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Items: 41


Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.

Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL.

ISME J. 2019 Sep 6. doi: 10.1038/s41396-019-0503-z. [Epub ahead of print]


Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.

Riffle M, Jaschob D, Zelter A, Davis TN.

J Proteome Res. 2019 Feb 1;18(2):759-764. doi: 10.1021/acs.jproteome.8b00726. Epub 2018 Dec 19.


Novel phosphorylation states of the yeast spindle pole body.

Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN.

Biol Open. 2018 Oct 8;7(10). pii: bio033647. doi: 10.1242/bio.033647.


Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments.

Helgeson LA, Zelter A, Riffle M, MacCoss MJ, Asbury CL, Davis TN.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2740-2745. doi: 10.1073/pnas.1718553115. Epub 2018 Feb 27.


MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.

Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL.

Proteomes. 2017 Dec 27;6(1). pii: E2. doi: 10.3390/proteomes6010002.


Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation.

Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB.

J Proteome Res. 2017 Sep 1;16(9):3298-3309. doi: 10.1021/acs.jproteome.7b00288. Epub 2017 Aug 11.


Efficacy of a 4-Food Elimination Diet for Children With Eosinophilic Esophagitis.

Kagalwalla AF, Wechsler JB, Amsden K, Schwartz S, Makhija M, Olive A, Davis CM, Manuel-Rubio M, Marcus S, Shaykin R, Sulkowski M, Johnson K, Ross JN, Riffle ME, Groetch M, Melin-Aldana H, Schady D, Palac H, Kim KA, Wershil BK, Collins MH, Chehade M.

Clin Gastroenterol Hepatol. 2017 Nov;15(11):1698-1707.e7. doi: 10.1016/j.cgh.2017.05.048. Epub 2017 Jun 8.


Direct measurement of the strength of microtubule attachment to yeast centrosomes.

Fong KK, Sarangapani KK, Yusko EC, Riffle M, Llauró A, Graczyk B, Davis TN, Asbury CL.

Mol Biol Cell. 2017 Jul 7;28(14):1853-1861. doi: 10.1091/mbc.E17-01-0034. Epub 2017 Mar 22.


Eosinophilic Esophagitis and Esophageal Granular Cell Tumor: An Unexpected Association.

Riffle ME, Polydorides AD, Niakan J, Chehade M.

Am J Surg Pathol. 2017 May;41(5):616-621. doi: 10.1097/PAS.0000000000000832.


The Ndc80 complex bridges two Dam1 complex rings.

Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN.

Elife. 2017 Feb 13;6. pii: e21069. doi: 10.7554/eLife.21069.


Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL.

ISME J. 2017 Feb;11(2):309-314. doi: 10.1038/ismej.2016.132. Epub 2016 Nov 8. No abstract available.


ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

Riffle M, Jaschob D, Zelter A, Davis TN.

J Proteome Res. 2016 Aug 5;15(8):2863-70. doi: 10.1021/acs.jproteome.6b00274. Epub 2016 Jun 24.


Eosinophilic esophagitis diagnosed in a patient with common variable immunodeficiency.

Chen M, Ko HM, Riffle ME, Andreae DA, Cunningham-Rundles C, Chehade M, Maglione PJ.

J Allergy Clin Immunol Pract. 2016 Sep-Oct;4(5):995-7. doi: 10.1016/j.jaip.2016.03.023. Epub 2016 May 4. No abstract available.


Early Comparison of Inflammatory vs. Fibrostenotic Phenotype in Eosinophilic Esophagitis in a Multicenter Longitudinal Study.

Singla MB, Chehade M, Brizuela D, Maydonovitch CL, Chen YJ, Riffle ME, Achem SR, Moawad FJ.

Clin Transl Gastroenterol. 2015 Dec 17;6:e132. doi: 10.1038/ctg.2015.62.


The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling.

Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN.

Nat Commun. 2015 Nov 12;6:8673. doi: 10.1038/ncomms9673.


Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex.

Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5583-9. doi: 10.1073/pnas.1513882112. Epub 2015 Oct 1.


Genetic Regulation of Dna2 Localization During the DNA Damage Response.

Yimit A, Riffle M, Brown GW.

G3 (Bethesda). 2015 Jul 10;5(9):1937-44. doi: 10.1534/g3.115.019208.


Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.

Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1827-36. doi: 10.1007/s13361-015-1193-z. Epub 2015 Jul 2.


Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.

Jaschob D, Davis TN, Riffle M.

BMC Res Notes. 2015 Mar 7;8:70. doi: 10.1186/s13104-015-1009-z.


Kojak: efficient analysis of chemically cross-linked protein complexes.

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.

J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15.


Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development.

Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law MJ, Lavigne R, Evrard B, Demougin P, Riffle M, Strich R, Davis RW, Pineau C, Primig M.

J Proteomics. 2015 Apr 24;119:30-44. doi: 10.1016/j.jprot.2015.01.015. Epub 2015 Feb 4.


Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex.

Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN.

Genetics. 2014 Dec;198(4):1483-93. doi: 10.1534/genetics.114.167775. Epub 2014 Sep 16.


Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data.

Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A.

Mol Cell Proteomics. 2014 Nov;13(11):2812-23. doi: 10.1074/mcp.M114.040824. Epub 2014 Aug 19.


Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.

Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM.

Genome Res. 2013 Sep;23(9):1496-504. doi: 10.1101/gr.155762.113. Epub 2013 May 29.


Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress.

Tkach JM, Yimit A, Lee AY, Riffle M, Costanzo M, Jaschob D, Hendry JA, Ou J, Moffat J, Boone C, Davis TN, Nislow C, Brown GW.

Nat Cell Biol. 2012 Sep;14(9):966-76. doi: 10.1038/ncb2549. Epub 2012 Jul 29.


A mass spectrometry proteomics data management platform.

Sharma V, Eng JK, Maccoss MJ, Riffle M.

Mol Cell Proteomics. 2012 Sep;11(9):824-31. doi: 10.1074/mcp.O111.015149. Epub 2012 May 18.


The Proteome Folding Project: proteome-scale prediction of structure and function.

Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R.

Genome Res. 2011 Nov;21(11):1981-94. doi: 10.1101/gr.121475.111. Epub 2011 Aug 8.


The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images.

Riffle M, Davis TN.

BMC Bioinformatics. 2010 May 19;11:263. doi: 10.1186/1471-2105-11-263.


Large-scale prediction of protein-protein interactions from structures.

Hue M, Riffle M, Vert JP, Noble WS.

BMC Bioinformatics. 2010 Mar 18;11:144. doi: 10.1186/1471-2105-11-144.


Proteomics data repositories.

Riffle M, Eng JK.

Proteomics. 2009 Oct;9(20):4653-63. doi: 10.1002/pmic.200900216. Review.


Bir1 is required for the tension checkpoint.

Shimogawa MM, Widlund PO, Riffle M, Ess M, Davis TN.

Mol Biol Cell. 2009 Feb;20(3):915-23. doi: 10.1091/mbc.E08-07-0723. Epub 2008 Dec 3.


Transmembrane topology and signal peptide prediction using dynamic bayesian networks.

Reynolds SM, Käll L, Riffle ME, Bilmes JA, Noble WS.

PLoS Comput Biol. 2008 Nov;4(11):e1000213. doi: 10.1371/journal.pcbi.1000213. Epub 2008 Nov 7.


"Lower extremity" amputation: conclusion.

Riffle MD.

Air Med J. 2007 Sep-Oct;26(5):202-4. No abstract available.


"Lower extremity" amputation.

Riffle MD, Ross DW, Wichman C, MacKinnon M.

Air Med J. 2007 Jul-Aug;26(4):164. No abstract available.


Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.

Malmström L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D.

PLoS Biol. 2007 Apr;5(4):e76.


The Yeast Resource Center Public Data Repository.

Riffle M, Malmström L, Davis TN.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D378-82.


Localization of proteins that are coordinately expressed with Cln2 during the cell cycle.

Sundin BA, Chiu CH, Riffle M, Davis TN, Muller EG.

Yeast. 2004 Jul 15;21(9):793-800.


Assigning function to yeast proteins by integration of technologies.

Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR 3rd, Davis TN.

Mol Cell. 2003 Dec;12(6):1353-65.


Devil's-claw (Proboscidea louisianica), essential oil and its components : Potential allelochemical agents on cotton and wheat.

Riffle MS, Waller GR, Murray DS, Sgaramello RP.

J Chem Ecol. 1990 Jun;16(6):1927-40. doi: 10.1007/BF01020506.


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