GronauLab @ IDC

Journal Publications

VonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK. (2016) Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Science Advances 12(32(7), e1501714
Freedman A, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva P, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante C, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. (2016) Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genetics 12(3), e1005851 PubMed
Kuhlwilm M*, Gronau I*, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gusic I, Marques-Bonet T, Andres AM, Viola B, Paabo S, Meyer M, Siepel A, Castellano S. (2016) Ancient gene flow from modern humans into Siberian Neanderthals . Nature 530, 429-433 PubMed ReadCube public view Dedicated page
Fan Z, Silva P, Gronau I, Wang S, Armero AS, Schweizer RM, Ramirez O, Pollinger J, Galaverni M, Ortega Del-Vecchyo D, Du L, Zhang W, Zhang Z, Xing J, Vila C, Marques-Bonet T, Godinho R, Yue B, Wayne RK. (2016) 26(2):163-73 Worldwide patterns of genomic variation and admixture in gray wolves. Genome Research 26(2):163-73 PubMed

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ. (2015) Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Molecular Ecology 24:4238-4251 PubMed
Gulko B, Hubisz MJ, Gronau I*, Siepel, A*. (2015) Probabilities of fitness consequences for point mutations across the human genome. Nature Genetics 47:276-283 PubMed Author post on Haldane's Sieve (by Adam)

Mohammed J, Bortolamiol-Becet D, Flynt A, Gronau I, Siepel A, Lai E. (2014) Adaptive evolution of testis-specic, recently-evolved, clustered miRNAs in Drosophila. RNA 20(8):1195-1209 PubMed
Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics 10(5):e1004342 PubMed Author post on Haldane's Sieve (by Adam)
Freedman A, Gronau I, Schweizer RM, Han E, Ortega-Del Vecchyo D, Silva P, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HGT, Lee C, Tadigotla V, Siepel A, Bustamante C, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. (2014) Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genetics 10(8), e1004631 PubMed Author post on Haldane's Sieve (by Ilan)

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nature Genetics 45:723-729 PubMed
Gronau I, Arbiza L, Mohammed J, Siepel A. (2013) Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence. Molecular Biology and Evolution 30(5):1159-1171 PubMed

Doerr D, Gronau I, Moran S, Yavneh I. (2012) Stochastic errors vs. modeling errors in distance based phylogenetic reconstruction. Algorithms in Molecular Biology 7(1):22 PubMed

Extended Abstract published in the proceedings of the 11th international conference on Algorithms in bioinformatics (WABI) 2011.
Gronau I, Moran S, Snir S. (2012) Fast and Reliable Reconstruction of Phylogenetic Trees with Indistinguishable Edges. Random Structures and Algorithms 40(3):350-384

Extended Abstract published in the proceedings of the 19th annual ACM-SIAM symposium on Discrete algorithms (SODA) 2008.
Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope, MJ, Siepel A. (2012) Replacing and additive horizontal gene transfer in Streptococcus. Molecular Biology and Evolution 29(11): 3309-3320 PubMed

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43:1031-1034 [supplementary methods] PubMed
Ben-Yehezkel T, Linshiz G, Kaplan T, Gronau I, Ravid S, Adar A, Shapiro E. (2011) Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA. Methods in Enzymology 498:207-245 PubMed

Gronau I, Moran S, Yavneh I. (2010) Adaptive Distance Measures for Resolving K2P Quartets: Metric Separation versus Stochastic Noise. Journal of Computational Biology 17:(11):1509-1518 PubMed

Gronau I, Moran S, Yavneh I. (2009) Towards Optimal Distance Functions for Stochastic Substitutions Models. Journal of Theoretical Biology 260:294-307 PubMed

Linshiz G, Ben-Yehezkel T, Kaplan T, Gronau I, Ravid S, Adar A, Shapiro E. (2008) Recursive Construction of Perfect DNA Molecules from Imperfect Oligonucleotides. Molecular Systems Biology 4:191 PubMed

Gronau I, Moran S. (2007) Neighbor Joining Algorithms for Inferring Phylogenies via LCA-Distances. Journal of Computational Biology 14(1):1-15 PubMed
Gronau I, Moran S. (2007) On the Hardness of Inferring Phylogenies from Triplet-Dissimilarities. Theoretical Computer Science 389(1-2):44-55
Gronau I Moran S. (2007) Optimal Implementations of UPGMA and Other Common Clustering Algorithms. Information Processing Letters 104(6):205-210