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Items: 1 to 50 of 150

1.

Spatial presentation of biological molecules to cells by localized diffusive transfer.

Regier MC, Olszewski E, Carter CC, Aitchison JD, Kaushansky A, Davis J, Berthier E, Beebe DJ, Stevens KR.

Lab Chip. 2019 Jun 11;19(12):2114-2126. doi: 10.1039/c9lc00122k.

PMID:
31111131
2.

Meta-analysis of Plasmodium falciparum var Signatures Contributing to Severe Malaria in African Children and Indian Adults.

Duffy F, Bernabeu M, Babar PH, Kessler A, Wang CW, Vaz M, Chery L, Mandala WL, Rogerson SJ, Taylor TE, Seydel KB, Lavstsen T, Gomes E, Kim K, Lusingu J, Rathod PK, Aitchison JD, Smith JD.

MBio. 2019 Apr 30;10(2). pii: e00217-19. doi: 10.1128/mBio.00217-19.

3.

Alterations in Phosphorylation of Hepatocyte Ribosomal Protein S6 Control Plasmodium Liver Stage Infection.

Glennon EKK, Austin LS, Arang N, Kain HS, Mast FD, Vijayan K, Aitchison JD, Kappe SHI, Kaushansky A.

Cell Rep. 2019 Mar 19;26(12):3391-3399.e4. doi: 10.1016/j.celrep.2019.02.085.

4.

Characterization of Peroxisomal Regulation Networks.

Mast FD, Aitchison JD.

Subcell Biochem. 2018;89:367-382. doi: 10.1007/978-981-13-2233-4_16. Review.

PMID:
30378032
5.

ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum.

Mast FD, Herricks T, Strehler KM, Miller LR, Saleem RA, Rachubinski RA, Aitchison JD.

J Cell Biol. 2018 Jun 4;217(6):2087-2102. doi: 10.1083/jcb.201706044. Epub 2018 Mar 27.

6.

Integrative structure and functional anatomy of a nuclear pore complex.

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP.

Nature. 2018 Mar 22;555(7697):475-482. doi: 10.1038/nature26003. Epub 2018 Mar 14.

7.

Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes.

Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC.

Mol Biol Cell. 2018 May 1;29(9):1100-1110. doi: 10.1091/mbc.E17-06-0430.

8.

The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria.

Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A.

Front Microbiol. 2017 Nov 16;8:2183. doi: 10.3389/fmicb.2017.02183. eCollection 2017. Review.

9.

Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria.

Kessler A, Dankwa S, Bernabeu M, Harawa V, Danziger SA, Duffy F, Kampondeni SD, Potchen MJ, Dambrauskas N, Vigdorovich V, Oliver BG, Hochman SE, Mowrey WB, MacCormick IJC, Mandala WL, Rogerson SJ, Sather DN, Aitchison JD, Taylor TE, Seydel KB, Smith JD, Kim K.

Cell Host Microbe. 2017 Nov 8;22(5):601-614.e5. doi: 10.1016/j.chom.2017.09.009. Epub 2017 Oct 26.

10.

Adaptive Prediction Emerges Over Short Evolutionary Time Scales.

López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS.

Genome Biol Evol. 2017 Jun 1;9(6):1616-1623. doi: 10.1093/gbe/evx116.

11.

ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth.

Herricks T, Mast FD, Li S, Aitchison JD.

J Vis Exp. 2017 Jul 3;(125). doi: 10.3791/55879.

12.

An indicator cell assay for blood-based diagnostics.

Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ.

PLoS One. 2017 Jun 8;12(6):e0178608. doi: 10.1371/journal.pone.0178608. eCollection 2017.

13.

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.

Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND.

PLoS Comput Biol. 2017 May 17;13(5):e1005489. doi: 10.1371/journal.pcbi.1005489. eCollection 2017 May.

14.

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

Herricks T, Dilworth DJ, Mast FD, Li S, Smith JJ, Ratushny AV, Aitchison JD.

G3 (Bethesda). 2017 Jan 5;7(1):279-288. doi: 10.1534/g3.116.037044.

15.

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.

Maishman L, Obado SO, Alsford S, Bart JM, Chen WM, Ratushny AV, Navarro M, Horn D, Aitchison JD, Chait BT, Rout MP, Field MC.

Nucleic Acids Res. 2016 Dec 15;44(22):10554-10570. Epub 2016 Sep 12.

16.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

17.

Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.

Bernabeu M, Danziger SA, Avril M, Vaz M, Babar PH, Brazier AJ, Herricks T, Maki JN, Pereira L, Mascarenhas A, Gomes E, Chery L, Aitchison JD, Rathod PK, Smith JD.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):E3270-9. doi: 10.1073/pnas.1524294113. Epub 2016 May 16.

18.

Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum.

Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD.

J Biol Chem. 2016 Jul 22;291(30):15408-27. doi: 10.1074/jbc.M116.728154. Epub 2016 Apr 29.

19.

The interactome challenge.

Aitchison JD, Rout MP.

J Cell Biol. 2015 Nov 23;211(4):729-32. doi: 10.1083/jcb.201510108. Epub 2015 Nov 16.

20.

Corrigendum: Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.

Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM.

Nature. 2015 Sep 3;525(7567):144. doi: 10.1038/nature14555. Epub 2015 Jul 8. No abstract available.

PMID:
26153856
21.

Signaling dynamics and peroxisomes.

Mast FD, Rachubinski RA, Aitchison JD.

Curr Opin Cell Biol. 2015 Aug;35:131-6. doi: 10.1016/j.ceb.2015.05.002. Epub 2015 May 29. Review.

22.

Rapid, optimized interactomic screening.

Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J.

Nat Methods. 2015 Jun;12(6):553-60. doi: 10.1038/nmeth.3395. Epub 2015 May 4.

23.

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.

BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15.

24.

Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.

Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR.

J Proteomics Bioinform. 2015;8(10):231-239.

25.

Systems cell biology.

Mast FD, Ratushny AV, Aitchison JD.

J Cell Biol. 2014 Sep 15;206(6):695-706. doi: 10.1083/jcb.201405027. Review.

26.

Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria.

Finney OC, Danziger SA, Molina DM, Vignali M, Takagi A, Ji M, Stanisic DI, Siba PM, Liang X, Aitchison JD, Mueller I, Gardner MJ, Wang R.

Mol Cell Proteomics. 2014 Oct;13(10):2646-60. doi: 10.1074/mcp.M113.036632. Epub 2014 Jul 14.

27.

Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection.

Carpp LN, Rogers RS, Moritz RL, Aitchison JD.

Mol Cell Proteomics. 2014 Nov;13(11):2836-54. doi: 10.1074/mcp.M114.038984. Epub 2014 May 22.

28.

The multifunctional nuclear pore complex: a platform for controlling gene expression.

Ptak C, Aitchison JD, Wozniak RW.

Curr Opin Cell Biol. 2014 Jun;28:46-53. doi: 10.1016/j.ceb.2014.02.001. Epub 2014 Mar 22. Review.

29.

An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.

Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS.

Mol Microbiol. 2014 Apr;92(2):369-82. doi: 10.1111/mmi.12564. Epub 2014 Mar 19.

30.

Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity.

Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC.

Mol Biol Cell. 2014 May;25(9):1421-36. doi: 10.1091/mbc.E13-12-0750. Epub 2014 Mar 5.

31.

Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.

Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM.

Nature. 2014 Jan 30;505(7485):691-5. doi: 10.1038/nature12862. Epub 2013 Nov 27. Erratum in: Nature. 2015 Sep 3;525(7567):144.

32.

Peroxisomes take shape.

Smith JJ, Aitchison JD.

Nat Rev Mol Cell Biol. 2013 Dec;14(12):803-17. doi: 10.1038/nrm3700. Review.

33.

Molecular mechanisms of system responses to novel stimuli are predictable from public data.

Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD.

Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31.

34.

PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.

Chen WM, Danziger SA, Chiang JH, Aitchison JD.

Bioinformatics. 2013 Oct 1;29(19):2435-44. doi: 10.1093/bioinformatics/btt387. Epub 2013 Jul 5.

35.

Multifunctional double-negative T cells in sooty mangabeys mediate T-helper functions irrespective of SIV infection.

Sundaravaradan V, Saleem R, Micci L, Gasper MA, Ortiz AM, Else J, Silvestri G, Paiardini M, Aitchison JD, Sodora DL.

PLoS Pathog. 2013;9(6):e1003441. doi: 10.1371/journal.ppat.1003441. Epub 2013 Jun 27.

36.

A role for the nucleoporin Nup170p in chromatin structure and gene silencing.

Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.

Cell. 2013 Feb 28;152(5):969-83. doi: 10.1016/j.cell.2013.01.049.

37.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3645-50. doi: 10.1073/pnas.1216918110. Epub 2013 Feb 6.

38.

Metallochaperones regulate intracellular copper levels.

Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.

PLoS Comput Biol. 2013;9(1):e1002880. doi: 10.1371/journal.pcbi.1002880. Epub 2013 Jan 17.

39.

Global analysis of condition-specific subcellular protein distribution and abundance.

Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.

Mol Cell Proteomics. 2013 May;12(5):1421-35. doi: 10.1074/mcp.O112.019166. Epub 2013 Jan 24.

40.

A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.

Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.

Nature. 2012 Oct 18;490(7420):421-5. doi: 10.1038/nature11428. Epub 2012 Sep 16.

41.

Asymmetric positive feedback loops reliably control biological responses.

Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD.

Mol Syst Biol. 2012 Apr 24;8:577. doi: 10.1038/msb.2012.10.

42.

NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.

DuBois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD, Navarro M, Horn D, Aitchison JD, Rout MP, Field MC.

PLoS Biol. 2012;10(3):e1001287. doi: 10.1371/journal.pbio.1001287. Epub 2012 Mar 27.

43.

The yeast nuclear pore complex and transport through it.

Aitchison JD, Rout MP.

Genetics. 2012 Mar;190(3):855-83. doi: 10.1534/genetics.111.127803.

44.

Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.

Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.

Mol Cell Proteomics. 2012 Apr;11(4):M111.014985. doi: 10.1074/mcp.M111.014985. Epub 2011 Dec 20.

45.

A regression model approach to enable cell morphology correction in high-throughput flow cytometry.

Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.

Mol Syst Biol. 2011 Sep 27;7:531. doi: 10.1038/msb.2011.64.

46.

Mathematical modeling of biomolecular network dynamics.

Ratushny AV, Ramsey SA, Aitchison JD.

Methods Mol Biol. 2011;781:415-33. doi: 10.1007/978-1-61779-276-2_21.

47.

Statistical analysis of dynamic transcriptional regulatory network structure.

Smith JJ, Saleem RA, Aitchison JD.

Methods Mol Biol. 2011;781:337-52. doi: 10.1007/978-1-61779-276-2_16.

PMID:
21877289
48.

Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

Ratushny AV, Shmulevich I, Aitchison JD.

PLoS Comput Biol. 2011 Jun;7(6):e1002091. doi: 10.1371/journal.pcbi.1002091. Epub 2011 Jun 30.

49.

The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast.

Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA.

Mol Biol Cell. 2011 May 15;22(10):1727-38. doi: 10.1091/mbc.E11-01-0084. Epub 2011 Mar 25.

50.

Faster, quantitative, and accurate precursor acquisition independent from ion count.

Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.

Anal Chem. 2011 Mar 15;83(6):2250-7. doi: 10.1021/ac103079q. Epub 2011 Feb 22.

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