john hawks weblog

paleoanthropology, genetics and evolution

Bibliography

Found 89 results
Filters: Keyword is genomics  [Clear All Filters]
2013
Gymrek M, McGuire AL, Golan D, Halperin E, and Erlich Y. 2013. Identifying Personal Genomes by Surname Inference. Science 339:321 - 324.
2012
Li S, and Jakobsson M. 2012. Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation. BMC genetics 13:22.
O'Bleness M, Searles VB, Varki A, Gagneux P, and Sikela JM. 2012. Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet 13:853-66.
Shendure J, and Aiden EL. 2012. The expanding scope of DNA sequencing. Nature Biotechnology 30:1084 - 1094.
Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, et al. 2012. A fine-scale chimpanzee genetic map from population sequencing. Science (New York, N.Y.) 336:193-8.
Chakravarti A, and Kapoor A. 2012. Mendelian Puzzles. Science 335:930 - 931.
Cerqueira CCS, Paixão-Côrtes VR, Zambra FMB, Salzano FM, Hünemeier T, and Bortolini M-C. 2012. Predicting Homo pigmentation phenotype through genomic data: From Neanderthal to James Watson. American Journal of Human Biology 24:705 - 709.
2011
Ju YS, Kim J-I, Kim S, Hong D, Park H, Shin J-Y, Lee S, Lee W-C, Kim S, Yu S-B, et al. 2011. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nature Genetics 43:745 - 752.
vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, Geffen E, Pilot M, Jedrzejewski W, Jedrzejewska B, et al. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Research [Internet]. Available from: http://dx.doi.org/10.1101/gr.116301.110
McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, et al. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature [Internet] 471:216–219. Available from: http://dx.doi.org/10.1038/nature09774
Hobolth A, Dutheil JY, Hawks J, Schierup MH, and Mailund T. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome research 21:349-56.
Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, and Kellis M. 2011. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome research.
Li H. 2011. A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography. Molecular Biology and Evolution [Internet] 28:365–375. Available from: http://dx.doi.org/10.1093/molbev/msq211
Tennessen JA, O'Connor TD, Bamshad MJ, and Akey JM. 2011. The promise and limitations of population exomics for human evolution studies. Genome biology 12:127.
2010
Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PF, Morrow B, Friedman E, Oddoux C, Burns E, et al. 2010. Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry. [Internet] 86:850–859. Available from: http://www.cell.com/AJHG/abstract/S0002-9297(10)00246-6
Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, and Rechavi G. 2010. Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the National Academy of Sciences [Internet] 107:12174–12179. Available from: http://dx.doi.org/10.1073/pnas.1006183107
Wang K, Li M, and Hakonarson H. 2010. Analysing biological pathways in genome-wide association studies. Nature Reviews Genetics [Internet] 11:843–854. Available from: http://dx.doi.org/10.1038/nrg2884
Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, et al. 2010. Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science [Internet] 328:636–639. Available from: http://dx.doi.org/10.1126/science.1186802
Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature [Internet] 463:536–539. Available from: http://dx.doi.org/10.1038/nature08700
Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, et al. 2010. A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science [Internet] 327:883–886. Available from: http://dx.doi.org/10.1126/science.1183863
Haygood R, Babbitt CC, Fedrigo O, and Wray GA. 2010. Contrasts between adaptive coding and noncoding changes during human evolution. Proceedings of the National Academy of Sciences [Internet] 107:7853–7857. Available from: http://dx.doi.org/10.1073/pnas.0911249107
Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, and Webster MT. 2010. Detecting positive selection within genomes: the problem of biased gene conversion. Philosophical Transactions of the Royal Society B: Biological Sciences [Internet] 365:2571–2580. Available from: http://dx.doi.org/10.1098/rstb.2010.0007
Liu F, Wollstein A, Hysi PG, Ankra-Badu GA, Spector TD, Park D, Zhu G, Larsson M, Duffy DL, Montgomery GW, et al. 2010. Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci. PLoS Genet [Internet] 6:e1000934+. Available from: http://dx.doi.org/10.1371/journal.pgen.1000934
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Project} G{1000, et al. 2010. Diversity of human copy number variation and multicopy genes. Science (New York, N.Y.) [Internet] 330:641–646. Available from: http://dx.doi.org/10.1126/science.1197005
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A Draft Sequence of the Neandertal Genome. Science [Internet] 328:710–722. Available from: http://dx.doi.org/10.1126/science.1188021
Carvalho CM, Zhang F, and Lupski JR. 2010. Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proceedings of the National Academy of Sciences of the United States of America [Internet] 107 Suppl 1:1765–1771. Available from: http://dx.doi.org/10.1073/pnas.0906222107
Lynch M. 2010. Evolution of the mutation rate. Trends in Genetics [Internet] 26:345–352. Available from: http://dx.doi.org/10.1016/j.tig.2010.05.003
Johansen CT, Wang J, Lanktree MB, Cao H, McIntyre AD, Ban MR, Martins RA, Kennedy BA, Hassell RG, Visser ME, et al. 2010. Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nature genetics [Internet] 42:684–687. Available from: http://dx.doi.org/10.1038/ng.628
Goecks J, Nekrutenko A, Taylor J, and Team TG. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology [Internet] 11:R86+. Available from: http://dx.doi.org/10.1186/gb-2010-11-8-r86
O'Dushlaine C, McQuillan R, Weale ME, Crouch DJM, Johansson A, Aulchenko Y, Franklin CS, Polasek O, Fuchsberger C, Corvin A, et al. 2010. Genes predict village of origin in rural Europe. European Journal of Human Genetics [Internet] 18:1269–1270. Available from: http://dx.doi.org/10.1038/ejhg.2010.92
Pritchard JK, Pickrell JK, and Coop G. 2010. The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation. Current Biology [Internet] 20:R208–R215. Available from: http://dx.doi.org/10.1016/j.cub.2009.11.055
Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, et al. 2010. The genome-wide structure of the Jewish people. Nature [Internet] 466:238–242. Available from: http://dx.doi.org/10.1038/nature09103
Sin H-S, Koh E, Kim D-S, Murayama M, Sugimoto K, Maeda Y, Yoshida A, and Namiki M. 2010. Human endogenous retrovirus K14C drove genomic diversification of the Y chromosome during primate evolution. Journal of Human Genetics [Internet] 55:717–725. Available from: http://dx.doi.org/10.1038/jhg.2010.94
Kayser M. 2010. The Human Genetic History of Oceania: Near and Remote Views of Dispersal. Current Biology [Internet] 20:R194–R201. Available from: http://dx.doi.org/10.1016/j.cub.2009.12.004
Barbujani G, and Colonna V. 2010. Human genome diversity: frequently asked questions. Trends in genetics : TIG [Internet] 26:285–295. Available from: http://dx.doi.org/10.1016/j.tig.2010.04.002
Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, et al. 2010. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature [Internet] 467:832–838. Available from: http://dx.doi.org/10.1038/nature09410
Fu W, Zhang F, Wang Y, Gu X, and Jin L. 2010. Identification of Copy Number Variation Hotspots in Human Populations. The American Journal of Human Genetics [Internet] 87:494–504. Available from: http://dx.doi.org/10.1016/j.ajhg.2010.09.006
Pemberton TJ, Wang C, Li JZ, and Rosenberg NA. 2010. Inference of Unexpected Genetic Relatedness among Individuals in HapMap Phase III. Am J Hum Genet [Internet] 87:457–464. Available from: http://www.cell.com/AJHG/abstract/S0002-9297(10)00427-1
Anon. 2010. Integrating common and rare genetic variation in diverse human populations. Nature [Internet] 467:52–58. Available from: http://dx.doi.org/10.1038/nature09298
Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, and Moran JV. 2010. LINE-1 Retrotransposition Activity in Human Genomes. [Internet] 141:1159–1170. Available from: http://www.cell.com//abstract/S0092-8674(10)00557-X
Anon. 2010. A map of human genome variation from population-scale sequencing. Nature [Internet] 467:1061–1073. Available from: http://dx.doi.org/10.1038/nature09534
Meader S, Ponting CP, and Lunter G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome research [Internet] 20:1335–1343. Available from: http://dx.doi.org/10.1101/gr.108795.110
Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, and Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nature Reviews Genetics [Internet] 11:446–450. Available from: http://dx.doi.org/10.1038/nrg2809
Iskow RC, McCabe MT, Mills RE, Torene S, Pittard SW, Neuwald AF, Van Meir EG, Vertino PM, and Devine SE. 2010. Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons. Cell [Internet] 141:1253–1261. Available from: http://dx.doi.org/10.1016/j.cell.2010.05.020
Noonan JP. 2010. Neanderthal genomics and the evolution of modern humans. Genome research [Internet] 20:547–553. Available from: http://dx.doi.org/10.1101/gr.076000.108
Hawkins DR, Hon GC, and Ren B. 2010. Next-generation genomics: an integrative approach. Nature reviews. Genetics [Internet] 11:476–486. Available from: http://dx.doi.org/10.1038/nrg2795
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews DT, Barnes C, Campbell P, et al. 2010. Origins and functional impact of copy number variation in the human genome. Nature [Internet] 464:704–712. Available from: http://dx.doi.org/10.1038/nature08516
Kaessmann H. 2010. Origins, evolution, and phenotypic impact of new genes. Genome Research [Internet] 20:1313–1326. Available from: http://dx.doi.org/10.1101/gr.101386.109
Altman RB, Kroemer HK, McCarty CA, Ratain MJ, and Roden D. 2010. Pharmacogenomics: will the promise be fulfilled?. Nature Reviews Genetics [Internet] 12:69–73. Available from: http://dx.doi.org/10.1038/nrg2920
Chen H, Patterson N, and Reich D. 2010. Population differentiation as a test for selective sweeps. Genome Research [Internet] 20:393–402. Available from: http://dx.doi.org/10.1101/gr.100545.109

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About the bibliography

My bibliography database represents years of work by many people. The core of the database was compiled by Milford Wolpoff, with contributions from many students and coauthors. I have added substantially to the database during the last fifteen years, and since I have been blogging all new entries are linked by Digital Object Identifier numbers to their place of publication.

If you find the database useful, please take time to thank the people who worked hard to compile it. I know they will appreciate hearing it.

This database began as a flat text file of bibliographic entries, which I have over the years scripted into a computer-readable format. Many errors have slipped in, including typos from the initial data entry, script fragments from my BibTeX database, and some entries that began in a non-standard format and were scrambled by scripts. Please do not write me expecting that I will fix these errors. It would take me weeks of work to do this. Works will be fixed as I cite them or enter updated information for them.

There are also errors of omission. Most entries are here because they got cited, in Milford's books, in the many research articles by him or his students, or in my work. I mention this mainly because I know that some of you will look up your own names, and find many important papers missing from the database. If you're disappointed in the representation of your articles here, by all means contact me and I will work with you. This database is mirrored on CiteULike and Mendeley and I can import your bibliographic data from these sites, EndNote, BibTeX or other standard formats.

A fuller introduction to the bibliography is in my initial announcement.

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.