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Items: 25


Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species.

Wunderlich Z, Fowlkes CC, Eckenrode KB, Bragdon MDJ, Abiri A, DePace AH.

G3 (Bethesda). 2019 Jul 9;9(7):2171-2182. doi: 10.1534/g3.118.200953.


Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies.

Rajendran PS, Challis RC, Fowlkes CC, Hanna P, Tompkins JD, Jordan MC, Hiyari S, Gabris-Weber BA, Greenbaum A, Chan KY, Deverman BE, Münzberg H, Ardell JL, Salama G, Gradinaru V, Shivkumar K.

Nat Commun. 2019 Apr 26;10(1):1944. doi: 10.1038/s41467-019-09770-1.


Intermittent Stem Cell Cycling Balances Self-Renewal and Senescence of the C. elegans Germ Line.

Cinquin A, Chiang M, Paz A, Hallman S, Yuan O, Vysniauskaite I, Fowlkes CC, Cinquin O.

PLoS Genet. 2016 Apr 14;12(4):e1005985. doi: 10.1371/journal.pgen.1005985. eCollection 2016 Apr.


Visual Recognition Software for Binary Classification and Its Application to Spruce Pollen Identification.

Tcheng DK, Nayak AK, Fowlkes CC, Punyasena SW.

PLoS One. 2016 Feb 11;11(2):e0148879. doi: 10.1371/journal.pone.0148879. eCollection 2016.


Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images.

Chiang M, Hallman S, Cinquin A, de Mochel NR, Paz A, Kawauchi S, Calof AL, Cho KW, Fowlkes CC, Cinquin O.

BMC Bioinformatics. 2015 Nov 25;16:397. doi: 10.1186/s12859-015-0814-7.


Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V.

Nat Protoc. 2015 Nov;10(11):1860-1896. doi: 10.1038/nprot.2015.122. Epub 2015 Oct 22.


A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate.

Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH.

Development. 2015 Feb 1;142(3):587-96. doi: 10.1242/dev.117796.


Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

Mander L, Li M, Mio W, Fowlkes CC, Punyasena SW.

Proc Biol Sci. 2013 Sep 18;280(1770):20131905. doi: 10.1098/rspb.2013.1905. Print 2013 Nov 7.


Feed-forward hierarchical model of the ventral visual stream applied to functional brain image classification.

Keator DB, Fallon JH, Lakatos A, Fowlkes CC, Potkin SG, Ihler A; Alzheimer's Disease Neuroimaging Initiative.

Hum Brain Mapp. 2014 Jan;35(1):38-52. doi: 10.1002/hbm.22149. Epub 2012 Jul 30.


Layered object models for image segmentation.

Yang Y, Hallman S, Ramanan D, Fowlkes CC.

IEEE Trans Pattern Anal Mach Intell. 2012 Sep;34(9):1731-43. doi: 10.1109/TPAMI.2011.208.


Quantitative analysis of axonal transport by using compartmentalized and surface micropatterned culture of neurons.

Kim HJ, Park JW, Byun JH, Poon WW, Cotman CW, Fowlkes CC, Jeon NL.

ACS Chem Neurosci. 2012 Jun 20;3(6):433-8.


Analysis of gap gene regulation in a 3D organism-scale model of the Drosophila melanogaster embryo.

Hengenius JB, Gribskov M, Rundell AE, Fowlkes CC, Umulis DM.

PLoS One. 2011;6(11):e26797. doi: 10.1371/journal.pone.0026797. Epub 2011 Nov 16.


Shrink-film configurable multiscale wrinkles for functional alignment of human embryonic stem cells and their cardiac derivatives.

Chen A, Lieu DK, Freschauf L, Lew V, Sharma H, Wang J, Nguyen D, Karakikes I, Hajjar RJ, Gopinathan A, Botvinick E, Fowlkes CC, Li RA, Khine M.

Adv Mater. 2011 Dec 22;23(48):5785-91. doi: 10.1002/adma.201103463. Epub 2011 Nov 8.


A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, Eisen MB, DePace AH.

PLoS Genet. 2011 Oct;7(10):e1002346. doi: 10.1371/journal.pgen.1002346. Epub 2011 Oct 27.


Multiscale biomimetic topography for the alignment of neonatal and embryonic stem cell-derived heart cells.

Luna JI, Ciriza J, Garcia-Ojeda ME, Kong M, Herren A, Lieu DK, Li RA, Fowlkes CC, Khine M, McCloskey KE.

Tissue Eng Part C Methods. 2011 May;17(5):579-88. doi: 10.1089/ten.TEC.2010.0410. Epub 2011 Feb 27.


Nonparametric identification of regulatory interactions from spatial and temporal gene expression data.

Aswani A, Keränen SV, Brown J, Fowlkes CC, Knowles DW, Biggin MD, Bickel P, Tomlin CJ.

BMC Bioinformatics. 2010 Aug 4;11:413. doi: 10.1186/1471-2105-11-413.


Natural-scene statistics predict how the figure-ground cue of convexity affects human depth perception.

Burge J, Fowlkes CC, Banks MS.

J Neurosci. 2010 May 26;30(21):7269-80. doi: 10.1523/JNEUROSCI.5551-09.2010.


Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.

Rübel O, Ahern S, Bethel EW, Biggin MD, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, Hendriks CL, Malik J, Meredith J, Messmer P, Prabhat, Ushizima D, Weber GH, Wu K.

Procedia Comput Sci. 2010 May;1(1):1757-1764.


Integrating data clustering and visualization for the analysis of 3D gene expression data.

Rübel O, Weber GH, Huang MY, Bethel EW, Biggin MD, Fowlkes CC, Luengo Hendriks CL, Keränen SV, Eisen MB, Knowles DW, Malik J, Hagen H, Hamann B.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):64-79. doi: 10.1109/TCBB.2008.49.


Visual exploration of three-dimensional gene expression using physical views and linked abstract views.

Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, Hamann B.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):296-309. doi: 10.1109/TCBB.2007.70249.


A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.

Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J.

Cell. 2008 Apr 18;133(2):364-74. doi: 10.1016/j.cell.2008.01.053.


Local figure-ground cues are valid for natural images.

Fowlkes CC, Martin DR, Malik J.

J Vis. 2007 Jun 8;7(8):2.


Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics.

Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, Malik J, Biggin MD.

Genome Biol. 2006;7(12):R124.


Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline.

Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin MD, Knowles DW.

Genome Biol. 2006;7(12):R123.


Learning to detect natural image boundaries using local brightness, color, and texture cues.

Martin DR, Fowlkes CC, Malik J.

IEEE Trans Pattern Anal Mach Intell. 2004 May;26(5):530-49.


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