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Hochreiter, S. (2013)
HapFABIA: Identification of very short segments of identity by descent
characterized by rare variants in large sequencing data.
Nucleic Acids Res.,.
- 2
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The 1000 Genomes Project Consortium (2012)
An integrated map of genetic variation from 1,092 human genomes.
Nature, 491(7422), 56-65.
- 3
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Strachan, T. and Read, A. P. (2004)
Human Molecular Genetics,
Garland Science/Taylor & Francis Group, London and New York 3rd edition.
- 4
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Hochreiter, S., Bodenhofer, U., Heusel, M., Mayr, A., Mitterecker, A., Kasim,
A., VanSanden, S., Lin, D., Talloen, W., Bijnens, L., Göhlmann, H. W. H.,
Shkedy, Z., and Clevert, D.-A. (2010)
FABIA: factor analysis for bicluster acquisition.
Bioinformatics, 26(12), 1520-1527.
- 5
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Klambauer, G., Unterthiner, T., and Hochreiter, S. (2013)
DEXUS: Identifying Differential Expression in RNA-Seq Studies with Unknown
Conditions.
Nucleic Acids Res.,.
- 6
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Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A.,
Bodenhofer, U., and Hochreiter, S. (2012)
cn.MOPS: mixture of Poissons for discovering copy number variations in next
generation sequencing data with a low false discovery rate.
Nucleic Acids Res., 40(9), e69.
- 7
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Talloen, W., Clevert, D.-A., Hochreiter, S., Amaratunga, D., Bijnens, L., Kass,
S., and Göhlmann, H. (2007)
I/NI-calls for the exclusion of non-informative genes: a highly effective
filtering tool for microarray data.
Bioinformatics, 23(21), 2897-2902.
- 8
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Talloen, W., Hochreiter, S., Bijnens, L., Kasim, A., Shkedy, Z., and
Amaratunga, D. (2010)
Filtering data from high-throughput experiments based on measurement
reliability.
Proc. Natl. Acad. Sci. USA, 107(46), 173-174.
- 9
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Clevert, D.-A., Mitterecker, A., Mayr, A., Klambauer, G., Tuefferd, M.,
DeBondt, A., Talloen, W., Göhlmann, H. W. H., and Hochreiter, S. (2011)
cn.FARMS: a latent variable model to detect copy number variations in
microarray data with a low false discovery rate.
Nucleic Acids Res., 39(12), e79.
- 10
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Hochreiter, S., Clevert, D.-A., and Obermayer, K. (2006)
A new summarization method for Affymetrix probe level data.
Bioinformatics, 22(8), 943-949.
- 11
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Schwarzbauer, K., Bodenhofer, U., and Hochreiter, S. (2012)
Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free
regions.
PLoS ONE, 7(11), e47924.
- 12
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Mahrenholz, C. C., Abfalter, I., Bodenhofer, U., Volkmer, R., and Hochreiter,
S. (2011)
Complex networks govern coiled coil oligomerization -- Predicting and
profiling by means of a machine learning approach.
Mol. Cell. Proteomics, 10, M110.004994.
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Browning, S. R. and Browning, B. L. (2012)
Identity by Descent Between Distant Relatives: Detection and Applications.
Annu. Rev. Genet., 46, 617-633.
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Leibon, G., Rockmore, D. N., and Polla, M. R. (2008)
A SNP Streak Model for the Identification of Genetic Regions
Identical-by-descent.
Stat. Appl. Genet. Mol., 7(1), Article v16.
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Halldorsson, B. V., Aguiar, D., Tarpine, R., and Istrail, S. (2011)
The Clark phaseable sample size problem: long-range phasing and loss of
heterozygosity in GWAS.
J. Comput. Biol., 18(3), 323-333.
- 16
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Gusev, A., Palamara, P. F., Aponte, G., Zhuang, Z., Darvasi, A., Gregersen, P.,
and Pe'er, I. (2012)
The architecture of long-range haplotypes shared within and across populations.
Mol. Biol. Evol., 29(2), 473-486.
- 17
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Browning, S. R. (2008)
Estimation of pairwise identity by descent from dense genetic marker data in a
population sample of haplotypes.
Genetics, 178(4), 2123-2132.
- 18
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Thomas, A., Skolnick, M. H., and Lewis, C. M. (1994)
Genomic mismatch scanning in pedigrees.
Math. Med. Biol., 11(1), 1-16.
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Thomas, A., Camp, N. J., Farnham, J. M., Allen-Brady, K., and Cannon-Albright,
L. A. (2008)
Shared genomic segment analysis. Mapping disease predisposition genes in
extended pedigrees using SNP genotype assays.
Ann. Hum. Genet., 72(Pt 2), 279-287.
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Fu, W., O'Connor, T. D., Jun, G., Kang, H. M., Abecasis, G., Leal, S. M.,
Gabriel, S., Altshuler, D., Shendure, J., Nickerson, D. A., et al. (2013)
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding
variants.
Nature, 493(7431), 216-220.
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Wang, K., Li, M., and Hakonarson, H. (2010)
ANNOVAR: Functional annotation of genetic variants from next-generation
sequencing data.
Nucleic Acids Res., 38, e164.
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Kong, A., Thorleifsson, G., Gudbjartsson, D. F., Masson, G., Sigurdsson, A.,
Jonasdottir, A., Walters, G. B., Jonasdottir, A., Gylfason, A., Kristinsson,
K. T., et al. (2010)
Fine-scale recombination rate differences between sexes, populations and
individuals.
Nature, 467(7319), 1099-1103.
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Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G. T., Clark,
A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, and Bustamante,
C. D. (2011)
Demographic history and rare allele sharing among human populations.
P. Natl. Acad. Sci. USA, 108(29), 11983-11988.
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Bryc, K., Auton, A., Nelson, M. R., Oksenberg, J. R., Hauser, S. L., Williams,
S., Froment, A., Bodo, J.-M., Wambebe, C., Tishkoff, S. A., et al. (2009)
Genome-wide patterns of population structure and admixture in West Africans and
African Americans.
P. Natl. Acad. Sci. USA, 107(2), 786-791.
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Blum, M. G. B. and Jakobsson, M. (2011)
Deep Divergences of Human Gene Trees and Models of Human Origins.
Mol. Biol. Evol., 28(2), 889-898.
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Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S.,
Schraiber, J. G., Jay, F., Prüfer, K., deFilippo, C., et al. (2012)
A High-Coverage Genome Sequence from an Archaic Denisovan Individual.
Science, 338(6104), 222-226.
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Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth,
G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing
Subgroup (2009)
The Sequence alignment/map (SAM) format and SAMtools.
Bioinformatics, 25(16), 2078-2079.
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Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M.,
Patterson, N., Li, H., Zhai, W., Fritz, M. H., et al. (2010)
A draft sequence of the Neandertal genome.
Science, 328(5979), 710-722.
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Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y.,
Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L., et al. (2010)
Genetic history of an archaic hominin group from Denisova Cave in Siberia.
Nature, 468, 1053-1060.
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Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S.,
Gignoux, C., Woerner, A., Hammer, M. F., and Slatkin, M. (2013)
Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans.
Genetics, 194(1), 199-209.
- 31
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Palamara, P. F., Lencz, T., Darvasi, A., and Pe'er, I. (2012)
Length Distributions of Identity by Descent Reveal Fine-Scale Demographic
History.
Am. J. Hum. Genet., 91(5), 809-822.
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Ulgen, A. and Li, W. (2005)
Comparing single-nucleotide-polymorphism marker-based and microsatellite
marker-based linkage analyses.
BMC Genet., 6, S13.
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Yu, A., Zhao, C., Fan, Y., Jang, W., Mungall, A. J., Deloukas, P., Olsen, A.,
Doggett, N. A., Ghebranious, N., Broman, K. W., et al. (2001)
Comparison of human genetic and sequence-based physical maps.
Nature, 409, 951-953.
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Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C., and Wall, J. D.
(2011)
Genetic evidence for archaic admixture in Africa.
P. Natl. Acad. Sci. USA, 10(37), 15123-15128.
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Pennisi, E. (2013)
More Genomes From Denisova Cave Show Mixing of Early Human Groups.
Science, 340(6134), 799.
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Meuwissen, T. H. E. and Goddard, M. E. (2001)
Prediction of identity by descent probabilities from marker-haplotypes.
Genet. Sel. Evol., 33(6), 605-634.
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Hacia, J. G., Fan, J.-B., Ryder, O., Jin, L., Edgemon, K., Ghandour, G., Mayer,
R. A., Sun, B., Hsie, L., Robbins, C. M., et al. (1999)
Determination of ancestral alleles for human single-nucleotide polymorphisms
using high-density oligonucleotide arrays.
Nat. Genet., 22(2), 164-167.
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The Chimpanzee Sequencing and Analysis Consortium (2005)
Initial sequence of the chimpanzee genome and comparison with the human genome.
Nature, 437, 69-87.
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Leffler, E. M., Gao, Z., Pfeifer, S., Ségurel, L., Auton, A., Venn, O.,
Bowden, R., Bontrop, R., Wall, J. D., Sella, G., et al. (2013)
Multiple instances of ancient balancing selection shared between humans and
chimpanzees.
Science, 339(6127), 1578-1582.
Sepp Hochreiter
2013-11-13