Genetics

• Waiting for cancer
  With Deena Schmidt and Jason Schweinsberg
• Regulatory sequence evolution. With Deena Schmidt.
  in humans Ann. Appl. Prob. 17 (2007), 1-32
  in Drosophila
• Fluctuating selection.
  With Emilia Huerta-Sanchez and Carlos Bustamante. Genetics 178 (2008), 325-337
• Wagner's Canalization Model
  With Emilia Huerta-Sanchez. Theoret. Pop. Biol. 71 (2007), 121-130
• Approximating selective sweeps
  With Jason Schweinsberg. Theoret Pop. Biol. 66 (2004), 129-138,
  Ann. Appl. Prob. 15 (2005), 1591-1651,
  Stoch. Proc. Appl. 115 (2005), 1628-1657
• Single nucleotide polymorphisms
  With Vlada Limic. Stoch. Proc. Appl. 93 (2001), 1-24
  
• A simple formula useful for positional cloning
  With K.Y. Chen and Steve Tanksley. Genetics 160 (2002), 353-355
• Selective mapping strategies
  With Todd Vision, David Brown, David Shmoys, and Steve Tanksley.
  Genetics 155 (2000), 407-420
  

Stepping Stone Model

• Two dimensions
  With Ted Cox. Ann. Appl. Probab. 12 (2002), 1348-1377
  With Ted Cox and Iljana Zahle. Ann. Appl. Probab. 15 (2005), 671-699
• Linkage diseqeuilibrium, site frequency spectrum, etc.
  With Arkendra De. Genetics. 176 (2007), 969-981
• One dimensional stepping stone model
  With Mateo Restrepo. Ann. Appl. Prob. 18 (2008), 334-358

Genome Rearrangement

• Survey article
  In Statistical Methods of Molecular Evolution, edited by R. Nielsen
• Chromosome size evolution
  With Arkedra De, Mike Ferguson, and Suzanne Sindi. J. Appl. Prob. 38 (2001), 324-334
• Shuffling chromosomes
  J. Theoret. Prob. 16 (2003), 725-750
• A phase transition
  With Nathanael Berestycki. Prob. Theor. Rel. Fields. 136 (2006), 203-233
• Computing genomic midpoints
  With Yannet Interian

Rearrangement papers with Tom York and Rasmus Nielsen

• Estimating the number of inversions
  J. Comp. Bio. 9 (2002), 805-818
• Estimating genomic distance
  Genetics. 166 (2004), 621-629
• Estimating genetic maps
  With Tom York, Rasmus Nielsen and Steve Tanksley. Genetical Research. 85 (2006), 159-168
• Inversion Tract Lengths
  BioMedCentral Bioinformatics. 8 (2008), paper 146
  

Gene Duplication

• Subfunctionalization
  With Rachel Ward. Theoret. Pop. Biol. 66 (2004), 93-100
• Zinc finger genes
  With Deena Schmidt. Mol. Biol. Evol. 21 (2004), 2326-2339
• Power laws for gene family sizes
  With Jason Schwweinsberg. Ann. Prob., 33 (2006), 2094-2126
• Degenerate diffusion limits
  With Lea Popovic

Microsatellites

• KDSA model
  With Semyon Kruglyak, Malcolm Schug, and Chipa Aquadro. Proc. Nat. Acad. Sci. 95 (1998), 10774-10778
  With Semyon Kruglyak. J. Appl. Probab. 36 (1999), 621-631
• Microsatellites in yeast
  With Semyon Kruglyak, Malcolm Schug, and Chipa Aquadro. Mol. Biol. Evol. 17 (2000), 120-1219
• Dynamics of Microsatellite Divergence
  With Peter Calabrese and Chip Aquadro. Genetics 159 (2001), 839-852
• Microsatellites in Drosophilia and Humans
  With Peter Calabrese. Mol. Biol. Evol. 20 (2003), 715-725
• Estimates from comparing humans and chimps
  With Raaz Sainudiin, Chip Aquadro, and Rasmus Nielsen. Genetics. 168, 383-395