Publications by authors named "Daniel G Brown"

49Publications

Mean and Variance of Phylogenetic Trees.

Syst Biol 2020 01;69(1):139-154

Department of Mathematics, Lehman College, City University of New York, 250 Bedford Park Blvd West, Bronx, New York, NY 10468, USA.

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http://dx.doi.org/10.1093/sysbio/syz041DOI Listing
January 2020

Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity.

Ecology 2016 Aug;97(8):1949-1960

Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, 09200, Moulis, France.

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http://dx.doi.org/10.1890/15-1759.1DOI Listing
August 2016

Multi-scale heterogeneity in vegetation and soil carbon in exurban residential land of southeastern Michigan, USA.

Ecol Appl 2016 Jul;26(5):1421-1436

School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan, 48109, USA.

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http://dx.doi.org/10.1890/15-0817DOI Listing
July 2016

Insufficient research on land grabbing.

Science 2016 Jul;353(6295):131

School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1126/science.aaf6565DOI Listing
July 2016

An assessment of air pollutant exposure methods in Mexico City, Mexico.

J Air Waste Manag Assoc 2015 May;65(5):581-91

a Department of Environmental Health Sciences , University of Michigan, School of Public Health , Ann Arbor , MI , USA.

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http://dx.doi.org/10.1080/10962247.2015.1020974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670782PMC
May 2015

Exploring agent-level calculations of risk and returns in relation to observed land-use changes in the US Great Plains, 1870-1940.

Reg Environ Change 2015 Feb;15(2):301-315

School of Natural Resources and Environment, University of Michigan, 440 Church St, Ann Arbor, MI 48109.

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http://dx.doi.org/10.1007/s10113-014-0628-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340090PMC
February 2015

Pollux: platform independent error correction of single and mixed genomes.

BMC Bioinformatics 2015 Jan 16;16:10. Epub 2015 Jan 16.

Department of Biology, University of Waterloo, 200 University Ave W, N2L3G1 Waterloo, Canada.

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http://dx.doi.org/10.1186/s12859-014-0435-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307147PMC
January 2015

Effects of rooting via out-groups on in-group topology in phylogeny.

Int J Bioinform Res Appl 2014 ;10(4-5):426-46

Cheriton School of Computer Science, Waterloo, Ontario, Canada.

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http://dx.doi.org/10.1504/IJBRA.2014.062993DOI Listing
March 2015

Cross-site comparison of land-use decision-making and its consequences across land systems with a generalized agent-based model.

PLoS One 2014 29;9(1):e86179. Epub 2014 Jan 29.

Department of Geography and Environmental Systems, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086179PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906050PMC
September 2014

Exploring agricultural livelihood transitions with an agent-based virtual laboratory: global forces to local decision-making.

PLoS One 2013 5;8(9):e73241. Epub 2013 Sep 5.

Department of Geography and Environmental Systems, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073241PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764159PMC
June 2014

Fast half-sibling population reconstruction: theory and algorithms.

Algorithms Mol Biol 2013 Jul 12;8(1):20. Epub 2013 Jul 12.

David R Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada.

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http://dx.doi.org/10.1186/1748-7188-8-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738158PMC
July 2013

Land Transitions in the American Plains: Multilevel Modeling of Drivers of Grassland Conversion (1950 to 2000).

Agric Ecosyst Environ 2013 Mar;168:7-15

Inter-University Consortium for Political and Social Research, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA 48106.

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http://dx.doi.org/10.1016/j.agee.2013.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634617PMC
March 2013

LSHPlace: fast phylogenetic placement using locality-sensitive hashing.

Pac Symp Biocomput 2013 :310-9

David R. Cheriton School of Computer Science, University of Waterloo, Waterloo ON N2L 3G1, Canada.

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December 2013

Towards a practical O(nlogn) phylogeny algorithm.

Algorithms Mol Biol 2012 Nov 26;7(1):32. Epub 2012 Nov 26.

David R, Cheriton School of Computer Science, University of Waterloo, Waterloo ON N2L 3G1 Canada.

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http://dx.doi.org/10.1186/1748-7188-7-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561654PMC
November 2012

PANDAseq: paired-end assembler for illumina sequences.

BMC Bioinformatics 2012 Feb 14;13:31. Epub 2012 Feb 14.

Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471323PMC
February 2012

Exploring walking differences by socioeconomic status using a spatial agent-based model.

Health Place 2012 Jan;18(1):96-9

Department of Epidemiology, Center for Social Epidemiology and Population Health, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1016/j.healthplace.2011.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3345574PMC
January 2012

Geostatistical exploration of spatial variation of summertime temperatures in the Detroit metropolitan region.

Environ Res 2011 Nov 14;111(8):1046-53. Epub 2011 Sep 14.

Department of Environmental Health Sciences, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1016/j.envres.2011.08.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345124PMC
November 2011

More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs.

BMC Bioinformatics 2011 May 17;12:168. Epub 2011 May 17.

David R Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada.

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http://dx.doi.org/10.1186/1471-2105-12-168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123234PMC
May 2011

A spatial agent-based model for the simulation of adults' daily walking within a city.

Am J Prev Med 2011 Mar;40(3):353-61

Department of Epidemiology, Center for Social Epidemiology and Population Health, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1016/j.amepre.2010.11.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306662PMC
March 2011

An agent-based model of income inequalities in diet in the context of residential segregation.

Am J Prev Med 2011 Mar;40(3):303-11

Department of Epidemiology and Biostatistics, Drexel University, 1505 Race Street, Philadelphia, PA 19102, USA.

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http://dx.doi.org/10.1016/j.amepre.2010.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625685PMC
March 2011

FEAST: sensitive local alignment with multiple rates of evolution.

IEEE/ACM Trans Comput Biol Bioinform 2011 May-Jun;8(3):698-709

David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.

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http://dx.doi.org/10.1109/TCBB.2010.76DOI Listing
August 2011

A spatial analysis of health-related resources in three diverse metropolitan areas.

Health Place 2010 Sep 15;16(5):885-92. Epub 2010 May 15.

Center for Social Epidemiology and Population Health, School of Public Health, University of Michigan, 109 Observatory Street, 3rd Floor, Ann Arbor, MI 48109-2029, USA.

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http://dx.doi.org/10.1016/j.healthplace.2010.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297427PMC
September 2010

New decoding algorithms for Hidden Markov Models using distance measures on labellings.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S40. Epub 2010 Jan 18.

David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009513PMC
January 2010

Decoding HMMs using the k best paths: algorithms and applications.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S28. Epub 2010 Jan 18.

Cheriton School of Computer Science, University of Waterloo, 200 University Avenue W, Waterloo, Ontario, Canada N2L 3G1.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009499PMC
January 2010

Mapping community determinants of heat vulnerability.

Environ Health Perspect 2009 Nov 10;117(11):1730-6. Epub 2009 Jun 10.

Environmental Health Sciences Division, School of Public Health, University of California at Berkeley, California 94720-7360, USA.

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http://dx.doi.org/10.1289/ehp.0900683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801183PMC
November 2009

US local action on heat and health: are we prepared for climate change?

Int J Public Health 2010 Apr 23;55(2):105-12. Epub 2009 Sep 23.

University of Michigan School of Public Health, 6631 SPH Tower, 109 South Observatory, Ann Arbor, MI 48109-2029, USA.

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http://dx.doi.org/10.1007/s00038-009-0071-5DOI Listing
April 2010

A tutorial of techniques for improving standard Hidden Markov Model algorithms.

J Bioinform Comput Biol 2009 Aug;7(4):737-54

David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.

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http://dx.doi.org/10.1142/s0219720009004242DOI Listing
August 2009

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.

Nucleic Acids Res 2009 Apr 5;37(7):e52. Epub 2009 Mar 5.

Department of Computer Science, Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia.

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http://dx.doi.org/10.1093/nar/gkp052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673418PMC
April 2009

Neighborhood resources for physical activity and healthy foods and their association with insulin resistance.

Epidemiology 2008 Jan;19(1):146-57

Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2029, USA.

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http://dx.doi.org/10.1097/EDE.0b013e31815c480DOI Listing
January 2008

Filling the gaps: spatial interpolation of residential survey data in the estimation of neighborhood characteristics.

Epidemiology 2007 Jul;18(4):469-78

Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan 48104, USA.

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http://dx.doi.org/10.1097/EDE.0b013e3180646320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772132PMC
July 2007

Toward an algebraic understanding of haplotype inference by pure parsimony.

Comput Syst Bioinformatics Conf 2006 :211-22

David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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June 2007

Availability of recreational resources and physical activity in adults.

Am J Public Health 2007 Mar 31;97(3):493-9. Epub 2007 Jan 31.

Center for Social Epidemiology and Population Health, University of Michigan, Ann Arbor, USA.

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http://dx.doi.org/10.2105/AJPH.2006.087734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805019PMC
March 2007

Association of insulin resistance with distance to wealthy areas: the multi-ethnic study of atherosclerosis.

Am J Epidemiol 2007 Feb 5;165(4):389-97. Epub 2006 Dec 5.

Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48103, USA.

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http://dx.doi.org/10.1093/aje/kwk028DOI Listing
February 2007

Integer programming approaches to haplotype inference by pure parsimony.

IEEE/ACM Trans Comput Biol Bioinform 2006 Apr-Jun;3(2):141-54

David R. Cheriton School of Computer Science, University of Waterloo, 200 University Ave. West, Waterloo, ON N2L 3G1 Canada.

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http://dx.doi.org/10.1109/TCBB.2006.24DOI Listing
November 2006

Optimizing multiple seeds for protein homology search.

Authors:
Daniel G Brown

IEEE/ACM Trans Comput Biol Bioinform 2005 Jan-Mar;2(1):29-38

School of Computer Science, University of Waterloo, 200 University Ave., West, Waterloo, ON N2L 3G1, Canada.

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http://dx.doi.org/10.1109/TCBB.2005.13DOI Listing
November 2006

The use of functional domains to improve transmembrane protein topology prediction.

J Bioinform Comput Biol 2006 Feb;4(1):109-23

Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, HS-1150, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.

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http://dx.doi.org/10.1142/s0219720006001722DOI Listing
February 2006

Ancestral sequence alignment under optimal conditions.

BMC Bioinformatics 2005 Nov 17;6:273. Epub 2005 Nov 17.

School of Computer Science, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.

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http://dx.doi.org/10.1186/1471-2105-6-273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310622PMC
November 2005

ExonHunter: a comprehensive approach to gene finding.

Bioinformatics 2005 Jun;21 Suppl 1:i57-65

School of Computer Science, University of Waterloo 200 University Avenue West, Waterloo, ON, Canada N2L 3G1.

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http://dx.doi.org/10.1093/bioinformatics/bti1040DOI Listing
June 2005

A tutorial of recent developments in the seeding of local alignment.

J Bioinform Comput Biol 2004 Dec;2(4):819-42

Department of Computer Science, University of Waterloo, Waterloo, ON, Canada, N2L 3G1, Canada.

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http://dx.doi.org/10.1142/s0219720004000983DOI Listing
December 2004

Optimal spaced seeds for homologous coding regions.

J Bioinform Comput Biol 2004 Jan;1(4):595-610

School of Computer Science, University of Waterloo, 200 University Ave West, Waterloo, ON N2L3G1, Canada.

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http://dx.doi.org/10.1142/s0219720004000326DOI Listing
January 2004

Integra v. Merck: a mixed bag for research tool patents.

Nat Biotechnol 2003 Sep;21(9):1099-101

Frommer Lawrence & Haug LLP, 745 Fifth Avenue, New York, New York 10151, USA.

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http://dx.doi.org/10.1038/nbt0903-1099DOI Listing
September 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002