48-59 Epub 2019 Apr 01
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  3. Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L, Erskine CL, Van Keulen VP, Kosari F, Murphy SJ, Ren H, Serla VV, Schaefer Klein JL, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G. Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma. J Thorac Oncol. 2019 Feb; 14 (2):276-287 Epub 2018 Oct 10
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  4. Thompson JJ, Kaur R, Sosa CP, Lee JH, Kashiwagi K, Zhou D, Robertson KD. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation. Nucleic Acids Res. 2018 Nov 2; 46 (19):10034-10051
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  5. Sugihara T, Werneburg NW, Hernandez MC, Yang L, Kabashima A, Hirsova P, Yohanathan L, Sosa C, Truty MJ, Vasmatzis G, Gores GJ, Smoot RL. YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity. Mol Cancer Res. 2018 Oct; 16 (10):1556-1567 Epub 2018 June 14
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  6. Giridhar KV, Sosa CP, Hillman DW, Sanhueza C, Dalpiaz CL, Costello BA, Quevedo FJ, Pitot HC, Dronca RS, Ertz D, Cheville JC, Donkena KV, Kohli M. Whole Blood mRNA Expression-Based Prognosis of Metastatic Renal Cell Carcinoma. Int J Mol Sci. 2017 Nov 3; 18 (11) Epub 2017 Nov 03
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  7. Sosa C, Sosa DN, Vastmatzis G. Toward the Integration of Mate Pair and RNA Sequencing to Identify Gene Fusions in Cancer Research: A Mini Review MOJ Proteomics Bioinformatics. 2017; 5(6):162. Epub 2017 May 15.
  8. Godzaridis E, Boisvert E, Xia F, Kandel M, Behling S, Long B, Sosa C, Laviolette F, Corbeil J. Human analysts at superhuman scales: What has friendly software to do? Big Data. 2014; 1(4):227-236. Epub 2014 Jan 07.
  9. Wang J, Sosa C, Cembran A, Truhlar DG, Gao J. Multilevel X-Pol: A Fragment-Based Method with Mixed Quantum Mechanical Representations of Different Fragments Journal of Physical Chemistry. 2012; 116(23):6781-6788. Epub 2012 Mar 19.
  10. Li J, Mottamal M, Li H, Liu K, Zhu F, Cho Y-Y, Sosa C, Zhou K, Bowden T, Bode AM, Dong Z. Quercetin-3-methyl ether suppresses proliferation of mouse epidermal JB6 P+ cells by targeting ERKs Carcinogenesis. 2011; 33(2):459-465.
  11. Li J, Malakhova M, Mottama M, Reddy K, Kurinov I, Carper A, Langfald A, Oi N, Kim O, Zhu F, Sosa C, Zhou K, Bode AM, Dong Z. Norathyriol Suppresses Skin Cancers Induced by Solar Ultraviolet Radiation by Targeting ERK Kinases Cancer Research. 2011; 72(1):260-270. Epub 2012 Jan 01.
  12. Jevremovic D, Trinh CT, Srienc F, Sosa C, Boley D. Parallelization of Nullspace Algorithm for the computation of metabolic pathways Parallel Computing. 2011; 37(6-7):261-278.
  13. Vank JC, Sosa C, Perczel A, Ciszmadia IG. Peptide models XXVII. An exploratory ab initio study on the 21st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe) in their ?L backbone conformation Canadian Journal of Chemistry. 2011; 78(3):395-408.
  14. Norgan AP, Coffman PK, Kocher JP, Katzmann DJ, Sosa CP. Multilevel Parallelization of AutoDock 4.2. J Cheminform. 2011; 3(1):12. Epub 2011 Apr 28.
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  15. Giambasu GM, Lee T-S, Sosa C, Robertson MP, Scott WG, York DM. Identification of dynamical hinge points of the L1 ligase molecular switch RNA. 2010; 16(4):769-780. Epub 2010 Apr 01.
  16. Lee T-S, Giambasu GM, Sosa C, Martick M, Scott WG, York DM. Threshold Occupancy and Specific Cation Binding Modes in the Hammerhead Ribozyme Active Site are Required for Active Conformation Journal of Molecular Biology. 2009; 388(1):195-206. Epub 2009 Apr 24.
  17. Jiang K, Thorsen O, Peters A, Smith B, Sosa C. An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System IEEE Transactions on Parallel and Distributed Systems. 2008.
  18. Klee EW, Sosa CP. Computational classification of classically secreted proteins. Drug Discov Today. 2007 Mar; 12 (5-6):234-40 Epub 2007 Feb 09
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  19. Sosa C, Carriero N. How to Write Parallel Programs on the T3E Using Linda Semantics Scholar. 2007. Epub 1997 Sep 01.
  20. Sosa C, Milledge T, Mcallister J, Milledge GZ. Molecular Dynamics Applications on the IBM System Blue Gene Solution : Performance Overview Semantic Scholar. 2006. Epub 2006 Mar 01.
  21. Csonka GI, Schubert A, Perczel A, Sosa C, Ciszmadia IG. Ab Initio Conformational Space Study of Model Compounds of O-Glycosides of Serine Diamide Chemistry. 2002; 8(20):4718-4733. Epub 2002 Sep 02.
  22. Vank JC, Zamora MA, Csizmadia IG, Baldoni HA, Rodriguez AM, Enriz RD, Sosa C, Perczel A, Kucsman A, Farkas O, Deretey A. Peptide model XXVIII: An exploratory ab initio and density functional study on the side-chain-backbone interaction in N -acetyl- L -cysteine- N -methylamide and N -formyl- L -cysteinamide in their ? L -backbone conformations Canadian Journal of Chemistry. 2002; 80(7):832-844. Epub 2002 Jan 01.
  23. Sosa C, Hewitt M, Lee MR, Case DA. Vectorization of the generalized Born model for molecular dynamics on shared-memory computers Journal of Molecular Structure Theochem. 2001; 549(1-2):193-2001.
  24. Sander W, Block K, Kappert W, Kirschfeld A, Muthusamy S, Schroeder K, Sosa C, Kraka E, Cremer D. Dimesitylketone O-Oxide: Spectroscopic Characterization, Conformation, and Reaction Modes: OH Formation and OH Capture Journal of the American Chemical Society. 2001; 123(11):2618-2627. Epub 2001 Feb 23.
  25. Chasse GA, Rodriguez AM, Mak ML, Deretey E, Perczel A, Sosa C, Enriz RD, Csizmadia IG. Peptide and protein folding Journal of Molecular Structure Theochem. 2001; 537:319-361. Epub 2001 Jan 01.
  26. Cremer D, Kraka E, Sosa C. First evidence for the production of OH radicals by carbonyl oxides in solution phase – A DFT investigation Chemical Physics Letters. 2001; 337(1-3):199-208. Epub 2001 Mar 30.
  27. Sosa C, Scalmani G, Gomperts R, Frisch MJ. Ab initio quantum chemistry on a ccNUMA architecture using openMP. III Parallel Computing. 2000; 26(7-8):843-856.
  28. Csonka GI, Sosa C. Ab initio conformational study of two lewis X analogues Journal of Physical Chemistry. 2000; 104(30):7113-7122. Epub 2000 Jul 06.
  29. Vank JC, Sosa C, Perczel A, Csizmadia IG. Peptide models XXVII. An e×ploratory ab initio study on the 21 st amino acid side-chain conformations of N -formyl-L-selenocysteinamide (For-L-Sec-NH2 ) and N -acetyl-L-selenocysteine- N -methylamide (Ac-L-Sec-NHMe) in their ? L backbone conformation Canadian Journal of Chemistry. 2000; 78:395-408.
  30. Jakli I, Perczel A, Farkas O, Csaszar AG, Sosa C, Enriz RD. Peptide models XXIII. Conformational model for polar side-chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO-L-SER-NH2 Journal of Computational Chemistry. 2000; 21:626-655. Epub 2020 Aug 15.
  31. Baldoni HA, Rodriguez AM, Zamora MA, Zamarbide GN, Enriz RD, Farkas O, Csaszar P, Torday LL, Sosa C, Jakli I, Perzel A, Gy J, Hollosi M, Cizmadia IG. Peptide models XXIV: An ab initio study on N-formyl-L-prolinamide with trans peptide bond. The existence or non-existence of a(L) and e(L) conformations Theochem. 1999; 465(1):79-91. Epub 1999 May 31.
  32. Rodrigues AM, Giannini FA, Baldoni HA, Santagata LN, Zamora MA, Zacchino S, Sosa C, Enriz RD. Conformational potential energy curves of acetophenone and a-substituted acetophenones. Theochem. 1999; 464:271-281. Epub 1999 May 03.
  33. Sosa C, Ochterski J, Carpenter J, Frisch MJ. Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: I Journal of Computational Chemistry. 1998; 19:1053-1063. Epub 1998 Dec 07.
  34. Goh SK, Sosa C, St-Amant A. A scalable divide-and-conquer algorithm combining coarse and fine-grain parallelization. Theoretical Chemistry Accounts. 1998; 99:197-206.
  35. Csonka GI, Elias K, Kolossvary I, Sosa C, Csizmadia IG. Theoretical Study of Alternative Ring Forms of a-l-Fucopyranose. Journal of Physical Chemistry. 1998; 102(7):1219-1229. Epub 1998 Jan 23.
  36. Kraka E, Sosa C, Grafenstein J, Cremer D. Trimesitylsilylium cation verification of a free silylium cation in solution by NMR chemical shift calculations. Chemical Physics Letters. 1997; 279(1-2):9-16. Epub 1997 Nov 07.
  37. Sander W, Schroeder K, Muthusamy S, Kirschfeld A, Kapert W, Böse R, Kraka E, Sosa C, Cremer D. Dimesityldioxirane Journal of American Chemical Society. 1997; 119(31):7265-7270. Epub 1997 Aug 06.
  38. Tozer D, Sosa C. The alkali metal trifluorides M F3: how well can theory predict experiment? +Kohn-Sham. Molecular Physics. 1997; 90(4):515-524. Epub 1997 Jan 01.
  39. Kraka E, Sosa C, Cremer D. Dimesitylketone O-oxide: Verification of an unusually stable carbonyl oxide by NMR chemical shift calculations. Chemical Physics Letters. 1996; 260(1-2):43-50.
  40. Lee C, Sosa C, Planas M, Novoa JJ. A theoretical study of the ionic dissociation of HF, HCl, and H2S in water clusters. Journal of Chemical Physics. 1996; 104(18):7081.
  41. Novoa JJ, Sosa C. Evaluation of the Density Functional Approximation on the Computation of Hydrogen Bond Interactions. Journal of Physical Chemistry. 1995; 99:15837-15845.
  42. Lee C, Sosa C, Novoa JJ. Evidence of the existence of dissociated water molecules in water clusters. Journal of Chemical Physics. 1995; 103:4360. Epub 1998 Jun 04.
  43. Natchtigall P, Jordan KD, Sosa C. Theoretical study of the mechanism of recombinative hydrogen desorption from the monohydride phase of Si(100): The role of defect migration. Journal of Chemical Physics. 1994; 101:8073. Epub 1998 Jun 04.
  44. Carpenter JE, Sosa C. Density functional studies of representative pericyclic reactions. Journal of Molecular Structure. Journal of Molecular Structure. 1994; 311:325-330. Epub 1994 Jul 20.
  45. Lee C, Sosa C. Local density component of the Lee-Yang-Parr correlation energy functional. Journal of Chemical Physics. 1994; 100:9018. Epub 1998 Jun 04.
  46. Bach RD, Schlegel HB, Andres JL, Sosa C. A Model for the Free Radical and Electrophilic Hydroxylation of Bicyclo[2.1.0]pentane. Journal of the American Chemical Society. 1994; 116(8):3475-3482.
  47. Sosa C, Andzelm JA, Lee C, Blake JF, Chenard BL, Butler TW. Electronic structure calculations of 1,3-dipolar cycloadditions using density functional and Hartree–Fock methods. International Journal of Quantum Chemistry. 1994; 49(4):511-526.
  48. Nachtigall P, Jordan KD, Sosa C. Ab initio calculation of the energy of recombinative hydrogen desorption from the monohydride phase of Si(100). Journal of Physical Chemistry. 1993; 97(45):11666-11672.
  49. Sosa C, Lee C, Fitzgerald G, Eades RA. Chemical applications of density functional theory: F¦(-@3)anion dissociation (F¦(-@3) ? F2 + F-) Chemical Physics Letters. 1993; 211(2-3):1993. Epub 1993 Aug 13.
  50. Raghavachari K, Sosa C. Fullerene derivatives. Comparative theoretical study of C60O and C60CH2. Chemical Physics Letters. 1993; 209(3):223-228. Epub 1993 Jul 02.
  51. Andzelm J, Sosa C, Eades RA. Theoretical study of chemical reactions using density functional methods with nonlocal corrections. Journal of Physical Chemistry. 1993; 97(18):4664-4669.
  52. Sosa C, Lee C. Density functional description of transition structures using nonlocal corrections. Silylene insertion reactions into the hydrogen molecule. Journal of Chemical Physics. 1993; 98(10):8004. Epub 1998 Aug 31.
  53. Sosa C, Schlegel HB. First Principles Study of Aluminum Deposition on Hydrogenterminated Si(100) Surface MRS Online Proceedings Library Archive. 1993; 334:289. Epub 2011 Feb 22.
  54. Sosa C, Andzelm J, Elkin BC, Wimmer E, Dobbs D, Dixon DA. A local density functional study of the structure and vibrational frequencies of molecular transition-metal compounds. Journal of Physical Chemistry. 1992; 96(16):6630-6636.
  55. Ferris KF, Franz JA, Sosa C, Bartlett RJ. Alkyl radical displacement reactions at sulfur: On the question of intermediacy in alkylsulfuranyl radicals. Journal of Organic Chemistry. 1992; 57(2):777-778.
  56. Sosa C, Ferris KF, Noga J. A theoretical study of the harmonic vibrational frequencies of SiO4H3X (XH,Li and Na): model structures for silicate surfaces. Journal of Molecular Structure. 1992; 265(1):163-177.
  57. Ferris KF, Franz JA, Sosa C, Bartlett RJ. Theoretical investigation of the relative stabilities of singlet and triplet disulfides. Chemical Physics Letters. 1991; 185(3-4):251-255.
  58. Gonzalez C, Sosa C, Schlegel HB. Ab initio study of the addition reaction of the methyl radical to ethylene and formaldehyde [Erratum to document cited in CA111(3):22775u]. Journal of Physical Chemistry. 1989; 93(26):8388. Epub 1998 Dec 01.
  59. Sosa C, Geertsen J, Trucks GW, Bartlett RJ. Selection of the reduced virtual space for correlated calculations. An application to the energy and dipole moment of H2O. Chemical Physics Letters. 1989; 159(2-3):148-154.
  60. Gonzalez C, Sosa C, Schlegel HB. Ab initio study of the addition reaction of the methyl radical to ethylene and formaldehyde. Journal of Physical Chemistry. 1989; 93(6):2435-2440.
  61. Sosa C, Trucks GW, Purvis GD, Bartlett Bartjett RJ. An application of the SCF, MBPT and CC correlated densities: a graphical display along the potential energy surface of CH4 ? CH3 + H. Journal of Molecular Graphics. 1989; 7(1):28-32.
  62. Sosa C, Bartlett RJ, KuBulat K, Person WB. A Theoretical Study of the Harmonic Vibrational Frequencies and IR Intensities of XCH2CH2SCH2CH2X and XCH2CH2SH (X: H, Cl). Journal of Physical Chemistry. 1989; 93(2):577-588.
  63. Ferris KF, Sosa C. Chemical Reactions at Glass/Liquid Interfaces. MRS Online Proceeding Library Archive. 1989; 65:172. Epub 2011 Feb 21.
  64. Sosa C, Noga J, Purvis GD, Bartlett RJ. An application of the full CCSDT coupled-cluster method to potential energy curves: The CH4?CH3+H dissociation. Chemical Physics Letters. 1988; 153(2-3):139-146.
  65. Trucks GW, Salter EA, Sosa C, Bartlett RJ. Theory and implementation of the MBPT density matrix. An application to one-electron properties. Journal of Chemical Physics. 1988; 147(4):359-366.
  66. Sosa C, Noga J, Bartlett RJ. A study of the Be2 potential curve using the full (CCSDT) coupled-cluster method: The importance of T4 clusters. Journal of Chemical Physics. 1988; 88(9):5974.
  67. Schlegel HD, Sosa C. Ab initio molecular orbital calculations on F+H2?HF+H and OH+H2? H2O+H using unrestricted Møller-Plesset perturbation theory with spin projection. Chemical Physics Letters. 1988; 145(4):329-333. Epub 1988 Apr 08.
  68. Sosa C, Schlegel HB. Ab initio study of the reaction pathways for OH + C2H4 ? HOCH2CH2 ? products. Journal of the American Chemical Society. 1987; 109(23):7007-7015.
  69. Sosa C, Schlegel HB. Calculated barrier heights for OH + C2H2 and OH + C2H4 using unrestricted Møller-Plesset perturbation theory with spin annihilation. Journal of the American Chemical Society. 1987; 109(14):4193-4198.
  70. Sosa C, Schlegel HB. A theoretical study of the infrared vibrational intensities of CH3F. Journal of Chemical Physics. 1987; 86(12):6937. Epub 1998 Aug 31.
  71. Sosa C, Schlegel HB. Ab initio calculations on H + C2H2 ? C2H3 using unrestricted Møller–Plesset perturbation theory with spin projection. International Journal of Quantum Chemistry. 1987; 32(S21):267-282.
  72. Sosa C, Schlegel HB. Ab initio calculations on the barrier height for the hydrogen addition to ethylene and formaldehyde. The importance of spin projection. International Journal of Quantum Chemistry. 1986; 29(4):1001-1015.
  73. Schlegel HB, Sosa C. SiH2 + SiH3F ? Si2H5F. An ab initio study of silylene insertion into a silicon-fluorine bond Journal of Physical Chemistry. 1985.
  74. Sosa C, Schlegel HB. Carbene and silylene insertion reactions. Ab initio calculations on the effects of fluorine substitution. Journal of American Chemical Society. 1984; 106(20):5847-5852.
  75. Schlegel H Bernhard, Sosa C. Ab initio molecular orbital studies of atomic chlorine + ethylene and atomic hydrogen + chloroethylene. Journal of Physical Chemistry. 1984; 88(6):1141-1145.