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Results: 1 to 20 of 22

1.

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.

PMID:
24675765
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24501640
[PubMed]
Free PMC Article
3.

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.

PMID:
24397936
[PubMed - in process]
Free PMC Article
4.
5.

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
[PubMed - indexed for MEDLINE]
6.

Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling.

An G, Christley S.

Crit Rev Biomed Eng. 2012;40(4):323-40. Review.

PMID:
23140123
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23110640
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
22217195
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21535899
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
20946637
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20929810
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
20696053
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
20663171
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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].

PMID:
20566863
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
19710931
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
19028744
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Human genomes as email attachments.

Christley S, Lu Y, Li C, Xie X.

Bioinformatics. 2009 Jan 15;25(2):274-5. doi: 10.1093/bioinformatics/btn582. Epub 2008 Nov 7.

PMID:
18996942
[PubMed - indexed for MEDLINE]
Free Article
19.

Multiple organism algorithm for finding ultraconserved elements.

Christley S, Lobo NF, Madey G.

BMC Bioinformatics. 2008 Jan 11;9:15. doi: 10.1186/1471-2105-9-15.

PMID:
18186941
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Multiscale models for vertebrate limb development.

Newman SA, Christley S, Glimm T, Hentschel HG, Kazmierczak B, Zhang YT, Zhu J, Alber M.

Curr Top Dev Biol. 2008;81:311-40. Review.

PMID:
18023733
[PubMed - indexed for MEDLINE]

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