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Results: 1 to 20 of 25

1.

Pseudomonas aeruginosa wound infection involves activation of its iron acquisition system in response to fascial contact.

Kim M, Christley S, Khodarev NN, Fleming I, Huang Y, Chang E, Zaborina O, Alverdy JC.

J Trauma Acute Care Surg. 2015 Apr;78(4):823-9. doi: 10.1097/TA.0000000000000574.

PMID:
25807409
2.

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

Cockrell RC, Christley S, Chang E, An G.

PLoS One. 2015 Mar 25;10(3):e0122192. doi: 10.1371/journal.pone.0122192. eCollection 2015.

3.

Intestinal anastomotic injury alters spatially defined microbiome composition and function.

Shogan BD, Smith DP, Christley S, Gilbert JA, Zaborina O, Alverdy JC.

Microbiome. 2014 Sep 15;2:35. doi: 10.1186/2049-2618-2-35. eCollection 2014.

4.

Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT).

Cockrell C, Christley S, An G.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003507. doi: 10.1371/journal.pcbi.1003507. eCollection 2014 Mar.

5.

The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013.

Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC Jr, Levin H, Rosenthal M, Foxman B, Chang EB, Siegel J, Cobey S, An G, Alverdy JC, Olsiewski PJ, Martin MO, Marrs R, Hernandez M, Christley S, Morowitz M, Weber S, Gilbert J.

Stand Genomic Sci. 2013 Jul 25;8(3):571-9. doi: 10.4056/sigs.4187859. eCollection 2013 Jul 30. No abstract available.

6.

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.

Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q.

BMC Syst Biol. 2014 Jan 8;8:3. doi: 10.1186/1752-0509-8-3.

7.
8.

Bayesian inference of the lung alveolar spatial model for the identification of alveolar mechanics associated with acute respiratory distress syndrome.

Christley S, Emr B, Ghosh A, Satalin J, Gatto L, Vodovotz Y, Nieman GF, An G.

Phys Biol. 2013 Jun;10(3):036008. doi: 10.1088/1478-3975/10/3/036008. Epub 2013 Apr 18.

PMID:
23598859
9.
10.

Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution.

Stern JR, Christley S, Zaborina O, Alverdy JC, An G.

Wound Repair Regen. 2012 Nov-Dec;20(6):862-71. doi: 10.1111/j.1524-475X.2012.00852.x. Epub 2012 Oct 30.

11.

Multiscale model of fibrin accumulation on the blood clot surface and platelet dynamics.

Xu Z, Christley S, Lioi J, Kim O, Harvey C, Sun W, Rosen ED, Alber M.

Methods Cell Biol. 2012;110:367-88. doi: 10.1016/B978-0-12-388403-9.00014-X.

PMID:
22482956
12.

Immature oxidative stress management as a unifying principle in the pathogenesis of necrotizing enterocolitis: insights from an agent-based model.

Kim M, Christley S, Alverdy JC, Liu D, An G.

Surg Infect (Larchmt). 2012 Feb;13(1):18-32. doi: 10.1089/sur.2011.057. Epub 2012 Jan 4.

13.

An automated homology-based approach for identifying transposable elements.

Kennedy RC, Unger MF, Christley S, Collins FH, Madey GR.

BMC Bioinformatics. 2011 May 3;12:130. doi: 10.1186/1471-2105-12-130.

14.

Data structures and compression algorithms for high-throughput sequencing technologies.

Daily K, Rigor P, Christley S, Xie X, Baldi P.

BMC Bioinformatics. 2010 Oct 14;11:514. doi: 10.1186/1471-2105-11-514.

15.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.

Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.

16.

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms.

Christley S, Lee B, Dai X, Nie Q.

BMC Syst Biol. 2010 Aug 9;4:107. doi: 10.1186/1752-0509-4-107.

17.

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.

Wang Y, Christley S, Mjolsness E, Xie X.

BMC Syst Biol. 2010 Jul 21;4:99. doi: 10.1186/1752-0509-4-99.

18.

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR.

Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12168-73. doi: 10.1073/pnas.1003379107. Epub 2010 Jun 21. Erratum in: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6335. Krause, Emily [corrected to Kraus, Emily].

19.

Incorporating existing network information into gene network inference.

Christley S, Nie Q, Xie X.

PLoS One. 2009 Aug 27;4(8):e6799. doi: 10.1371/journal.pone.0006799.

20.

VectorBase: a data resource for invertebrate vector genomics.

Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.

Nucleic Acids Res. 2009 Jan;37(Database issue):D583-7. doi: 10.1093/nar/gkn857. Epub 2008 Nov 21.

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