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Items: 1 to 50 of 80

1.

A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes.

Li GXL, Munro D, Fermin D, Vogel C, Choi H.

Hum Mutat. 2020 Jan 12. doi: 10.1002/humu.23979. [Epub ahead of print]

PMID:
31930623
2.

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.

Koh HWL, Fermin D, Vogel C, Choi KP, Ewing RM, Choi H.

NPJ Syst Biol Appl. 2019 Jul 9;5:22. doi: 10.1038/s41540-019-0099-y. eCollection 2019.

3.

Disruption of the exocyst induces podocyte loss and dysfunction.

Nihalani D, Solanki AK, Arif E, Srivastava P, Rahman B, Zuo X, Dang Y, Fogelgren B, Fermin D, Gillies CE, Sampson MG, Lipschutz JH.

J Biol Chem. 2019 Jun 28;294(26):10104-10119. doi: 10.1074/jbc.RA119.008362. Epub 2019 May 9.

PMID:
31073028
4.

Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis.

Graham SE, Nielsen JB, Zawistowski M, Zhou W, Fritsche LG, Gabrielsen ME, Skogholt AH, Surakka I, Hornsby WE, Fermin D, Larach DB, Kheterpal S, Brummett CM, Lee S, Kang HM, Abecasis GR, Romundstad S, Hallan S, Sampson MG, Hveem K, Willer CJ.

Nat Commun. 2019 Apr 23;10(1):1847. doi: 10.1038/s41467-019-09861-z.

5.

Mapping Shunting Paths at the Surface of Cu2ZnSn(S,Se)4 Films via Energy-Filtered Photoemission Microscopy.

Tiwari D, Cattelan M, Harniman RL, Sarua A, Abbas A, Bowers JW, Fox NA, Fermin DJ.

iScience. 2018 Nov 30;9:36-46. doi: 10.1016/j.isci.2018.10.004. Epub 2018 Oct 13.

6.

Effect of Ba Content on the Activity of La1-x Ba x MnO3 Towards the Oxygen Reduction Reaction.

Gobaille-Shaw GPA, Celorrio V, Calvillo L, Morris LJ, Granozzi G, Fermín DJ.

ChemElectroChem. 2018 Jul 11;5(14):1922-1927. doi: 10.1002/celc.201800052. Epub 2018 Apr 6.

7.

An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.

Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, Hoover P, Lieb D, Li S, Eddy S, Fermin D, McNulty MT; Nephrotic Syndrome Study Network (NEPTUNE), Hacohen N, Kiryluk K, Kretzler M, Wen X, Sampson MG.

Am J Hum Genet. 2018 Aug 2;103(2):232-244. doi: 10.1016/j.ajhg.2018.07.004. Epub 2018 Jul 26.

8.

Investigating the Role of the Organic Cation in Formamidinium Lead Iodide Perovskite Using Ultrafast Spectroscopy.

Taylor VCA, Tiwari D, Duchi M, Donaldson PM, Clark IP, Fermin DJ, Oliver TAA.

J Phys Chem Lett. 2018 Feb 15;9(4):895-901. doi: 10.1021/acs.jpclett.7b03296. Epub 2018 Feb 8.

9.

A comparative global phosphoproteomics analysis of obinutuzumab (GA101) versus rituximab (RTX) against RTX sensitive and resistant Burkitt lymphoma (BL) demonstrates differential phosphorylation of signaling pathway proteins after treatment.

Awasthi A, Rolland DCM, Ayello J, van de Ven C, Basrur V, Conlon K, Fermin D, Barth MJ, Klein C, Elenitoba-Johnson KSJ, Lim MS, Cairo MS.

Oncotarget. 2017 Dec 9;8(69):113895-113909. doi: 10.18632/oncotarget.23040. eCollection 2017 Dec 26.

10.

AMnO3 (A = Sr, La, Ca, Y) Perovskite Oxides as Oxygen Reduction Electrocatalysts.

Celorrio V, Calvillo L, Granozzi G, Russell AE, Fermin DJ.

Top Catal. 2018;61(3):154-161. doi: 10.1007/s11244-018-0886-5. Epub 2018 Jan 16.

11.

Prevention and Treatment of Thrombotic and Hemorrhagic Complications in Patients Supported by Continuous-Flow Left Ventricular Assist Devices.

Loyaga-Rendon RY, Jani M, Fermin D, McDermott JK, Vancamp D, Lee S.

Curr Heart Fail Rep. 2017 Dec;14(6):465-477. doi: 10.1007/s11897-017-0367-3. Review.

PMID:
29075955
12.

Real-time tracking of metal nucleation via local perturbation of hydration layers.

Harniman RL, Plana D, Carter GH, Bradley KA, Miles MJ, Fermín DJ.

Nat Commun. 2017 Oct 17;8(1):971. doi: 10.1038/s41467-017-01087-1.

13.

Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.

Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6581-6586. doi: 10.1073/pnas.1701263114. Epub 2017 Jun 12.

14.

Single Molecular Precursor Solution for CuIn(S,Se)2 Thin Films Photovoltaic Cells: Structure and Device Characteristics.

Tiwari D, Koehler T, Lin X, Sarua A, Harniman R, Wang L, Klenk R, Fermin DJ.

ACS Appl Mater Interfaces. 2017 Jan 25;9(3):2301-2308. doi: 10.1021/acsami.6b12306. Epub 2017 Jan 12.

15.

Nanopores: general discussion.

Mount A, Kang M, Fermin D, Albrecht T, Gooding J, Crooks R, Tao N, Schmickler W, MacPherson J, Chen S, Actis P, Magnussen O, Baker L, Bartlett P, Faez S, Clausmeyer J, Thomas B, Ash PA, Kanoufi F, Long Y, Unwin P, Koper M, Lemay S, Ewing A, Tian Z, Johnson R, Eikerling M, Platt M.

Faraday Discuss. 2016 Dec 12;193:507-531. No abstract available.

PMID:
27892975
16.

Electrochemistry of single nanoparticles: general discussion.

Albrecht T, MacPherson J, Magnussen O, Fermin D, Crooks R, Gooding J, Hersbach T, Kanoufi F, Schuhmann W, Bentley C, Tao N, Mitra S, Krischer K, Tschulik K, Faez S, Nogala W, Unwin P, Long Y, Koper M, Tian Z, Alpuche-Aviles MA, White H, Brasiliense V, Kranz C, Schmickler W, Stevenson K, Jing C, Edwards M.

Faraday Discuss. 2016 Dec 12;193:387-413. No abstract available.

PMID:
27892971
17.

From single cells to single molecules: general discussion.

Gooding J, Magnussen O, Fermin D, Crooks R, Kanoufi F, Schuhmann W, Nichols R, Schmickler W, Tao N, Chen S, Actis P, Page A, Tschulik K, Faez S, Edwards M, Johnson R, Nogala W, Kranz C, Eikerling M, Unwin P, Thomas B, Prabhakaran V, Clausmeyer J, Vincent K, Koper M, Tian Z, Mount A, Alpuche-Aviles MA, White H, Ewing A, Higgins S, Baker L, Zhan D, Ulstrup J, Bohn PW, Lemay S.

Faraday Discuss. 2016 Dec 12;193:141-170. doi: 10.1039/c6fd90066f. No abstract available.

PMID:
27892970
18.

Reactions at the nanoscale: general discussion.

Hersbach T, MacPherson J, Magnussen O, Crooks R, Higgins S, Fermin D, Kanoufi F, Schuhmann W, Nichols R, Mitra S, Schmickler W, Tschulik K, Bartlett P, Faez S, Nogala W, Eikerling M, Kranz C, Unwin P, Koper M, Lemay S, Mount A, Ewing A, Tian Z, White H, Chen S, Clausmeyer J, Krischer K.

Faraday Discuss. 2016 Dec 12;193:265-292. No abstract available.

PMID:
27892968
19.

Enhanced MFC power production and struvite recovery by the addition of sea salts to urine.

Merino-Jimenez I, Celorrio V, Fermin DJ, Greenman J, Ieropoulos I.

Water Res. 2017 Feb 1;109:46-53. doi: 10.1016/j.watres.2016.11.017. Epub 2016 Nov 4.

20.

Effect of Bioconjugation on the Reduction Potential of Heme Proteins.

Risbridger TA, Watkins DW, Armstrong JP, Perriman AW, Anderson JL, Fermin DJ.

Biomacromolecules. 2016 Nov 14;17(11):3485-3492. Epub 2016 Oct 3.

PMID:
27650815
21.

Observation of antisite domain boundaries in Cu2ZnSnS4 by atomic-resolution transmission electron microscopy.

Kattan NA, Griffiths IJ, Cherns D, Fermín DJ.

Nanoscale. 2016 Aug 14;8(30):14369-73. doi: 10.1039/c6nr04185j. Epub 2016 Jul 13.

PMID:
27405278
22.

SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data.

Teo G, Koh H, Fermin D, Lambert JP, Knight JD, Gingras AC, Choi H.

Proteomics. 2016 Aug;16(15-16):2238-45. doi: 10.1002/pmic.201500499. Epub 2016 May 27.

PMID:
27119218
23.

Over 75% incident-photon-to-current efficiency without solid electrodes.

Plana D, Bradley KA, Tiwari D, Fermín DJ.

Phys Chem Chem Phys. 2016 May 14;18(18):12428-33. doi: 10.1039/c6cp02231f. Epub 2016 Apr 22.

PMID:
27103001
24.

Ion flow in a zeolitic imidazolate framework results in ionic diode phenomena.

Madrid E, Buckingham MA, Stone JM, Rogers AT, Gee WJ, Burrows AD, Raithby PR, Celorrio V, Fermin DJ, Marken F.

Chem Commun (Camb). 2016 Feb 14;52(13):2792-4. doi: 10.1039/c5cc09780k.

PMID:
26771027
25.

Fast One-Pot Synthesis of MoS2/Crumpled Graphene p-n Nanonjunctions for Enhanced Photoelectrochemical Hydrogen Production.

Carraro F, Calvillo L, Cattelan M, Favaro M, Righetto M, Nappini S, Píš I, Celorrio V, Fermín DJ, Martucci A, Agnoli S, Granozzi G.

ACS Appl Mater Interfaces. 2015 Nov 25;7(46):25685-92. doi: 10.1021/acsami.5b06668. Epub 2015 Nov 10.

PMID:
26517577
26.

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;129:121-126. doi: 10.1016/j.jprot.2015.07.036. Epub 2015 Aug 4.

27.

Surface activation of Pt nanoparticles synthesised by "hot injection" in the presence of oleylamine.

Humphrey JJ, Sadasivan S, Plana D, Celorrio V, Tooze RA, Fermín DJ.

Chemistry. 2015 Sep 1;21(36):12694-701. doi: 10.1002/chem.201501496. Epub 2015 Jul 17.

28.

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.

29.

EBprot: Statistical analysis of labeling-based quantitative proteomics data.

Koh HW, Swa HL, Fermin D, Ler SG, Gunaratne J, Choi H.

Proteomics. 2015 Aug;15(15):2580-91. doi: 10.1002/pmic.201400620. Epub 2015 May 28.

PMID:
25913743
30.

Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma.

El-Mallawany NK, Day N, Ayello J, Van de Ven C, Conlon K, Fermin D, Basrur V, Elenitoba-Johnson K, Lim M, Cairo MS.

Eur J Cancer. 2015 Jan;51(1):92-100. doi: 10.1016/j.ejca.2014.10.017. Epub 2014 Nov 6.

PMID:
25466511
31.

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

Fermin D, Avtonomov D, Choi H, Nesvizhskii AI.

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.

32.

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas.

Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS.

Am J Pathol. 2014 May;184(5):1331-42. doi: 10.1016/j.ajpath.2014.01.036. Epub 2014 Mar 22.

33.

Porous boron-doped diamond/carbon nanotube electrodes.

Zanin H, May PW, Fermin DJ, Plana D, Vieira SM, Milne WI, Corat EJ.

ACS Appl Mater Interfaces. 2014 Jan 22;6(2):990-5. doi: 10.1021/am4044344. Epub 2014 Jan 6.

PMID:
24392640
34.

Lactose as a "Trojan horse" for quantum dot cell transport.

Benito-Alifonso D, Tremel S, Hou B, Lockyear H, Mantell J, Fermin DJ, Verkade P, Berry M, Galan MC.

Angew Chem Int Ed Engl. 2014 Jan 13;53(3):810-4. doi: 10.1002/anie.201307232. Epub 2013 Dec 5.

35.

Redox transitions in an electrolyte-free myoglobin fluid.

Sharma KP, Bradley K, Brogan AP, Mann S, Perriman AW, Fermin DJ.

J Am Chem Soc. 2013 Dec 11;135(49):18311-4. doi: 10.1021/ja4104606. Epub 2013 Nov 26.

PMID:
24245589
36.

Initial stages in the formation of Cu2ZnSn(S,Se)4 nanoparticles.

Hou B, Benito-Alifonso D, Kattan N, Cherns D, Galan MC, Fermín DJ.

Chemistry. 2013 Nov 18;19(47):15847-51. doi: 10.1002/chem.201302722. Epub 2013 Oct 21. No abstract available.

PMID:
24151102
37.

Reconstructing targetable pathways in lung cancer by integrating diverse omics data.

Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM.

Nat Commun. 2013;4:2617. doi: 10.1038/ncomms3617.

38.

Tuning CO2 electroreduction efficiency at Pd shells on Au nanocores.

Plana D, Flórez-Montaño J, Celorrio V, Pastor E, Fermín DJ.

Chem Commun (Camb). 2013 Dec 4;49(93):10962-4. doi: 10.1039/c3cc46543h.

PMID:
24131917
39.

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.

40.

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI.

Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5.

41.

Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma.

McDonnell SR, Hwang SR, Rolland D, Murga-Zamalloa C, Basrur V, Conlon KP, Fermin D, Wolfe T, Raskind A, Ruan C, Jiang JK, Thomas CJ, Hogaboam CM, Burant CF, Elenitoba-Johnson KS, Lim MS.

Blood. 2013 Aug 8;122(6):958-68. doi: 10.1182/blood-2013-01-482026. Epub 2013 Jun 27.

42.

Charge transport across high surface area metal/diamond nanostructured composites.

Plana D, Humphrey JJ, Bradley KA, Celorrio V, Fermín DJ.

ACS Appl Mater Interfaces. 2013 Apr 24;5(8):2985-90. doi: 10.1021/am302397p. Epub 2013 Apr 4.

PMID:
23510528
43.

Sparsely correlated hidden Markov models with application to genome-wide location studies.

Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS.

Bioinformatics. 2013 Mar 1;29(5):533-41. doi: 10.1093/bioinformatics/btt012. Epub 2013 Jan 16.

44.

Contrast in electron-transfer mediation between graphene oxide and reduced graphene oxide.

Hongthani W, Patil AJ, Mann S, Fermín DJ.

Chemphyschem. 2012 Aug 27;13(12):2956-63. doi: 10.1002/cphc.201200407. Epub 2012 Aug 2.

PMID:
22865797
45.

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

Ning K, Fermin D, Nesvizhskii AI.

J Proteome Res. 2012 Apr 6;11(4):2261-71. doi: 10.1021/pr201052x. Epub 2012 Feb 29.

46.

Anionic surfactant ionic liquids with 1-butyl-3-methyl-imidazolium cations: characterization and application.

Brown P, Butts CP, Eastoe J, Fermin D, Grillo I, Lee HC, Parker D, Plana D, Richardson RM.

Langmuir. 2012 Feb 7;28(5):2502-9. doi: 10.1021/la204557t. Epub 2012 Jan 19.

PMID:
22208500
47.

NPM-ALK signals through glycogen synthase kinase 3β to promote oncogenesis.

McDonnell SR, Hwang SR, Basrur V, Conlon KP, Fermin D, Wey E, Murga-Zamalloa C, Zeng Z, Zu Y, Elenitoba-Johnson KS, Lim MS.

Oncogene. 2012 Aug 9;31(32):3733-40. doi: 10.1038/onc.2011.542. Epub 2011 Dec 19.

48.

Electrochemical charge transfer mediated by metal nanoparticles and quantum dots.

Kissling GP, Miles DO, Fermín DJ.

Phys Chem Chem Phys. 2011 Dec 28;13(48):21175-85. doi: 10.1039/c1cp21996k. Epub 2011 Oct 5.

PMID:
21971063
49.

Insulating diamond particles as substrate for Pd electrocatalysts.

Moore A, Celorrio V, de Oca MM, Plana D, Hongthani W, Lázaro MJ, Fermín DJ.

Chem Commun (Camb). 2011 Jul 21;47(27):7656-8. doi: 10.1039/c1cc12387d. Epub 2011 Jun 7.

PMID:
21647528
50.

Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma.

Vareed SK, Bhat VB, Thompson C, Vasu VT, Fermin D, Choi H, Creighton CJ, Gayatri S, Lan L, Putluri N, Thangjam GS, Kaur P, Shabahang M, Giri JG, Nesvizhskii AI, Asea AA, Cashikar AG, Rao A, McLoughlin J, Sreekumar A.

PLoS One. 2011 Mar 23;6(3):e17177. doi: 10.1371/journal.pone.0017177.

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