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Items: 1 to 50 of 93

1.

Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment.

Rossenkhan R, Rolland M, Labuschagne JPL, Ferreira RC, Magaret CA, Carpp LN, Matsen Iv FA, Huang Y, Rudnicki EE, Zhang Y, Ndabambi N, Logan M, Holzman T, Abrahams MR, Anthony C, Tovanabutra S, Warth C, Botha G, Matten D, Nitayaphan S, Kibuuka H, Sawe FK, Chopera D, Eller LA, Travers S, Robb ML, Williamson C, Gilbert PB, Edlefsen PT.

Viruses. 2019 Jul 3;11(7). pii: E607. doi: 10.3390/v11070607.

2.

Metabolomic profiling of urine: response to a randomised, controlled feeding study of select fruits and vegetables, and application to an observational study.

May DH, Navarro SL, Ruczinski I, Hogan J, Ogata Y, Schwarz Y, Levy L, Holzman T, McIntosh MW, Lampe JW.

Br J Nutr. 2013 Nov;110(10):1760-70. doi: 10.1017/S000711451300127X. Epub 2013 May 9.

3.

Integrative analysis of N-linked human glycoproteomic data sets reveals PTPRF ectodomain as a novel plasma biomarker candidate for prostate cancer.

Whitmore TE, Peterson A, Holzman T, Eastham A, Amon L, McIntosh M, Ozinsky A, Nelson PS, Martin DB.

J Proteome Res. 2012 May 4;11(5):2653-65. doi: 10.1021/pr201200n. Epub 2012 Apr 19.

PMID:
22494190
4.

Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer.

Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng LC, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, Moore RJ, Camp DG 2nd, Chodosh LA, Smith RD, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG.

Proteomics Clin Appl. 2011 Apr;5(3-4):179-88. doi: 10.1002/prca.201000037. Epub 2011 Feb 15.

5.

Structural characterization of a soluble amyloid beta-peptide oligomer.

Yu L, Edalji R, Harlan JE, Holzman TF, Lopez AP, Labkovsky B, Hillen H, Barghorn S, Ebert U, Richardson PL, Miesbauer L, Solomon L, Bartley D, Walter K, Johnson RW, Hajduk PJ, Olejniczak ET.

Biochemistry. 2009 Mar 10;48(9):1870-7. doi: 10.1021/bi802046n.

PMID:
19216516
6.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M.

Mol Cell Proteomics. 2008 Nov;7(11):2270-8. doi: 10.1074/mcp.M700504-MCP200. Epub 2008 Jul 18.

7.

From bacterial genomes to novel antibacterial agents: discovery, characterization, and antibacterial activity of compounds that bind to HI0065 (YjeE) from Haemophilus influenzae.

Lerner CG, Hajduk PJ, Wagner R, Wagenaar FL, Woodall C, Gu YG, Searle XB, Florjancic AS, Zhang T, Clark RF, Cooper CS, Mack JC, Yu L, Cai M, Betz SF, Chovan LE, McCall JO, Black-Schaefer CL, Kakavas SJ, Schurdak ME, Comess KM, Walter KA, Edalji R, Dorwin SA, Smith RA, Hebert EJ, Harlan JE, Metzger RE, Merta PJ, Baranowski JL, Coen ML, Thornewell SJ, Shivakumar AG, Saiki AY, Soni N, Bui M, Balli DJ, Sanders WJ, Nilius AM, Holzman TF, Fesik SW, Beutel BA.

Chem Biol Drug Des. 2007 Jun;69(6):395-404.

PMID:
17581233
8.

A platform for accurate mass and time analyses of mass spectrometry data.

May D, Fitzgibbon M, Liu Y, Holzman T, Eng J, Kemp CJ, Whiteaker J, Paulovich A, McIntosh M.

J Proteome Res. 2007 Jul;6(7):2685-94. Epub 2007 Jun 9.

PMID:
17559252
9.

Activation of TRPA1 channels by the fatty acid amide hydrolase inhibitor 3'-carbamoylbiphenyl-3-yl cyclohexylcarbamate (URB597).

Niforatos W, Zhang XF, Lake MR, Walter KA, Neelands T, Holzman TF, Scott VE, Faltynek CR, Moreland RB, Chen J.

Mol Pharmacol. 2007 May;71(5):1209-16. Epub 2007 Feb 21.

PMID:
17314320
10.

Head-to-head comparison of serum fractionation techniques.

Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp DG 2nd, Anderson L, Watts J, Smith RD, McIntosh MW, Paulovich AG.

J Proteome Res. 2007 Feb;6(2):828-36.

PMID:
17269739
11.

Utility of large-scale transiently transfected cells for cell-based high-throughput screens to identify transient receptor potential channel A1 (TRPA1) antagonists.

Chen J, Lake MR, Sabet RS, Niforatos W, Pratt SD, Cassar SC, Xu J, Gopalakrishnan S, Pereda-Lopez A, Gopalakrishnan M, Holzman TF, Moreland RB, Walter KA, Faltynek CR, Warrior U, Scott VE.

J Biomol Screen. 2007 Feb;12(1):61-9. Epub 2006 Nov 12.

PMID:
17099245
12.

A high throughput fluorescent assay for measuring the activity of fatty acid amide hydrolase.

Kage KL, Richardson PL, Traphagen L, Severin J, Pereda-Lopez A, Lubben T, Davis-Taber R, Vos MH, Bartley D, Walter K, Harlan J, Solomon L, Warrior U, Holzman TF, Faltynek C, Surowy CS, Scott VE.

J Neurosci Methods. 2007 Mar 30;161(1):47-54. Epub 2006 Nov 2.

PMID:
17083980
13.

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments.

Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW.

J Proteome Res. 2006 Jan;5(1):112-21. Erratum in: J Proteome Res. 2006 Apr;5(4):1024. Whitaker, Jeffrey [corrected to Whiteaker, Jeffrey].

PMID:
16396501
14.

Genomewide scan for real-word reading subphenotypes of dyslexia: novel chromosome 13 locus and genetic complexity.

Igo RP Jr, Chapman NH, Berninger VW, Matsushita M, Brkanac Z, Rothstein JH, Holzman T, Nielsen K, Raskind WH, Wijsman EM.

Am J Med Genet B Neuropsychiatr Genet. 2006 Jan 5;141B(1):15-27.

15.

Structure of MurF from Streptococcus pneumoniae co-crystallized with a small molecule inhibitor exhibits interdomain closure.

Longenecker KL, Stamper GF, Hajduk PJ, Fry EH, Jakob CG, Harlan JE, Edalji R, Bartley DM, Walter KA, Solomon LR, Holzman TF, Gu YG, Lerner CG, Beutel BA, Stoll VS.

Protein Sci. 2005 Dec;14(12):3039-47.

16.

Variants in Apaf-1 segregating with major depression promote apoptosome function.

Harlan J, Chen Y, Gubbins E, Mueller R, Roch JM, Walter K, Lake M, Olsen T, Metzger P, Dorwin S, Ladror U, Egan DA, Severin J, Johnson RW, Holzman TF, Voelp K, Davenport C, Beck A, Potter J, Gopalakrishnan M, Hahn A, Spear BB, Halbert DN, Sullivan JP, Abkevich V, Neff CD, Skolnick MH, Shattuck D, Katz DA.

Mol Psychiatry. 2006 Jan;11(1):76-85.

PMID:
16231040
17.

A highly potent and selective farnesyltransferase inhibitor ABT-100 in preclinical studies.

Gu WZ, Joseph I, Wang YC, Frost D, Sullivan GM, Wang L, Lin NH, Cohen J, Stoll VS, Jakob CG, Muchmore SW, Harlan JE, Holzman T, Walten KA, Ladror US, Anderson MG, Kroeger P, Rodriguez LE, Jarvis KP, Ferguson D, Marsh K, Ng S, Rosenberg SH, Sham HL, Zhang H.

Anticancer Drugs. 2005 Nov;16(10):1059-69.

PMID:
16222147
18.
19.

Protein fragmentation via liquid chromatography-quadrupole time-of-flight mass spectrometry: the use of limited sequence information in structural characterization.

Johnson RW Jr, Ahmed TF, Miesbauer LJ, Edalji R, Smith R, Harlan J, Dorwin S, Walter K, Holzman T.

Anal Biochem. 2005 Jun 1;341(1):22-32.

PMID:
15866524
20.

Analysis of xbx genes in C. elegans.

Efimenko E, Bubb K, Mak HY, Holzman T, Leroux MR, Ruvkun G, Thomas JH, Swoboda P.

Development. 2005 Apr;132(8):1923-34.

21.

A genome scan in multigenerational families with dyslexia: Identification of a novel locus on chromosome 2q that contributes to phonological decoding efficiency.

Raskind WH, Igo RP, Chapman NH, Berninger VW, Thomson JB, Matsushita M, Brkanac Z, Holzman T, Brown M, Wijsman EM.

Mol Psychiatry. 2005 Jul;10(7):699-711.

PMID:
15753956
22.

Chkl binds and phosphorylates BAD protein.

Han EK, Butler C, Zhang H, Severin JM, Qin W, Holzman TF, Gubbins EJ, Simmer RL, Rosenberg S, Giranda VL, Ng SC, Luo Y.

Anticancer Res. 2004 Nov-Dec;24(6):3907-10. Erratum in: Anticancer Res. 2005 Jan-Feb;25(1b):681. Severin, Jean M [added]; Qin, Wenying [added]; Holzman, Tom F [added]; Gubbins, Earl J [added]; Simmer, Robert L [added]. Anticancer Res. 2005 May-Jun;25(3c):2599.

23.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2099-104. Epub 2005 Jan 31.

24.

Transforming the work of early-stage drug discovery through bioprocess informatics.

Holzman TF, Hebert EJ.

Drug Discov Today. 2005 Jan 1;10(1):61-7. Review.

PMID:
15676300
25.

Linkage analyses of four regions previously implicated in dyslexia: confirmation of a locus on chromosome 15q.

Chapman NH, Igo RP, Thomson JB, Matsushita M, Brkanac Z, Holzman T, Berninger VW, Wijsman EM, Raskind WH.

Am J Med Genet B Neuropsychiatr Genet. 2004 Nov 15;131B(1):67-75.

PMID:
15389770
26.

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.

Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS Jr, Kolesov G, Frishman D, Galperin MY.

Nucleic Acids Res. 2004 Apr 30;32(8):2353-61. Print 2004.

27.

Statistical analysis of global gene expression data: some practical considerations.

Holzman T, Kolker E.

Curr Opin Biotechnol. 2004 Feb;15(1):52-7.

PMID:
15102467
28.

Driving affinity selection by centrifugal force.

Harlan JE, Egan DA, Ladror US, Snyder S, Tang MI, Buko A, Holzman TF.

Assay Drug Dev Technol. 2003 Aug;1(4):507-19.

PMID:
15090247
29.

Pseudosubstrate peptides inhibit Akt and induce cell growth inhibition.

Luo Y, Smith RA, Guan R, Liu X, Klinghofer V, Shen J, Hutchins C, Richardson P, Holzman T, Rosenberg SH, Giranda VL.

Biochemistry. 2004 Feb 10;43(5):1254-63.

PMID:
14756561
30.

Familial aggregation patterns in mathematical ability.

Wijsman EM, Robinson NM, Ainsworth KH, Rosenthal EA, Holzman T, Raskind WH.

Behav Genet. 2004 Jan;34(1):51-62.

PMID:
14739696
31.

Characterization of protein kinase A phosphorylation: multi-technique approach to phosphate mapping.

Shen J, Smith RA, Stoll VS, Edalji R, Jakob C, Walter K, Gramling E, Dorwin S, Bartley D, Gunasekera A, Yang J, Holzman T, Johnson RW.

Anal Biochem. 2004 Jan 15;324(2):204-18.

PMID:
14690684
32.

Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein.

Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG.

J Virol. 2003 Jun;77(11):6367-75.

33.

Pharmacotherapy for severe aggression in a child with autism: "open label" evaluation of multiple medications on response frequency and intensity of behavioral intervention.

Luiselli JK, Blew P, Keane J, Thibadeau S, Holzman T.

J Behav Ther Exp Psychiatry. 2000 Sep-Dec;31(3-4):219-30.

PMID:
11494958
34.

Abrogation of G2 checkpoint specifically sensitize p53 defective cells to cancer chemotherapeutic agents.

Luo Y, Rockow-Magnone SK, Joseph MK, Bradner J, Butler CC, Tahir SK, Han EK, Ng SC, Severin JM, Gubbins EJ, Reilly RM, Rueter A, Simmer RL, Holzman TF, Giranda VL.

Anticancer Res. 2001 Jan-Feb;21(1A):23-8.

PMID:
11299740
35.

Design of adenosine kinase inhibitors from the NMR-based screening of fragments.

Hajduk PJ, Gomtsyan A, Didomenico S, Cowart M, Bayburt EK, Solomon L, Severin J, Smith R, Walter K, Holzman TF, Stewart A, McGaraughty S, Jarvis MF, Kowaluk EA, Fesik SW.

J Med Chem. 2000 Dec 14;43(25):4781-6.

PMID:
11123986
36.

Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome.

Mahairas GG, Wallace JC, Smith K, Swartzell S, Holzman T, Keller A, Shaker R, Furlong J, Young J, Zhao S, Adams MD, Hood L.

Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9739-44.

37.

Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.

Bussiere DE, Kong X, Egan DA, Walter K, Holzman TF, Lindh F, Robins T, Giranda VL.

Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1367-76.

PMID:
10089498
38.

Domain structure analysis of elongation factor-3 from Saccharomyces cerevisiae by limited proteolysis and differential scanning calorimetry.

Ladror US, Egan DA, Snyder SW, Capobianco JO, Goldman RC, Dorwin SA, Johnson RW, Edalji R, Sarthy AV, McGonigal T, Walter KA, Holzman TF.

Protein Sci. 1998 Dec;7(12):2595-601.

39.

The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance.

Bussiere DE, Pratt SD, Katz L, Severin JM, Holzman T, Park CH.

Mol Cell. 1998 Jul;2(1):75-84.

40.

Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria.

Bussiere DE, Muchmore SW, Dealwis CG, Schluckebier G, Nienaber VL, Edalji RP, Walter KA, Ladror US, Holzman TF, Abad-Zapatero C.

Biochemistry. 1998 May 19;37(20):7103-12.

PMID:
9585521
41.

High-level overexpression of yeast elongation factor 3 and detailed kinetic analysis using a coupled spectrophotometric assay.

Sarthy AV, McGonigal T, Capobianco JO, Holzman TH, Walter KA, Egan DA, Goldman RC.

Anal Biochem. 1997 Dec 15;254(2):288-90. No abstract available.

PMID:
9417791
42.

NMR-based discovery of lead inhibitors that block DNA binding of the human papillomavirus E2 protein.

Hajduk PJ, Dinges J, Miknis GF, Merlock M, Middleton T, Kempf DJ, Egan DA, Walter KA, Robins TS, Shuker SB, Holzman TF, Fesik SW.

J Med Chem. 1997 Sep 26;40(20):3144-50.

PMID:
9379433
43.

Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance.

Yu L, Petros AM, Schnuchel A, Zhong P, Severin JM, Walter K, Holzman TF, Fesik SW.

Nat Struct Biol. 1997 Jun;4(6):483-9. Erratum in: Nat Struct Biol 1997 Jul;4(7):592.

PMID:
9187657
44.

Initial characterization of autoprocessing and active-center mutants of CMV proteinase.

Snyder SW, Edalji RP, Lindh FG, Walter KA, Solomon L, Pratt S, Steffy K, Holzman TF.

J Protein Chem. 1996 Nov;15(8):763-74.

PMID:
9008301
45.

Autocatalyzed protein folding.

Veeraraghavan S, Holzman TF, Nall BT.

Biochemistry. 1996 Aug 20;35(33):10601-7.

PMID:
8718848
46.

Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions.

Liang H, Petros AM, Meadows RP, Yoon HS, Egan DA, Walter K, Holzman TF, Robins T, Fesik SW.

Biochemistry. 1996 Feb 20;35(7):2095-103.

PMID:
8652551
47.

The nanometer-scale structure of amyloid-beta visualized by atomic force microscopy.

Stine WB Jr, Snyder SW, Ladror US, Wade WS, Miller MF, Perun TJ, Holzman TF, Krafft GA.

J Protein Chem. 1996 Feb;15(2):193-203.

PMID:
8924204
48.

Clusterin (apoJ) alters the aggregation of amyloid beta-peptide (A beta 1-42) and forms slowly sedimenting A beta complexes that cause oxidative stress.

Oda T, Wals P, Osterburg HH, Johnson SA, Pasinetti GM, Morgan TE, Rozovsky I, Stine WB, Snyder SW, Holzman TF, et al.

Exp Neurol. 1995 Nov;136(1):22-31.

PMID:
7589331
49.

Substrate requirements for ErmC' methyltransferase activity.

Zhong P, Pratt SD, Edalji RP, Walter KA, Holzman TF, Shivakumar AG, Katz L.

J Bacteriol. 1995 Aug;177(15):4327-32.

50.

Cathepsin D from Alzheimer's-diseased and normal brains.

Kohnken RE, Ladror US, Wang GT, Holzman TF, Miller BE, Krafft GA.

Exp Neurol. 1995 Jun;133(2):105-12.

PMID:
7649217

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