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Items: 30

1.

Laboratory information management software for engineered mini-protein therapeutic workflow.

Brusniak MY, Ramos H, Lee B, Olson JM.

BMC Bioinformatics. 2019 Jun 17;20(1):343. doi: 10.1186/s12859-019-2935-x.

2.

Simultaneous extraction and analysis of multiple cystine-dense peptides by μSPE and microflow-MS/MS from plasma.

Brusniak MY, Christianson C, Witthuhn E, Needham S, Olson JM.

Bioanalysis. 2019 Mar;11(6):485-493. doi: 10.4155/bio-2018-0276. Epub 2019 Mar 20.

PMID:
30892059
3.

Publisher Correction: Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets.

Crook ZR, Sevilla GP, Friend D, Brusniak MY, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ, Baker D, Strong RK, Bradley P, Olson JM.

Nat Commun. 2018 Mar 9;9(1):1072. doi: 10.1038/s41467-018-03350-5.

4.

Screening, large-scale production and structure-based classification of cystine-dense peptides.

Correnti CE, Gewe MM, Mehlin C, Bandaranayake AD, Johnsen WA, Rupert PB, Brusniak MY, Clarke M, Burke SE, De Van Der Schueren W, Pilat K, Turnbaugh SM, May D, Watson A, Chan MK, Bahl CD, Olson JM, Strong RK.

Nat Struct Mol Biol. 2018 Mar;25(3):270-278. doi: 10.1038/s41594-018-0033-9. Epub 2018 Feb 26.

5.

Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets.

Crook ZR, Sevilla GP, Friend D, Brusniak MY, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ, Baker D, Strong RK, Bradley P, Olson JM.

Nat Commun. 2017 Dec 21;8(1):2244. doi: 10.1038/s41467-017-02098-8. Erratum in: Nat Commun. 2018 Mar 9;9(1):1072.

6.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

7.

An integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples.

Li XJ, Lee LW, Hayward C, Brusniak MY, Fong PY, McLean M, Mulligan J, Spicer D, Fang KC, Hunsucker SW, Kearney P.

Clin Proteomics. 2015 Jan 29;12(1):3. doi: 10.1186/1559-0275-12-3. eCollection 2015.

8.

A cross-platform toolkit for mass spectrometry and proteomics.

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P.

Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. No abstract available.

9.

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology.

Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL.

Proteomics. 2012 Apr;12(8):1176-84. doi: 10.1002/pmic.201100571. Review.

10.

PASSEL: the PeptideAtlas SRMexperiment library.

Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL.

Proteomics. 2012 Apr;12(8):1170-5. doi: 10.1002/pmic.201100515.

11.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Proteomics Clin Appl. 2011 Dec;5(11-12):580-9. doi: 10.1002/prca.201100097.

PMID:
22213554
12.

TraML--a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.

Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040. Epub 2011 Dec 12.

13.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics. 2012 Jan;12(1):11-20. doi: 10.1002/pmic.201100562. Epub 2011 Dec 14.

PMID:
22069307
14.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

J Proteome Res. 2012 Feb 3;11(2):1412-9. doi: 10.1021/pr201071t. Epub 2011 Dec 8.

15.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Mol Cell Proteomics. 2011 Dec;10(12):O111.015446. doi: 10.1074/mcp.O111.015446. Epub 2011 Nov 3.

16.

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.

J Proteome Res. 2011 Nov 4;10(11):5260-3. doi: 10.1021/pr200664h. Epub 2011 Oct 13.

17.

mProphet: automated data processing and statistical validation for large-scale SRM experiments.

Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.

Nat Methods. 2011 May;8(5):430-5. doi: 10.1038/nmeth.1584. Epub 2011 Mar 20.

PMID:
21423193
18.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.

Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R.

BMC Bioinformatics. 2011 Mar 18;12:78. doi: 10.1186/1471-2105-12-78.

19.

The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.

Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R.

Proteomics. 2011 Jan;11(1):154-8. doi: 10.1002/pmic.201000459. Epub 2010 Dec 6.

20.

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.

Sci Signal. 2010 Dec 21;3(153):rs4. doi: 10.1126/scisignal.2001182.

21.

Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry.

Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R.

Mol Cell Proteomics. 2009 Aug;8(8):1934-46. doi: 10.1074/mcp.M800569-MCP200. Epub 2009 May 1.

22.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

23.

Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.

Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS, Vitek O, Zhang H, Aebersold R, Watts JD.

Clin Proteomics. 2008 Dec 1;4(3-4):105.

24.

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.

Lange V, Malmström JA, Didion J, King NL, Johansson BP, Schäfer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, Bühlmann P, Björck L, Domon B, Aebersold R.

Mol Cell Proteomics. 2008 Aug;7(8):1489-500. doi: 10.1074/mcp.M800032-MCP200. Epub 2008 Apr 13.

25.

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

Mueller LN, Brusniak MY, Mani DR, Aebersold R.

J Proteome Res. 2008 Jan;7(1):51-61. doi: 10.1021/pr700758r. Epub 2008 Jan 4. Review.

PMID:
18173218
26.

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.

Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M.

Proteomics. 2007 Oct;7(19):3470-80.

PMID:
17726677
27.

High-affinity interactions of ligands at recombinant guinea pig 5HT7 receptors.

Wilcox RE, Ragan JE, Pearlman RS, Brusniak MY, Eglen RM, Bonhaus DW, Tenner TE Jr, Miller JD.

J Comput Aided Mol Des. 2001 Oct;15(10):883-909.

PMID:
11918075
28.

CoMFA-based prediction of agonist affinities at recombinant wild type versus serine to alanine point mutated D2 dopamine receptors.

Wilcox RE, Huang WH, Brusniak MY, Wilcox DM, Pearlman RS, Teeter MM, DuRand CJ, Wiens BL, Neve KA.

J Med Chem. 2000 Aug 10;43(16):3005-19.

PMID:
10956209
29.

CoMFA-based prediction of agonist affinities at recombinant D1 vs D2 dopamine receptors.

Wilcox RE, Tseng T, Brusniak MY, Ginsburg B, Pearlman RS, Teeter M, DuRand C, Starr S, Neve KA.

J Med Chem. 1998 Oct 22;41(22):4385-99.

PMID:
9784114
30.

Comparative molecular field analysis-based prediction of drug affinities at recombinant D1A dopamine receptors.

Brusniak MY, Pearlman RS, Neve KA, Wilcox RE.

J Med Chem. 1996 Feb 16;39(4):850-9.

PMID:
8632409

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