Gronau Lab - publications

Journal publications

Hejase HA, Salman-Minkov A, Campagna L, Hubisz MJ, Lovette IJ, Gronau I*+, Siepel A* (2020) Genomic islands of differentiation in a rapid avian radiation are driven by recent selective sweeps. Accepted to PNAS, in print. BioRxiv preprint
Adrion J, Cole CB, Dukler N, Galloway JG, Gladstein A, gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Del-Vecchyo DO, Racimo F, Struck TJ, Gravel S, Gutenkunst RN, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD (2020) A community-maintained standard library of population genetic models. eLife 9:e54967 PubMed

Chavez DE, Gronau I, Hains T, Kliver S, Koepfli KP, Wayne RK. (2019) Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). Scientic Reports, 9:8329 PubMed

Damty Y, Gronau I, Moran S, Yavneh I. (2018) Comparing evolutionary distances via adaptive distance functions. Journal of Theoretical Biology, 440:88-99 PubMed

VonHoldt BM, Cahill JA, Gronau I, Shapiro B, Wall J, Wayne RK. (2017) Response to Hohenlohe et al. Science Advances, 3(6)e1701233 PubMed

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 PubMed
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, et al. (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

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
Freedman A, Gronau I, Schweizer RM, Han E, Ortega-Del Vecchyo D, et al. (2014) Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genetics 10(8), e1004631 PubMed

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 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