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A likelihood ratio test for changes in homeolog expression bias.

Smith RD, Kinser TJ, Smith GDC, Puzey JR.

BMC Bioinformatics. 2019 Mar 20;20(1):149. doi: 10.1186/s12859-019-2709-5.


Long-term outcomes of deep brain stimulation in severe Parkinson's disease utilizing UPDRS III and modified Hoehn and Yahr as a severity scale.

Kahn L, Mathkour M, Lee SX, Gouveia EE, Hanna JA, Garces J, Scullen T, McCormack E, Riffle J, Glynn R, Houghton D, Lea G, Biro EE, Bui CJ, Sulaiman OA, Smith RD.

Clin Neurol Neurosurg. 2019 Apr;179:67-73. doi: 10.1016/j.clineuro.2019.02.018. Epub 2019 Feb 21.


Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells.

Yi L, Tsai CF, Dirice E, Swensen AC, Chen J, Shi T, Gritsenko MA, Chu RK, Piehowski PD, Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, Qian WJ.

Anal Chem. 2019 Mar 15. doi: 10.1021/acs.analchem.9b00024. [Epub ahead of print]


Author Correction: Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Mar 6. doi: 10.1038/s41588-019-0380-4. [Epub ahead of print]


Dual Polarity Ion Confinement and Mobility Separations.

Attah IK, Garimella SVB, Webb IK, Nagy G, Norheim RV, Schimelfenig CE, Ibrahim YM, Smith RD.

J Am Soc Mass Spectrom. 2019 Mar 4. doi: 10.1007/s13361-019-02138-1. [Epub ahead of print]


Glomerular filtrate proteins in acute cardiorenal syndrome.

Wakasaki R, Matsushita K, Golgotiu K, Anderson S, Eiwaz MB, Orton DJ, Han SJ, Lee HT, Smith RD, Rodland KD, Piehowski PD, Hutchens MP.

JCI Insight. 2019 Feb 21;4(4). pii: 122130. doi: 10.1172/jci.insight.122130. eCollection 2019 Feb 21.


Separation of β-Amyloid Tryptic Peptide Species with Isomerized and Racemized l-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations.

Nagy G, Kedia K, Attah IK, Garimella SVB, Ibrahim YM, Petyuk VA, Smith RD.

Anal Chem. 2019 Mar 12. doi: 10.1021/acs.analchem.8b04696. [Epub ahead of print]


Plasma lipidome reveals critical illness and recovery from human Ebola virus disease.

Kyle JE, Burnum-Johnson KE, Wendler JP, Eisfeld AJ, Halfmann PJ, Watanabe T, Sahr F, Smith RD, Kawaoka Y, Waters KM, Metz TO.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3919-3928. doi: 10.1073/pnas.1815356116. Epub 2019 Feb 11.


Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Mar;51(3):541-547. doi: 10.1038/s41588-019-0356-4. Epub 2019 Feb 25. Erratum in: Nat Genet. 2019 Mar 6;:.


Global Disease Outbreaks Associated with the 2015-2016 El Niño Event.

Anyamba A, Chretien JP, Britch SC, Soebiyanto RP, Small JL, Jepsen R, Forshey BM, Sanchez JL, Smith RD, Harris R, Tucker CJ, Karesh WB, Linthicum KJ.

Sci Rep. 2019 Feb 13;9(1):1930. doi: 10.1038/s41598-018-38034-z.


Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.

Clark JJ, Benson ML, Smith RD, Carlson HA.

PLoS Comput Biol. 2019 Jan 30;15(1):e1006705. doi: 10.1371/journal.pcbi.1006705. eCollection 2019 Jan.


H/D Isotope Effects Reveal Factors Controlling Catalytic Activity in Co-Based Oxides for Water Oxidation.

Pasquini C, Zaharieva I, González-Flores D, Chernev P, Mohammadi MR, Guidoni L, Smith RDL, Dau H.

J Am Chem Soc. 2019 Feb 20;141(7):2938-2948. doi: 10.1021/jacs.8b10002. Epub 2019 Feb 6.


Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells.

Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs JM, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, Smith RD, Liu T, Wiley HS, Shi T.

Anal Chem. 2018 Dec 17. doi: 10.1021/acs.analchem.8b04258. [Epub ahead of print]


Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations.

Nagy G, Veličković D, Chu RK, Carrell AA, Weston DJ, Ibrahim YM, Anderton CR, Smith RD.

Chem Commun (Camb). 2019 Jan 2;55(3):306-309. doi: 10.1039/c8cc07482h.


Design methodology for a simulator of a robotic surgical system.

Julian DL, Smith RD, Tanaka ADS, Dubin A.

J Robot Surg. 2018 Nov 30. doi: 10.1007/s11701-018-0897-z. [Epub ahead of print]


Shifting global health governance towards the sustainable development goals.

Marten R, Kadandale S, Nordström A, Smith RD.

Bull World Health Organ. 2018 Dec 1;96(12):798-798A. doi: 10.2471/BLT.18.209668. No abstract available.


Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses.

Dou M, Chouinard CD, Zhu Y, Nagy G, Liyu AV, Ibrahim YM, Smith RD, Kelly RT.

Anal Bioanal Chem. 2018 Nov 5. doi: 10.1007/s00216-018-1452-5. [Epub ahead of print]


Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy.

Matsushita K, Golgotiu K, Orton DJ, Smith RD, Rodland KD, Piehowski PD, Hutchens MP.

J Vis Exp. 2018 Oct 11;(140). doi: 10.3791/58206.


Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection.

Stevens SL, Liu T, Bahjat FR, Petyuk VA, Schepmoes AA, Sontag RL, Gritsenko MA, Wu C, Wang S, Shukla AK, Jacobs JM, Smith RD, Rodland KD, Alexander West G, Kohama SG, Glynn C, Stenzel-Poore MP.

Transl Stroke Res. 2018 Oct 19. doi: 10.1007/s12975-018-0670-7. [Epub ahead of print]


Identification and Evaluation of Self-Report Physical Activity Instruments in Adults With Osteoarthritis: A Systematic Review.

Smith RD, Dziedzic KS, Quicke JG, Holden MA, McHugh GA, Healey EL.

Arthritis Care Res (Hoboken). 2019 Feb;71(2):237-251. doi: 10.1002/acr.23787.


Utilizing ion mobility spectrometry and mass spectrometry for the analysis of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polybrominated diphenyl ethers and their metabolites.

Zheng X, Dupuis KT, Aly NA, Zhou Y, Smith FB, Tang K, Smith RD, Baker ES.

Anal Chim Acta. 2018 Dec 11;1037:265-273. doi: 10.1016/j.aca.2018.02.054. Epub 2018 Mar 2.


Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ.

Commun Biol. 2018 Aug 6;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018.


Comparison of elderly and young patient populations treated with deep brain stimulation for Parkinson's disease: long-term outcomes with up to 7 years of follow-up.

Hanna JA, Scullen T, Kahn L, Mathkour M, Gouveia EE, Garces J, Evans LM, Lea G, Houghton DJ, Biro E, Bui CJ, Sulaiman OA, Smith RD.

J Neurosurg. 2018 Sep 1:1-6. doi: 10.3171/2018.4.JNS171909. [Epub ahead of print]


Unraveling the isomeric heterogeneity of glycans: ion mobility separations in structures for lossless ion manipulations.

Nagy G, Attah IK, Garimella SVB, Tang K, Ibrahim YM, Baker ES, Smith RD.

Chem Commun (Camb). 2018 Oct 25;54(83):11701-11704. doi: 10.1039/c8cc06966b. Epub 2018 Sep 28.


Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.

Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P.

Tuberculosis (Edinb). 2018 Sep;112:52-61. doi: 10.1016/ Epub 2018 Jul 18.


Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations.

Nagy G, Chouinard CD, Attah IK, Webb IK, Garimella SVB, Ibrahim YM, Baker ES, Smith RD.

Electrophoresis. 2018 Dec;39(24):3148-3155. doi: 10.1002/elps.201800294. Epub 2018 Sep 17.


Cost-effectiveness of internet-based training for primary care clinicians on antibiotic prescribing for acute respiratory tract infections in Europe.

Oppong R, Smith RD, Little P, Verheij T, Butler CC, Goossens H, Coenen S, Jowett S, Roberts TE, Achana F, Stuart B, Coast J.

J Antimicrob Chemother. 2018 Nov 1;73(11):3189-3198. doi: 10.1093/jac/dky309.


The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target.

Petyuk VA, Chang R, Ramirez-Restrepo M, Beckmann ND, Henrion MYR, Piehowski PD, Zhu K, Wang S, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, De Jager P, Schneider JA, Morris CM, McKeith IG, Perry RH, Lovestone S, Woltjer RL, Beach TG, Sue LI, Serrano GE, Lieberman AP, Albin RL, Ferrer I, Mash DC, Hulette CM, Ervin JF, Reiman EM, Hardy JA, Bennett DA, Schadt E, Smith RD, Myers AJ.

Brain. 2018 Sep 1;141(9):2721-2739. doi: 10.1093/brain/awy215.


Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry.

Chouinard CD, Nagy G, Webb IK, Shi T, Baker ES, Prost SA, Liu T, Ibrahim YM, Smith RD.

Anal Chem. 2018 Sep 18;90(18):10889-10896. doi: 10.1021/acs.analchem.8b02397. Epub 2018 Aug 29.


Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations.

Chouinard CD, Nagy G, Webb IK, Garimella SVB, Baker ES, Ibrahim YM, Smith RD.

Anal Chem. 2018 Sep 18;90(18):11086-11091. doi: 10.1021/acs.analchem.8b02990. Epub 2018 Aug 24.


Residual tissue repositories as a resource for population-based cancer proteomic studies.

Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD.

Clin Proteomics. 2018 Aug 3;15:26. doi: 10.1186/s12014-018-9202-4. eCollection 2018.


Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.

MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES.

J Am Soc Mass Spectrom. 2018 Nov;29(11):2182-2188. doi: 10.1007/s13361-018-2028-5. Epub 2018 Jul 25.


Representation of ICD-10-AM/ACHI Using Classification Markup Language (ClaML).

Smith RD, Ginige JA, Boulamatsis C.

Stud Health Technol Inform. 2018;252:126-131.


Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.

Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, Carr SA.

Nat Protoc. 2018 Jul;13(7):1632-1661. doi: 10.1038/s41596-018-0006-9.


Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation.

Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ, Worden AZ.

Nat Microbiol. 2018 Jul;3(7):781-790. doi: 10.1038/s41564-018-0178-7. Epub 2018 Jun 25.


Use of a novel electronic maternal surveillance system to generate automated alerts on the labor and delivery unit.

Klumpner TT, Kountanis JA, Langen ES, Smith RD, Tremper KK.

BMC Anesthesiol. 2018 Jun 26;18(1):78. doi: 10.1186/s12871-018-0540-6.


Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets.

Zhu Y, Dou M, Piehowski PD, Liang Y, Wang F, Chu RK, Chrisler WB, Smith JN, Schwarz KC, Shen Y, Shukla AK, Moore RJ, Smith RD, Qian WJ, Kelly RT.

Mol Cell Proteomics. 2018 Sep;17(9):1864-1874. doi: 10.1074/mcp.TIR118.000686. Epub 2018 Jun 24.


The MPLEx Protocol for Multi-omic Analyses of Soil Samples.

Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA 3rd, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES.

J Vis Exp. 2018 May 30;(135). doi: 10.3791/57343.


Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia.

Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA.

Ann Neurol. 2018 Jul;84(1):78-88. doi: 10.1002/ana.25266. Epub 2018 Jul 3.


Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA.

Otwell AE, Callister SJ, Sherwood RW, Zhang S, Goldman AR, Smith RD, Richardson RE.

Geobiology. 2018 Sep;16(5):522-539. doi: 10.1111/gbi.12295. Epub 2018 Jun 15.


Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.

Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0.


Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS.

Zhu Y, Clair G, Chrisler WB, Shen Y, Zhao R, Shukla AK, Moore RJ, Misra RS, Pryhuber GS, Smith RD, Ansong C, Kelly RT.

Angew Chem Int Ed Engl. 2018 Sep 17;57(38):12370-12374. doi: 10.1002/anie.201802843. Epub 2018 Jun 14.


Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics.

Rodland KD, Piehowski P, Smith RD.

Cancer J. 2018 May/Jun;24(3):121-125. doi: 10.1097/PPO.0000000000000315. Review.


An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies.

Bilbao A, Gibbons BC, Slysz GW, Crowell KL, Monroe ME, Ibrahim YM, Smith RD, Payne SH, Baker ES.

Int J Mass Spectrom. 2018 Apr;427:91-99. doi: 10.1016/j.ijms.2017.11.003. Epub 2017 Nov 6.


Are sweet snacks more sensitive to price increases than sugar-sweetened beverages: analysis of British food purchase data.

Smith RD, Cornelsen L, Quirmbach D, Jebb SA, Marteau TM.

BMJ Open. 2018 Apr 26;8(4):e019788. doi: 10.1136/bmjopen-2017-019788. Erratum in: BMJ Open. 2018 May 17;8(5):e019788corr1.


Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data.

Stanfill BA, Nakayasu ES, Bramer LM, Thompson AM, Ansong CK, Clauss TR, Gritsenko MA, Monroe ME, Moore RJ, Orton DJ, Piehowski PD, Schepmoes AA, Smith RD, Webb-Robertson BM, Metz TO; TEDDY Study Group.

Mol Cell Proteomics. 2018 Sep;17(9):1824-1836. doi: 10.1074/mcp.RA118.000648. Epub 2018 Apr 17.


Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway.

Yi L, Shi T, Gritsenko MA, X'avia Chan CY, Fillmore TL, Hess BM, Swensen AC, Liu T, Smith RD, Wiley HS, Qian WJ.

Anal Chem. 2018 Apr 17;90(8):5256-5263. doi: 10.1021/acs.analchem.8b00071. Epub 2018 Apr 3.


Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples.

Zhu Y, Zhao R, Piehowski PD, Moore RJ, Lim S, Orphan VJ, Paša-Tolić L, Qian WJ, Smith RD, Kelly RT.

Int J Mass Spectrom. 2018 Apr;427:4-10. doi: 10.1016/j.ijms.2017.08.016. Epub 2017 Sep 1.


A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry.

Zheng X, Aly NA, Zhou Y, Dupuis KT, Bilbao A, Paurus VL, Orton DJ, Wilson R, Payne SH, Smith RD, Baker ES.

Chem Sci. 2017 Nov 1;8(11):7724-7736. doi: 10.1039/c7sc03464d. Epub 2017 Sep 28.


Characterization of the Ovarian Tumor Peptidome.

Liu T, Rodland KD, Smith RD.

Vitam Horm. 2018;107:515-531. doi: 10.1016/bs.vh.2018.01.020. Epub 2018 Feb 22.

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