Index Journal Papers

[1] Judea Pearl, Dan Geiger, and Tom Verma. Conditional independence and its representations. Kybernetika, 25(7):33–44, 1989. [bib | http | .pdf ]
[2] Dan Geiger, Tom Verma, and Judea Pearl. Identifying independence in Bayesian networks. Networks, 20(5):507–534, 1990. [ bib |  http  | .pdf ]
[3] Dan Geiger and Judea Pearl. Logical and algorithmic properties of independence and their application to Bayesian networks. Annals of Mathematics and Artificial Intelligence, 2(1):165–178, 1990. [ bib | http | .pdf ]
[4] Dan Geiger, Azaria Paz, and Judea Pearl. Axioms and algorithms for inferences involving probabilistic independence. Information and Computation, 91(1):128–141, 1991. [ bib | http | .pdf ]
[5] Dan Geiger, Azaria Paz, and Judea Pearl. Learning simple causal structures. International Journal of Intelligent Systems, 8(2):231–247, 1993. [ bib ]
[6] Dan Geiger and Judea Pearl. Logical and algorithmic properties of conditional independence and graphical models. The Annals of Statistics, 21(4):2001–2021, 1993. [ bib | http | .pdf ]
[7] David Maxwell Chickering, Dan Geiger, and David Heckerman. On finding a cycle basis with a shortest maximal cycle. Information processing letters, 54(1):55–58, 1995. [ bib | http | .pdf ]
[8] David Heckerman, Dan Geiger, and David M. Chickering. Learning Bayesian networks: The combination of knowledge and statistical data. Machine learning, 20(3):197–243, 1995. [ bib | http | .pdf ]
[9] Amir Eliaz and Dan Geiger. Word-level recognition of small sets of hand-written words. Pattern recognition letters, 16(10):999–1009, 1995. [ bib | http | .pdf ]
[10] Dan Geiger and Eyal Zussmann. Probabilistic reactive disassembly planning. CIRP Annals-Manufacturing Technology, 45(1):49–52, 1996. [ bib | http | .pdf ]
[11] Dan Geiger and David Heckerman. Knowledge representation and inference in similarity networks and Bayesian multinets. Artificial Intelligence, 82(1-2):45–74, 1996. [ bib | http | .pdf ]
[12] Ann Becker and Dan Geiger. Optimization of pearl’s method of conditioning and greedy-like approximation algorithms for the vertex feedback set problem. Artificial Intelligence, 83(1):167–188, 1996. [ bib | http | .pdf ]
[13] Nir Friedman, Dan Geiger, and Moises Goldszmidt. Bayesian network classifiers. Machine learning, 29(2):131–163, 1997. [ bib | http |.pdf ]
[14] Dan Geiger and David Heckerman. A characterization of the Dirichlet distribution through global and local parameter independence. The Annals of Statistics, pages 1344–1369, 1997. [ bib | http | .pdf ]
[15] Reuven Bar-Yehuda, Dan Geiger, Seffi Naor, and Ron Roth. Approximation algorithms for the feedback vertex set problem with applications to constraint satisfaction and Bayesian inference. SIAM Journal on Computing, 27(4):942–959, 1998. [ bib | http | .pdf ]
[16] Dan Geiger and David Heckerman. Probabilistic relevance relations. Systems, Man and Cybernetics, Part A: Systems and Humans, IEEE Transactions on, 28(1):17–25, 1998. [ bib | http | .pdf ]
[17] Dan Geiger and David Heckerman. A characterization of the bivariate Wishart distribution. Probability and Mathematical Statistics, 18(1):119–131, 1998. [ bib | http | .pdf ]
[18] Ann Becker, Dan Geiger, and Alejandro Schäffer. Automatic selection of loop breakers for genetic linkage analysis. Human heredity, 48(1):49–60, 1998. [ bib | http | .pdf ]
[19] Ann Becker, Reuven Bar-Yehuda, and Dan Geiger. Randomized algorithms for the loop cutset problem. Journal Artificial Intelligence Research, 12:219–234, 2000. [ bib | .html | .pdf ]
[20] Ann Becker and Dan Geiger. A sufficiently fast algorithm for finding close to optimal clique trees. Artificial Intelligence, 125(1-2):3–17, 2001. [ bib | http | .pdf ]
[21] Dan Geiger, David Heckerman, Henry King, and Christopher Meek. Stratified exponential families: graphical models and model selection. Annals of Statistics, pages 505–529, 2001. [ bib | http | .pdf ]
[22] Dan Geiger and David Heckerman. Parameter priors for directed acyclic graphical models and the characterization of several probability distributions. Annals of statistics, pages 1412–1440, 2002. [ bib | http | .pdf ]
[23] Ma’ayan Fishelson and Dan Geiger. Exact genetic linkage computations for general pedigrees. Bioinformatics, 18(suppl 1):S189–S198, 2002. [ bib | http | .pdf ]
[24] Gideon Greenspan, Dan Geiger, F. Gotch, M. Bower, S. Patterson, M. Nelson, B. Gazzard, and J. Stebbing. Model-based inference of recombination hotspots in a highly, variable oncogene. Journal of molecular evolution, 58(3):239–251, 2004. [ bib | http | .pdf ]
[25] Ma’ayan Fishelson and Dan Geiger. Optimizing exact genetic linkage computations. Journal of Computational Biology, 11(2-3):263–275, 2004. [ bib | http | .pdf ]
[26] Gideon Greenspan and Dan Geiger. Model-based inference of haplotype block variation. Journal of computational biology, 11(2-3):493–504, 2004. [ bib | http | .pdf ]
[27] Ginat Narkis, Daniella Landau, Esther Manor, Khalil Elbedour, Anna Tzemach, Ma’ayan Fishelson, Dan Geiger, Rivka Ofir, Rivka Carmi, and Ohad S. Birk. Homozygosity mapping of lethal congenital contractural syndrome type 2 (lccs2) to a 6 cm interval on chromosome 12q13. American Journal of Medical Genetics Part A, 130(3):272–276, 2004. [ bib | http | .pdf ]
[28] Gideon Greenspan and Dan Geiger. High density linkage disequilibrium mapping using models of haplotype block variation.Bioinformatics, 20(suppl 1):i137–i144, 2004. [ bib | http | .pdf ]
[29] Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam Siepel, David Haussler, and David Heckerman. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics, 20(suppl 1):i161–i168, 2004. [ bib | http | .pdf ]
[30] Dmitry Rusakov and Dan Geiger. Asymptotic model selection for naive Bayesian networks. The Journal of Machine Learning Research, 6:1–35, 2005. [ bib | .html | .pdf ]
[31] Ma’ayan Fishelson, Nickolay Dovgolevsky, and Dan Geiger. Maximum likelihood haplotyping for general pedigrees. Human Heredity, 59:41–60, 2005. [ bib | http | .pdf ]
[32] Mordechai Mizrachi-Koren, Dan Geiger, Margarita Indelman, Ora Bitterman-Deutsch, Reuven Bergman, and Eli Sprecher. Identification of a novel locus associated with congenital recessive ichthyosis on 12p11. 2–q13. Journal of investigative dermatology, 125(3):456–462, 2005. [ bib | .html | .pdf ]
[33] Shimyn Slomovic, David Laufer, Dan Geiger, and Gadi Schuster. Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark. Molecular and cellular biology, 25(15):6427–6435, 2005. [ bib | http | .pdf ]
[34] Eli Sprecher, Akemi Ishida-Yamamoto, Mordechai Mizrahi-Koren, Debora Rapaport, Dorit Goldsher, Margarita Indelman, Orit Topaz, Ilana Chefetz, Hanni Keren, Timothy J. O’Brien, Dani Bercovich, Stavit Shalev, Dan Geiger, Reuven Bergman, Mia Horowitz, and Hanna Mandel. A mutation in snap29, coding for a snare protein involved in intracellular trafficking, causes a novel neurocutaneous syndrome characterized by cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma. The American Journal of Human Genetics, 77(2):242–251, 2005. [ bib | http | .pdf ]
[35] Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, and Dan Geiger. Finding approximate tandem repeats in genomic sequences. Journal of Computational Biology, 12(7):928–942, 2005. [ bib | http | .pdf ]
[36] Dan Geiger, Christopher Meek, and Bernd Sturmfels. On the toric algebra of graphical models. The Annals of Statistics, 34(3):1463–1492, 2006. [ bib | http | .pdf ]
[37] Gideon Greenspan and Dan Geiger. Modeling haplotype block variation using Markov chains. Genetics, 172(4):2583–2599, 2006. [ bib |http | .pdf ]
[38] Ann Becker, Dan Geiger, and Christopher Meek. Perfect tree-like Markovian distributions. Probability and Mathematical Statistics, 25(2):231–239, 2006. [ bib | .pdf ]
[39] Mark Silberstein, Anna Tzemach, Nickolay Dovgolevsky, Ma’ayan Fishelson, Assaf Schuster, and Dan Geiger. Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers. The American Journal of Human Genetics, 78(6):922–935, 2006. [ bib | http | .pdf ]
[40] Ron Zohar and Dan Geiger. Estimation of flows in flow networks. European journal of operational research, 176(2):691–706, 2007. [ bib | http | .pdf ]
[41] Shimyn Slomovic, David Laufer, Dan Geiger, and Gadi Schuster. Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Research, 34(10):2966–2975, 2006. [ bib | http | .pdf ]
[42] Ramon Y. Birnbaum, Alex Zvulunov, Dafna Hallel-Halevy, Emanuella Cagnano, Gal Finer, Rivka Ofir, Dan Geiger, Eldad Silberstein, Yael Feferman, and Ohad S. Birk. Seborrhea-like dermatitis with psoriasiform elements caused by a mutation in znf750, encoding a putative c2h2 zinc finger protein. Nature Genetics, 38(7):749–751, 2006. [ bib | .html | .pdf ]
[43] Dan Geiger, Christopher Meek, and Ydo Wexler. A variational inference procedure allowing internal structure for overlapping clusters and deterministic constraints. Journal of Artificial Intelligence Research, 27(1):1–23, 2006. [ bib | .html | .pdf ]
[44] Orit Topaz, Margarita Indelman, Ilana Chefetz, Dan Geiger, Aryeh Metzker, Yoram Altschuler, Mordechai Choder, Dani Bercovich, Jouni Uitto, Reuven Bergman, Gabriele Richard, and Eli Sprecher. A deleterious mutation in samd9 causes normophosphatemic familial tumoral calcinosis. The American Journal of Human Genetics, 79(4):759–764, 2006. [ bib | http | .pdf ]
[45] Jennie Lugassy, Peter Itin, Akemi Ishida-Yamamoto, Kristen Holland, Susan Huson, Dan Geiger, Hans Christian Hennies, Margarita Indelman, Dani Bercovich, Jouni Uitto, Reuven Bergman, John A. McGrath, Gabriele Richard, and Eli Sprecher. Naegeli-franceschetti-jadassohn syndrome and dermatopathia pigmentosa reticularis: two allelic ectodermal dysplasias caused by dominant mutations in krt14.The American Journal of Human Genetics, 79(4):724–730, 2006. [ bib | http | .pdf ]
[46] Daniel Landau, Tal Oved, Dan Geiger, Luba Abizov, Hanna Shalev, and Ruti Parvari. Familial steroid-sensitive nephrotic syndrome in southern israel: clinical and genetic observations. Pediatric Nephrology, 22(5):661–669, 2007. [ bib | http | .pdf ]
[47]J anna Nousbeck, Ronen Spiegel, Akemi Ishida-Yamamoto, Margarita Indelman, Ayelet Shani-Adir, Noam Adir, Ehud Lipkin, Sivan Bercovici, Dan Geiger, Maurice A. Van Steensel, Peter M. Steijlen, Reuven Bergman, Albrecht Bindereif, Mordechai Choder, Stavit Shalev, and Eli Sprecher. Alopecia, neurological defects, and endocrinopathy syndrome caused by decreased expression of rbm28, a nucleolar protein associated with ribosome biogenesis. The American Journal of Human Genetics, 82(5):1114–1121, 2008. [ bib | http |.pdf ]
[48] Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki, and Alan Templeton. Panel construction for mapping in admixed populations via expected mutual information. Genome Research, 18(4):661–667, 2008. [ bib | http | .pdf ]
[49] Ydo Wexler and Dan Geiger. Variational upper and lower bounds for probabilistic graphical models. Journal of Computational Biology, 15(7):721–735, 2008. [ bib | http | .pdf ]
[50] Paul Renbaum, Efrat Kellerman, Ranit Jaron, Dan Geiger, Reeval Segel, Ming Lee, Mary Claire King, and Ephrat Levy-Lahad. Spinal muscular atrophy with pontocerebellar hypoplasia is caused by a mutation in the vrk1 gene. The American Journal of Human Genetics, 85(2):281–289, 2009. [ bib | http | .pdf ]
[51] Dan Geiger, Christopher Meek, and Ydo Wexler. Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space. Bioinformatics, 25(12):i196–i203, 2009. [ bib | http | .pdf ]
[52] Sivan Bercovici and Dan Geiger. Inferring ancestries efficiently in admixed populations with linkage disequilibrium. Journal of Computational Biology, 16(8):1141–1150, 2009. [ bib | http | .pdf ]
[53] Mira Genzer-Nir, Morad Khayat, Leonid Kogan, Hector I. Cohen, Miriam Hershkowitz, Dan Geiger, and Tzipora C. Falik-Zaccai. Mammary-digital-nail (mdn) syndrome: a novel phenotype maps to human chromosome 22q12. 3–13.1. European Journal of Human Genetics, 18(6):662–667, 2010. [ bib | http | .pdf ]
[54] Meral Gunay-Aygun, Yifat Zivony-Elboum, Fatma Gumruk, Dan Geiger, Mualla Cetin, Morad Khayat, Robert Kleta, Nehama Kfir, Yair Anikster, Judith Chezar, Mauricio Arcos-Burgos, Adel Shalata, Horia Stanescu, Joseph Manaster, Mutlu Arat, Hailey Edwards, Andrew S. Freiberg, P. Suzanne Hart, Lauren C. Riney, Katherine Patzel, Pranoot Tanpaiboon, Tom Markello, Marjan Huizing, Irina Maric, McDonald Horne, Beate E. Kehrel, Kerstin Jurk, Nancy F. Hansen, Praveen F. Cherukuri, Marypat Jones, Pedro Cruz, Jim C. Mullikin, Alan Nurden, James G. White, William A. Gahl, and Tzippora Falik-Zaccai. Gray platelet syndrome: natural history of a large patient cohort and locus assignment to chromosome 3p. Blood, 116(23):4990–5001, 2010. [ bib | http | .pdf ]
[55] Sivan Bercovici, Christopher Meek, Ydo Wexler, and Dan Geiger. Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping. Bioinformatics, 26(12):i175–i182, 2010. [ bib | http | .pdf ]
[56] Liran Shlush, Sivan Bercovici, Walter G. Wasser, Guennady Yudkovsky, Alan Templeton, Dan Geiger, and Karl Skorecki. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers. BMC Medical Genomics, 3(1):47, 2010. [ bib | http | .pdf ]
[57] Dorit Baras, Shai Fine, Laurent Fournier, Dan Geiger, and Avi Ziv. Automatic boosting of cross-product coverage using Bayesian networks. International Journal on Software Tools for Technology Transfer (STTT), 13(3):247–261, 2011. [ bib | http | .pdf ]
[58] Barak Markus, Ohad Birk, and Dan Geiger. Integration of SNP genotyping confidence scores in IBD inference. Bioinformatics, 27(20):2880–2887, 2011. [ bib | http | .pdf ]
[59] Sivan Bercovici and Dan Geiger. Admixture aberration analysis: Application to mapping in admixed population using pooled DNA.Journal of Computational Biology, 18(3):237–249, 2011. [ bib | http | .pdf ]
[60] Omer Weissbrod and Dan Geiger. Genetic linkage analysis in the presence of germline mosaicism. Statistical Applications in Genetics and Molecular Biology, 10(1):46, 2011. [ bib | http | .pdf ]