-
1
-
-
13144271178
-
The methods and uses of a research museum
-
Grinnell J (1910) The methods and uses of a research museum. Popular Science Monthly 77: 163-169.
-
(1910)
Popular Science Monthly
, vol.77
, pp. 163-169
-
-
Grinnell, J.1
-
2
-
-
0021688630
-
DNA sequences from the quagga, an extinct member of the horse family
-
6504142
-
Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282-284. PMID: 6504142
-
(1984)
Nature
, vol.312
, pp. 282-284
-
-
Higuchi, R.1
Bowman, B.2
Freiberger, M.3
Ryder, O.A.4
Wilson, A.C.5
-
3
-
-
0035822055
-
PCR amplification of the Irish potato famine pathogen from historic specimens
-
11395772
-
Ristaino JB, Groves CT, Parra GR (2001) PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411: 695-697. doi: 10.1038/35079606 PMID: 11395772
-
(2001)
Nature
, vol.411
, pp. 695-697
-
-
Ristaino, J.B.1
Groves, C.T.2
Parra, G.R.3
-
4
-
-
41149138745
-
Explosive avian radiations and multi-directional dispersal across Wallacea: Evidence from the Campephagidae and other Crown Corvida (Aves)
-
18295511
-
Jønsson KA, Irestedt M, Fuchs J, Ericson PGP, Christidis L, Bowie RKC, et al. (2008) Explosive avian radiations and multi-directional dispersal across Wallacea: Evidence from the Campephagidae and other Crown Corvida (Aves). Molecular Phylogenetics and Evolution 47: 221-236. doi: 10.1016/j. ympev.2008.01.017 PMID: 18295511
-
(2008)
Molecular Phylogenetics and Evolution
, vol.47
, pp. 221-236
-
-
Jønsson, K.A.1
Irestedt, M.2
Fuchs, J.3
Ericson, P.G.P.4
Christidis, L.5
Bowie, R.K.C.6
-
5
-
-
84873149873
-
A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes, chimeras, and a novel phylogenetic hypothesis
-
23220516
-
Moyle RG, Jones RM, Andersen MJ (2013) A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes, chimeras, and a novel phylogenetic hypothesis. Molecular Phylogenetics and Evolution 66: 1060-1066. doi: 10.1016/j.ympev.2012.11.024 PMID: 23220516
-
(2013)
Molecular Phylogenetics and Evolution
, vol.66
, pp. 1060-1066
-
-
Moyle, R.G.1
Jones, R.M.2
Andersen, M.J.3
-
6
-
-
84855488333
-
Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons
-
Fulton TL, Wagner SM, Fisher C, Shapiro B (2012) Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Annals of Anatomy-Anatomischer Anzeiger 194: 52-57.
-
(2012)
Annals of Anatomy-Anatomischer Anzeiger
, vol.194
, pp. 52-57
-
-
Fulton, T.L.1
Wagner, S.M.2
Fisher, C.3
Shapiro, B.4
-
8
-
-
69549139892
-
Direct multiplex sequencing (DMPS)-A novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
-
19635845
-
Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M (2009) Direct multiplex sequencing (DMPS)-A novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Research 19: 1843-1848. doi: 10.1101/gr.095760.109 PMID: 19635845
-
(2009)
Genome Research
, vol.19
, pp. 1843-1848
-
-
Stiller, M.1
Knapp, M.2
Stenzel, U.3
Hofreiter, M.4
Meyer, M.5
-
10
-
-
76749141381
-
Ancient human genome sequence of an extinct Palaeo-Eskimo
-
20148029
-
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762. doi: 10.1038/nature08835 PMID: 20148029
-
(2010)
Nature
, vol.463
, pp. 757-762
-
-
Rasmussen, M.1
Li, Y.2
Lindgreen, S.3
Pedersen, J.S.4
Albrechtsen, A.5
Moltke, I.6
-
11
-
-
80053587649
-
The shaping of modern human immune systems by multiregional admixture with archaic humans
-
21868630
-
Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, et al. (2011) The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans. Science 334: 89-94. doi: 10.1126/science.1209202 PMID: 21868630
-
(2011)
Science
, vol.334
, pp. 89-94
-
-
Abi-Rached, L.1
Jobin, M.J.2
Kulkarni, S.3
McWhinnie, A.4
Dalva, K.5
Gragert, L.6
-
12
-
-
84890116555
-
Unlocking the vault: Next-generation museum population genomics
-
Bi K, Linderoth T, Vanderpool D, Good JM, Nielsen R, Moritz C. (2013) Unlocking the vault: Next-generation museum population genomics. Molecular Evolution 22: 6018-6032. doi: 10.1111/mec.12516
-
(2013)
Molecular Evolution
, vol.22
, pp. 6018-6032
-
-
Bi, K.1
Linderoth, T.2
Vanderpool, D.3
Good, J.M.4
Nielsen, R.5
Moritz, C.6
-
14
-
-
84901604272
-
-
Wong SQ, Li J, Tan AY-C, Vedururu R, Pang J-MB, Do H, et al. (2014) Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. 7: 1-10. doi: 10.1186/1755-8794-7-23
-
(2014)
Sequence Artefacts in a Prospective Series of Formalin-Fixed Tumours Tested for Mutations in Hotspot Regions by Massively Parallel Sequencing
, vol.7
, pp. 1-10
-
-
Wong, S.Q.1
Li, J.2
Tan, A.Y.-C.3
Vedururu, R.4
Pang, J.-M.B.5
Do, H.6
-
15
-
-
2942652786
-
In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR
-
15028125
-
Quach N, Goodman MF, Shibata D (2004) In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. BMC Clin Pathol 4: 1. doi: 10.1186/1472-6890-4-1 PMID: 15028125
-
(2004)
BMC Clin Pathol
, vol.4
, pp. 1
-
-
Quach, N.1
Goodman, M.F.2
Shibata, D.3
-
16
-
-
84856259511
-
DNA extraction from formalin-fixed material
-
In: Shapiro B, Hofreiter M, editors. Humana Press
-
Campos P, Gilbert TP (2012) DNA Extraction from Formalin-Fixed Material. In: Shapiro B, Hofreiter M, editors. Methods in Molecular Biology. Humana Press, Vol. 840. pp. 81-85. doi: 10.1007/978-1-61779-516-9-11
-
(2012)
Methods in Molecular Biology
, vol.840
, pp. 81-85
-
-
Campos, P.1
Gilbert, T.P.2
-
17
-
-
84867290918
-
Dramatic reduction of sequence artefacts from DNA isolated from formalinfixed cancer biopsies by treatment with uracil-DNA glycosylase
-
22643842
-
Do H, Dobrovic A (2012) Dramatic reduction of sequence artefacts from DNA isolated from formalinfixed cancer biopsies by treatment with uracil-DNA glycosylase. Oncotarget 3: 546-558. PMID: 22643842
-
(2012)
Oncotarget
, vol.3
, pp. 546-558
-
-
Do, H.1
Dobrovic, A.2
-
18
-
-
33744769979
-
Extraction of nuclear DNA from bone of skeletonized and fluid-preserved museum specimens
-
Stuart BL, Dugan KA, Allard MW, Kearney M (2006) Extraction of nuclear DNA from bone of skeletonized and fluid-preserved museum specimens. Systematics and Biodiversity 4: 133-136.
-
(2006)
Systematics and Biodiversity
, vol.4
, pp. 133-136
-
-
Stuart, B.L.1
Dugan, K.A.2
Allard, M.W.3
Kearney, M.4
-
19
-
-
80255134172
-
Illumina whole-genome complementary DNA-mediated annealing, selection, extension and ligation platform: Assessing its performance in formalin-fixed, paraffin-embedded samples and identifying invasion pattern-related genes in oral squamous cell carcinoma
-
21683979
-
Loudig O, Brandwein-Gensler M, Kim RS, Lin J, Isayeva T, Liu C, et al. (2011) Illumina whole-genome complementary DNA-mediated annealing, selection, extension and ligation platform: Assessing its performance in formalin-fixed, paraffin-embedded samples and identifying invasion pattern-related genes in oral squamous cell carcinoma. Human Pathology 42: 1911-1922. doi: 10.1016/j.humpath. 2011.02.011 PMID: 21683979
-
(2011)
Human Pathology
, vol.42
, pp. 1911-1922
-
-
Loudig, O.1
Brandwein-Gensler, M.2
Kim, R.S.3
Lin, J.4
Isayeva, T.5
Liu, C.6
-
20
-
-
80053173227
-
Targeted high throughput sequencing in clinical cancer Settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity
-
21958464
-
Kerick M, Isau M, Timmermann B, Sültmann H, Herwig R, Krobitsch S, et al. (2011) Targeted high throughput sequencing in clinical cancer Settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Medical Genomics 4: 68. doi: 10.1186/1755-8794-4-68 PMID: 21958464
-
(2011)
BMC Medical Genomics
, vol.4
, pp. 68
-
-
Kerick, M.1
Isau, M.2
Timmermann, B.3
Sültmann, H.4
Herwig, R.5
Krobitsch, S.6
-
21
-
-
84913590291
-
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
-
25236618
-
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Research 24: 2022-2032. doi: 10.1101/gr.175141.114 PMID: 25236618
-
(2014)
Genome Research
, vol.24
, pp. 2022-2032
-
-
Scheinin, I.1
Sie, D.2
Bengtsson, H.3
Van De Wiel, M.A.4
Olshen, A.B.5
Van Thuijl, H.F.6
-
22
-
-
80054062860
-
Efficient DNA extraction for HPV genotyping in formalin-fixed, paraffin-embedded tissues
-
Steinau M, Patel SS, Unger ER (2011) Efficient DNA Extraction for HPV Genotyping in Formalin-Fixed, Paraffin-Embedded Tissues. JMDI 13: 377-381. doi: 10.1016/j.jmoldx.2011.03.007
-
(2011)
JMDI
, vol.13
, pp. 377-381
-
-
Steinau, M.1
Patel, S.S.2
Unger, E.R.3
-
23
-
-
4243115072
-
Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones
-
15306287
-
Kearney M, Stuart BL (2004) Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones. Proceedings of the Royal Society B: Biological Sciences 271: 1677-1683. doi: 10.1098/rspb.2004.2771 PMID: 15306287
-
(2004)
Proceedings of the Royal Society B: Biological Sciences
, vol.271
, pp. 1677-1683
-
-
Kearney, M.1
Stuart, B.L.2
-
24
-
-
80054069357
-
Museum genomics: Low-cost and high-accuracy genetic data from historical specimens
-
21791033
-
Rowe KC, Singhal S, MacManes MD, Ayroles JF, Morelli TL, Rubidge EM, et al. (2011) Museum genomics: Low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources 11: 1082-1092. doi: 10.1111/j.1755-0998.2011.03052.x PMID: 21791033
-
(2011)
Molecular Ecology Resources
, vol.11
, pp. 1082-1092
-
-
Rowe, K.C.1
Singhal, S.2
MacManes, M.D.3
Ayroles, J.F.4
Morelli, T.L.5
Rubidge, E.M.6
-
25
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Meth 9: 357-359. doi: 10.1038/nmeth.1923
-
(2012)
Nat Meth
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
26
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
19261174
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
27
-
-
34848827224
-
Patterns of damage in genomic DNA sequences from a Neandertal
-
17715061
-
Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104: 14616-14621. doi: 10. 1073/pnas.0704665104 PMID: 17715061
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 14616-14621
-
-
Briggs, A.W.1
Stenzel, U.2
Johnson, P.L.F.3
Green, R.E.4
Kelso, J.5
Prüfer, K.6
-
28
-
-
84859112401
-
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
-
Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S (2012) Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA. PLoS ONE 7: E34131.
-
(2012)
PLoS ONE
, vol.7
, pp. e34131
-
-
Sawyer, S.1
Krause, J.2
Guschanski, K.3
Savolainen, V.4
Pääbo, S.5
-
29
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
30
-
-
84876321663
-
De novotranscriptomic analyses for non-model organisms: An evaluation of methods across a multi-species data set
-
Singhal S (2013) De novotranscriptomic analyses for non-model organisms: An evaluation of methods across a multi-species data set. Molecular Ecology Resources 13: 403-416.
-
(2013)
Molecular Ecology Resources
, vol.13
, pp. 403-416
-
-
Singhal, S.1
-
31
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
19251739
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. (2009) ABySS: A parallel assembler for short read sequence data. Genome Research 19: 1117-1123. doi: 10.1101/gr.089532.108 PMID: 19251739
-
(2009)
Genome Research
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
32
-
-
84865055419
-
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
-
Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM. (2012) Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics 13: 1-1.
-
(2012)
BMC Genomics
, vol.13
, pp. 1-1
-
-
Bi, K.1
Vanderpool, D.2
Singhal, S.3
Linderoth, T.4
Moritz, C.5
Good, J.M.6
-
33
-
-
84870431038
-
CD-HIT: Accelerated for clustering the next-generation sequencing data
-
23060610
-
Fu L, Niu B, Zhu Z, Wu S, LiW(2012) CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28: 3150-3152. doi: 10.1093/bioinformatics/bts565 PMID: 23060610
-
(2012)
Bioinformatics
, vol.28
, pp. 3150-3152
-
-
Fu, L.1
Niu, B.2
Zhu, Z.3
Wu S LiW.4
-
34
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent WJ (2002) BLAT-The BLAST-like alignment tool. Genome Research 12: 656-664.
-
(2002)
Genome Research
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
35
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
10508846
-
Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Research 9: 868-877. PMID: 10508846
-
(1999)
Genome Research
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
36
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. doi: 10.1016/S0022-2836(05)80360-2 PMID: 2231712
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
38
-
-
84906244271
-
A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0
-
2104
-
Bazinet AL, Zwickle DJ, Cummings MP (2104) A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0. Sys Bio 63(5): 812-818. doi: 10.1093/sysbio/syu031
-
Sys Bio
, vol.63
, Issue.5
, pp. 812-818
-
-
Bazinet, A.L.1
Zwickle, D.J.2
Cummings, M.P.3
-
39
-
-
84875500588
-
Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA
-
23493070
-
Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8: 737-748. doi: 10.1038/nprot.2013.038 PMID: 23493070
-
(2013)
Nat Protoc
, vol.8
, pp. 737-748
-
-
Gansauge, M.-T.1
Meyer, M.2
-
40
-
-
84902346093
-
Library construction for ancient genomics: Single strand or double strand?
-
289-90-292-6-298-passim
-
Bennett EA, Massilani D, Lizzo G, Daligault J, Geigl E-M, Grange T. (2014) Library construction for ancient genomics: Single strand or double strand? BioTechniques 56: 289-90-292-6-298-passim.
-
(2014)
BioTechniques
, vol.56
-
-
Bennett, E.A.1
Massilani, D.2
Lizzo, G.3
Daligault, J.4
Geigl, E.-M.5
Grange, T.6
-
41
-
-
84856448155
-
Optimal enzymes for amplifying sequencing libraries
-
Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, et al. (2012) Optimal enzymes for amplifying sequencing libraries. Nat Meth 9: 10-11. doi: 10.1038/nmeth.1814
-
(2012)
Nat Meth
, vol.9
, pp. 10-11
-
-
Quail, M.A.1
Otto, T.D.2
Gu, Y.3
Harris, S.R.4
Skelly, T.F.5
McQuillan, J.A.6
-
42
-
-
84879910635
-
MapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters
-
Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L (2013) mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. J Gerontol 29: 1682-1684. doi: 10.1093/bioinformatics/btt193
-
(2013)
J Gerontol
, vol.29
, pp. 1682-1684
-
-
Jónsson, H.1
Ginolhac, A.2
Schubert, M.3
Johnson, P.L.F.4
Orlando, L.5
-
43
-
-
84879207290
-
Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues
-
23603300
-
Paireder S, Werner B, Bailer J, Werther W, Schmid E, Patzak B, et al. (2013) Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues. Analytical Biochemistry 439: 152-160. doi: 10.1016/j.ab.2013.04.006 PMID: 23603300
-
(2013)
Analytical Biochemistry
, vol.439
, pp. 152-160
-
-
Paireder, S.1
Werner, B.2
Bailer, J.3
Werther, W.4
Schmid, E.5
Patzak, B.6
-
44
-
-
33846874137
-
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
-
17189378
-
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research 17: 240-248. doi: 10.1101/gr.5681207 PMID: 17189378
-
(2007)
Genome Research
, vol.17
, pp. 240-248
-
-
Miller, M.R.1
Dunham, J.P.2
Amores, A.3
Cresko, W.A.4
Johnson, E.A.5
-
45
-
-
79955783956
-
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
-
21573248
-
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE 6: E19379. doi: 10.1371/journal.pone.0019379.s004 PMID: 21573248
-
(2011)
PLoS ONE
, vol.6
, pp. e19379
-
-
Elshire, R.J.1
Glaubitz, J.C.2
Sun, Q.3
Poland, J.A.4
Kawamoto, K.5
Buckler, E.S.6
|