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Showing 1 to 12 of 38 entries
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Hole counts from X-ray absorption spectra.

Journal of synchrotron radiation

Ankudinov AL, Nesvizhskii AI, Rehr JJ.
PMID: 11512979
J Synchrotron Radiat. 2001 Mar 01;8:92-5. doi: 10.1107/s0909049500016435.

The interpretation of X-ray absorption spectra in terms of electronic structure has long been of interest. Hole counts derived from such spectra are often interpreted in terms of free-atom occupation numbers or Mülliken counts. It is shown here, however,...

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Omics : a journal of integrative biology

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.
PMID: 24456465
OMICS. 2014 Jan;18(1):10-4. doi: 10.1089/omi.2013.0149.

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full...

Stark effect near the type-I-type-II transition point in semiconductor quantum wells.

Physical review. B, Condensed matter

Kavokin AV, Nesvizhskii AI.
PMID: 10010882
Phys Rev B Condens Matter. 1994 Jun 15;49(24):17055-17058. doi: 10.1103/physrevb.49.17055.

No abstract available.

A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy.

Clinical proteomics

Weber SR, Zhao Y, Ma J, Gates C, da Veiga Leprevost F, Basrur V, Nesvizhskii AI, Gardner TW, Sundstrom JM.
PMID: 34861815
Clin Proteomics. 2021 Dec 03;18(1):28. doi: 10.1186/s12014-021-09328-8.

BACKGROUND: Vitreous is an accessible, information-rich biofluid that has recently been studied as a source of retinal disease-related proteins and pathways. However, the number of samples required to confidently identify perturbed pathways remains unknown. In order to confidently identify...

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.

Molecular & cellular proteomics : MCP

Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI.
PMID: 33568339
Mol Cell Proteomics. 2021;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub 2020 Dec 11.

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift...

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification.

Molecular & cellular proteomics : MCP

Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B.
PMID: 34737085
Mol Cell Proteomics. 2021 Nov 01;20:100171. doi: 10.1016/j.mcpro.2021.100171. Epub 2021 Nov 01.

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported...

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.

Molecular & cellular proteomics : MCP

Yu F, Haynes SE, Nesvizhskii AI.
PMID: 33813065
Mol Cell Proteomics. 2021 Apr 02;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02.

Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem...

Philosopher: a versatile toolkit for shotgun proteomics data analysis.

Nature methods

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
PMID: 32669682
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y.

No abstract available.

Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma.

Hepatology communications

Alcedo KP, Guerrero A, Basrur V, Fu D, Richardson ML, McLane JS, Tsou CC, Nesvizhskii AI, Welling TH, Lebrilla CB, Otey CA, Kim HJ, Omary MB, Snider NT.
PMID: 31592495
Hepatol Commun. 2019 Aug 09;3(10):1400-1414. doi: 10.1002/hep4.1410. eCollection 2019 Oct.

CD73, a cell-surface

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks.

Nature communications

Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B.
PMID: 34857745
Nat Commun. 2021 Dec 02;12(1):7036. doi: 10.1038/s41467-021-27280-x.

The molecular nanoscale organization of the surfaceome is a fundamental regulator of cellular signaling in health and disease. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would unlock theranostic opportunities to target...

Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook.

Journal of clinical medicine

Weber SR, Zhao Y, Gates C, Ma J, da Veiga Leprevost F, Basrur V, Nesvizhskii AI, Gardner TW, Sundstrom JM.
PMID: 34070658
J Clin Med. 2021 May 25;10(11). doi: 10.3390/jcm10112309.

Vitreous fluid is becoming an increasingly popular medium for the study of retinal disease. Numerous studies have demonstrated that proteomic analysis of the vitreous from patients with proliferative diabetic retinopathy yields valuable molecular information regarding known and novel proteins...

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.

Molecular & cellular proteomics : MCP

Yu F, Haynes SE, Nesvizhskii AI.
PMID: 33813065
Mol Cell Proteomics. 2021;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02.

Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem...

Showing 1 to 12 of 38 entries