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Items: 1 to 20 of 28

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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
10.

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.

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, Rodriguez H.

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

PMID:
22069307
12.

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.

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 3rd, Rodriguez H.

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

14.

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.

15.

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
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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