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Items: 1 to 20 of 108

1.

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI.

Nat Methods. 2017 Apr 10. doi: 10.1038/nmeth.4256. [Epub ahead of print]

PMID:
28394336
2.

BioContainers: An open-source and community-driven framework for software standardization.

Leprevost FD, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Mar 30. doi: 10.1093/bioinformatics/btx192. [Epub ahead of print]

PMID:
28379341
3.

New targeted approaches for the quantification of data-independent acquisition mass spectrometry.

Bruderer R, Sondermann J, Tsou CC, Barrantes-Freer A, Stadelmann C, Nesvizhskii AI, Schmidt M, Reiter L, Gomez-Varela D.

Proteomics. 2017 Mar 20. doi: 10.1002/pmic.201700021. [Epub ahead of print]

PMID:
28319648
4.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

5.

Data Independent Acquisition analysis in ProHits 4.0.

Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC.

J Proteomics. 2016 Oct 21;149:64-68. doi: 10.1016/j.jprot.2016.04.042. Epub 2016 Apr 29.

PMID:
27132685
6.

BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.

Avtonomov DM, Raskind A, Nesvizhskii AI.

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.

PMID:
27306858
7.

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Tsou CC, Tsai CF, Teo GC, Chen YJ, Nesvizhskii AI.

Proteomics. 2016 Aug;16(15-16):2257-71. doi: 10.1002/pmic.201500526. Epub 2016 Jul 22.

PMID:
27246681
8.

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam MN, Griss J, Tabb DL.

Anal Chem. 2016 Jun 7;88(11):5733-41. doi: 10.1021/acs.analchem.6b00021. Epub 2016 May 24.

PMID:
27186799
9.

MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency.

Zhang H, Gayen S, Xiong J, Zhou B, Shanmugam AK, Sun Y, Karatas H, Liu L, Rao RC, Wang S, Nesvizhskii AI, Kalantry S, Dou Y.

Cell Stem Cell. 2016 Apr 7;18(4):481-94. doi: 10.1016/j.stem.2016.02.004. Epub 2016 Mar 17.

10.

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.

Shanmugam AK, Nesvizhskii AI.

J Proteome Res. 2015 Dec 4;14(12):5169-78. doi: 10.1021/acs.jproteome.5b00504. Epub 2015 Nov 24.

11.

Two-pass alignment improves novel splice junction quantification.

Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI.

Bioinformatics. 2016 Jan 1;32(1):43-9. doi: 10.1093/bioinformatics/btv642. Epub 2015 Oct 30.

12.

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H.

J Proteomics. 2015 Nov 3;129:108-20. doi: 10.1016/j.jprot.2015.09.013. Epub 2015 Sep 15.

13.

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI.

J Proteomics. 2015 Nov 3;129:121-6. doi: 10.1016/j.jprot.2015.07.036. Epub 2015 Aug 4.

14.

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

Kitata RB, Dimayacyac-Esleta BR, Choong WK, Tsai CF, Lin TD, Tsou CC, Weng SH, Chen YJ, Yang PC, Arco SD, Nesvizhskii AI, Sung TY, Chen YJ.

J Proteome Res. 2015 Sep 4;14(9):3658-69. doi: 10.1021/acs.jproteome.5b00477. Epub 2015 Aug 6.

15.

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME.

Mol Endocrinol. 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16.

16.

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.

J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.

17.

The landscape of antisense gene expression in human cancers.

Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X, Wu YM, Robinson D, Wang R, Chen G, Beer DG, Nesvizhskii AI, Chinnaiyan AM.

Genome Res. 2015 Jul;25(7):1068-79. doi: 10.1101/gr.180596.114. Epub 2015 Jun 10.

18.

Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens.

Dytfeld D, Rosebeck S, Kandarpa M, Mayampurath A, Mellacheruvu D, Alonge MM, Ngoka L, Jasielec J, Richardson PG, Volchenboum S, Nesvizhskii AI, Sreekumar A, Jakubowiak AJ.

Br J Haematol. 2015 Jul;170(1):66-79. doi: 10.1111/bjh.13394. Epub 2015 Mar 30.

19.

Targeting the MLL complex in castration-resistant prostate cancer.

Malik R, Khan AP, Asangani IA, Cieślik M, Prensner JR, Wang X, Iyer MK, Jiang X, Borkin D, Escara-Wilke J, Stender R, Wu YM, Niknafs YS, Jing X, Qiao Y, Palanisamy N, Kunju LP, Krishnamurthy PM, Yocum AK, Mellacheruvu D, Nesvizhskii AI, Cao X, Dhanasekaran SM, Feng FY, Grembecka J, Cierpicki T, Chinnaiyan AM.

Nat Med. 2015 Apr;21(4):344-52. doi: 10.1038/nm.3830. Epub 2015 Mar 30.

20.

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics.

Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y, Chen YJ.

Nat Commun. 2015 Mar 27;6:6622. doi: 10.1038/ncomms7622.

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