• A.Clark.Inference of haplotypes from PCR-amplified samples of diploid populations.Molecular Biology and Evolution, 7(2): 111–22,1990.
• D. Gusfield, Inference of Haplotypes from Samples of Diploid Populations:Complexity and Algorithms. J.  COMPUTATIONAL  BIOLOGY Volume 8,Number 3,2001 Pp.305–323
• D. Gusfield. Haplotyping as Perfect Phylogeny:Conceptual Framework and Efficient Solutions. Proc. RECOMB 02.
• V.Bafna,D.Gusfield,G.Lancia,and S.Yooseph.Haplotyping as perfect phylogeny:A direct approach.Technical Report UCDavis CSE-2002-21,2002.
• E.Eskin,E.Halperin,and R.M.Karp.Efficient reconstruction of haplotype structure via perfect phylogeny.To appear in the Journal of Bioinformatics and Computational Biology (JBCB),2003 .
• L.Excoffier and M.Slatkin.Maximum-likelihood estimation of mollecular haplotype frequencies in a diploid population.Molecular Biology and Evolution,12(5):912–7,1995.
• M.Stephens et al.A new statistical method for haplotype reconstruction from population data.American Journal of Human Genetics,68(4):978–89, 2001.

Block Parititioning

• K.Zhang,M.Deng,T.Chen,M.S.Waterman,and F.Sun.A dynamic programming algorithm for haplotype block partitioning. Proc.Natl.Acad.Sci.USA,99(11):7335–9,2002.
• K. Zhang, F. Sun, M. Waterman, T. Chen  Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. Proc. RECOMB03 332-340 (2003)
• M.Koivisto et al.An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries.In Proc PSB 03, volume 8,pages 502–513, 2003 .
• Anderson and Novembere. Finding haplotype block boundaries by using the minimum-description-length principle. In American Journal of Human Genetics, volume 73, pages 336–354, 2003 .
• G.Kimmel,R.Sharan,and R.Shamir.Identifying blocks and sub-populations in noisy SNP data. In proc. WABI 2003.

Phasing and Block Partitioning

• G. Greenspan and D. Geiger. Model-based inference of haplotype block variationProc. RECOMB 03 131-137 (2003).
• Gad Kimmel and Ron Shamir.  Maximum Likelihood Resolution of Multi-block Genotypes. Technical Report (24 Sept 03)

Other Problems

• R. R. Hudson. Linkage disequilibrium and recombination. Handbook of Statistical Genetics. D. J. Balding, M. Bishop, C.Canning (editors), Wiley (2001) pp.309-324
•  Vineet Bafna, Bjarni V.Halld´orsson, Russell Schwartz, Andrew G.Clark, Sorin Istrail. Haplotypes and Informative SNP Selection Algorithms:Don’t Block Out Information. Proc. RECOMB03, pp 19-27.
• I. Pe’er and J. Beckmann. Resolution of haplotypes and haplotypes frequencies from snp genotypes of pooled samples. Proc. RECOMB 03 ,pages 237–246,2003.

Reviews and Background Material

•   The International HapMap Project webpage
• The SNP Consortium
• dbSNP
  
• B.V.Halldorsson et al. Combinatorial problems arising in SNP and haplotype analysis . Proc., DMTCS ’03 Conference.
•   Kaleigh Smith. Genetic Polymorphism and SNPs: Genotyping, Haplotype Assembly Problem, Haplotype Map, Functional Genomics and Proteomics pdf.
•   M. Chicurel, Faster, better, cheaper genotyping. Nature 412:580-82, 2001.
•   N.Patil et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human  chromosome 21. Science, 294: 1719–1723, 2001.
• Mark J. Daly, John D. Rioux, Stephen F. Schaffner, Thomas J. Hudson, Eric S. Lander , High-resolution haplotype structure in the human genome. Nature Genetics 29 (2) 229-232 (2001)
• S.B.Gabriel et al.The structure of haplotype blocks in the human genome.Science,296:2225–2229,  2001
• Wentian Li's bibliography on linkage disequilibrium (over 2000 references) . here

• Haploview (Broad Institute)
• Mathematical genetics software (Oxford)
• PHASE (M. Stephes, U. Washington)
• HaploBlock (G. Greenspan, D. Geiger, Technion)
• HAP (Eskin et al., ICSI and ICSD)