Bull JJ: Evolution of Sex Determining Mechanisms. 1983, The Benjamin/Cummings Publishing Company, Inc., San Francisco
Google Scholar
Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC: Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature. 2010, 466 (7306): 612-616. 10.1038/nature09172.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grutzner F, Kaessmann H: Origins and functional evolution of Y chromosomes across mammals. Nature. 2014, 508 (7497): 488-493. 10.1038/nature13151.
Article
PubMed
CAS
Google Scholar
Zhou Q, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MTP, Zhang G: Sex chromosomes demonstrate complex evolutionary trajectories across bird taxa. Science 2014, in press.,
Lahn BT, Page DC: Four evolutionary strata on the human X chromosome. Science. 1999, 286 (5441): 964-967. 10.1126/science.286.5441.964.
Article
PubMed
CAS
Google Scholar
Nam K, Ellegren H: The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics. 2008, 180 (2): 1131-1136. 10.1534/genetics.108.090324.
Article
PubMed
CAS
PubMed Central
Google Scholar
Roesti M, Moser D, Berner D: Recombination in the threespine stickleback genome–patterns and consequences. Mol Ecol. 2013, 22 (11): 3014-3027. 10.1111/mec.12322.
Article
PubMed
CAS
Google Scholar
Bergero R, Qiu S, Forrest A, Borthwick H, Charlesworth D: Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes. Genetics. 2013, 194 (3): 673-686. 10.1534/genetics.113.150755.
Article
PubMed
CAS
PubMed Central
Google Scholar
Natri HM, Shikano T, Merila J: Progressive recombination suppression and differentiation in recently evolved neo-sex chromosomes. Mol Biol Evol. 2013, 30 (5): 1131-1144. 10.1093/molbev/mst035.
Article
PubMed
CAS
PubMed Central
Google Scholar
Vicoso B, Charlesworth B: Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet. 2006, 7 (8): 645-653. 10.1038/nrg1914.
Article
PubMed
CAS
Google Scholar
Ellegren H: Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nat Rev Genet. 2011, 12 (3): 157-166. 10.1038/nrg2948.
Article
PubMed
CAS
Google Scholar
Xu K, Oh S, Park T, Presgraves DC, Yi SV: Lineage-specific variation in slow- and fast-X evolution in primates. Evolution. 2012, 66 (6): 1751-1761. 10.1111/j.1558-5646.2011.01556.x.
Article
PubMed
Google Scholar
Lu J, Wu CI: Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci U S A. 2005, 102 (11): 4063-4067. 10.1073/pnas.0500436102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li WH, Yi S, Makova K: Male-driven evolution. Curr Opin Genet Dev. 2002, 12 (6): 650-656. 10.1016/S0959-437X(02)00354-4.
Article
PubMed
CAS
Google Scholar
Charlesworth B, Coyne J, Barton N: The relative rates of evolution of sex chromosomes and autosomes. Am Nat. 1987, 130: 113-146. 10.1086/284701.
Article
Google Scholar
Meisel RP, Connallon T: The faster-X effect: integrating theory and data. Trends Genet. 2013, 29 (9): 537-544. 10.1016/j.tig.2013.05.009.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, JS J, Adams MD, Cargill M: A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 2005, 3(6):e170.,
Hvilsom C, Qian Y, Bataillon T, Li Y, Mailund T, Salle B, Carlsen F, Li R, Zheng H, Jiang T, Jiang H, Jin X, Munch K, Hobolth A, Siegismund HR, Wang J, Schierup MH: Extensive X-linked adaptive evolution in central chimpanzees. Proc Natl Acad Sci U S A. 2012, 109 (6): 2054-2059. 10.1073/pnas.1106877109.
Article
PubMed
CAS
PubMed Central
Google Scholar
Torgerson DG, Singh RS: Enhanced adaptive evolution of sperm-expressed genes on the mammalian X chromosome. Heredity. 2006, 96 (1): 39-44.
PubMed
CAS
Google Scholar
Torgerson DG, Singh RS: Sex-linked mammalian sperm proteins evolve faster than autosomal ones. Mol Biol Evol. 2003, 20 (10): 1705-1709. 10.1093/molbev/msg193.
Article
PubMed
CAS
Google Scholar
Sturgill D, Zhang Y, Parisi M, Oliver B: Demasculinization of X chromosomes in the Drosophila genus. Nature. 2007, 450 (7167): 238-241. 10.1038/nature06330.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang YE, Vibranovski MD, Landback P, Marais GA, Long M: Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol 2010, 8(10):e1000494.,
Wu CI, Xu EY: Sexual antagonism and X inactivation–the SAXI hypothesis. Trends Genet. 2003, 19 (5): 243-247. 10.1016/S0168-9525(03)00058-1.
Article
PubMed
CAS
Google Scholar
Potrzebowski L, Vinckenbosch N, Marques AC, Chalmel F, Jegou B, Kaessmann H: Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol 2008, 6(4):e80.,
Vicoso B, Charlesworth B: The deficit of male-biased genes on the d-melanogaster x chromosome is expression-dependent: a consequence of dosage compensation?. J Mol Evol. 2009, 68 (5): 576-583. 10.1007/s00239-009-9235-4.
Article
PubMed
CAS
Google Scholar
Bachtrog D, Toda NR, Lockton S: Dosage compensation and demasculinization of X chromosomes in Drosophila. Curr Biol. 2010, 20 (16): 1476-1481. 10.1016/j.cub.2010.06.076.
Article
PubMed
CAS
PubMed Central
Google Scholar
Guioli S, Lovell-Badge R, Turner JM: Error-prone ZW pairing and no evidence for meiotic sex chromosome inactivation in the chicken germ line. PLoS Genet 2012, 8(3):e1002560.,
Itoh Y, Replogle K, Kim YH, Wade J, Clayton DF, Arnold AP: Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res. 2010, 20 (4): 512-518. 10.1101/gr.102343.109.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schoenmakers S, Wassenaar E, Hoogerbrugge JW, Laven JS, Grootegoed JA, Baarends WM: Female meiotic sex chromosome inactivation in chicken. PLoS Genet 2009, 5(5):e1000466.,
Ellegren H, Fridolfsson AK: Male-driven evolution of DNA sequences in birds. Nat Genet. 1997, 17 (2): 182-184. 10.1038/ng1097-182.
Article
PubMed
CAS
Google Scholar
Axelsson E, Smith NG, Sundstrom H, Berlin S, Ellegren H: Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and Turkey. Mol Biol Evol. 2004, 21 (8): 1538-1547. 10.1093/molbev/msh157.
Article
PubMed
CAS
Google Scholar
Mank JE, Axelsson E, Ellegren H: Fast-X on the Z: rapid evolution of sex-linked genes in birds. Genome Res. 2007, 17 (5): 618-624. 10.1101/gr.6031907.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mank JE, Nam K, Ellegren H: Faster-Z evolution is predominantly due to genetic drift. Mol Biol Evol. 2010, 27 (3): 661-670. 10.1093/molbev/msp282.
Article
PubMed
CAS
Google Scholar
Mank JE, Vicoso B, Berlin S, Charlesworth B: Effective population size and the faster-X effect: empirical results and their interpretation. Evolution. 2010, 64 (3): 663-674. 10.1111/j.1558-5646.2009.00853.x.
Article
PubMed
Google Scholar
Vicoso B, Charlesworth B: Effective population size and the faster-X effect: an extended model. Evolution. 2009, 63 (9): 2413-2426. 10.1111/j.1558-5646.2009.00719.x.
Article
PubMed
Google Scholar
Tsuda Y, Nishida-Umehara C, Ishijima J, Yamada K, Matsuda Y: Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds. Chromosoma. 2007, 116 (2): 159-173. 10.1007/s00412-006-0088-y.
Article
PubMed
Google Scholar
Ayers KL, Davidson NM, Demiyah D, Roeszler KN, Grutzner F, Sinclair AH, Oshlack A, Smith CA: RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome. Genome Biol 2013, 14(3):R26.,
Zhang G, Li C, Li Q, Wang Z, Jarvis E, Gilbert T: Comparative genomics across modern bird species reveal insights into avian genome evolution and adaptation. Science 2014, in press.,
Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Schutz F, Daish T, Grutzner F, Kaessmann H: Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol 2012, 10(5):e1001328.,
Adolfsson S, Ellegren H: Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches. Mol Biol Evol. 2013, 30 (4): 806-810. 10.1093/molbev/mst009.
Article
PubMed
CAS
PubMed Central
Google Scholar
Vicoso B, Kaiser VB, Bachtrog D: Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. Proc Natl Acad Sci U S A. 2013, 110 (16): 6453-6458. 10.1073/pnas.1217027110.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wright AE, Moghadam HK, Mank JE: Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome. Genetics. 2012, 192 (4): 1433-1445. 10.1534/genetics.112.145102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jarvis E, Warnow T, Mirarab S, Houde P, Cracraft J, Boussau B, Howard J, Zhang G, Gilbert T: Whole genome analyses resolve the early branches to the tree of life of modern birds. Science 2014, in press.,
Nanda I, Schlegelmilch K, Haaf T, Schartl M, Schmid M: Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination. Cytogenet Genome Res. 2008, 122 (2): 150-156. 10.1159/000163092.
Article
PubMed
CAS
Google Scholar
Shetty S, Griffin DK, Graves JA: Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Res. 1999, 7 (4): 289-295. 10.1023/A:1009278914829.
Article
PubMed
CAS
Google Scholar
Derjusheva S, Kurganova A, Habermann F, Gaginskaya E: High chromosome conservation detected by comparative chromosome painting in chicken, pigeon and passerine birds. Chromosome Res. 2004, 12 (7): 715-723. 10.1023/B:CHRO.0000045779.50641.00.
Article
PubMed
CAS
Google Scholar
Nanda I, Benisch P, Fetting D, Haaf T, Schmid M: Synteny conservation of chicken macrochromosomes 1-10 in different avian lineages revealed by cross-species chromosome painting. Cytogenet Genome Res. 2011, 132 (3): 165-181. 10.1159/000322358.
Article
PubMed
CAS
Google Scholar
Nanda I, Karl E, Volobouev V, Griffin DK, Schartl M, Schmid M: Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes : Accipitridae). Cytogenet Genome Res. 2006, 112 (3–4): 286-295. 10.1159/000089883.
Article
PubMed
CAS
Google Scholar
Nishida C, Ishijima J, Kosaka A, Tanabe H, Habermann FA, Griffin DK, Matsuda Y: Characterization of chromosome structures of Falconinae (Falconidae, Falconiformes, Aves) by chromosome painting and delineation of chromosome rearrangements during their differentiation. Chromosome Res. 2008, 16 (1): 171-181. 10.1007/s10577-007-1210-6.
Article
PubMed
CAS
Google Scholar
Burt DW: Origin and evolution of avian microchromosomes. Cytogenet Genome Res. 2002, 96 (1–4): 97-112. 10.1159/000063018.
Article
PubMed
CAS
Google Scholar
Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T: Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harb Symp Quant Biol. 1987, 52: 863-867. 10.1101/SQB.1987.052.01.094.
Article
PubMed
CAS
Google Scholar
Carmichael AN, Fridolfsson AK, Halverson J, Ellegren H: Male-biased mutation rates revealed from Z and W chromosome-linked ATP synthase alpha-subunit (ATP5A1) sequences in birds. J Mol Evol. 2000, 50 (5): 443-447.
PubMed
CAS
Google Scholar
Bartosch-Harlid A, Berlin S, Smith NG, Moller AP, Ellegren H: Life history and the male mutation bias. Evolution. 2003, 57 (10): 2398-2406. 10.1554/03-036.
Article
PubMed
Google Scholar
Smith SA, Donoghue MJ: Rates of molecular evolution are linked to life history in flowering plants. Science. 2008, 322 (5898): 86-89. 10.1126/science.1163197.
Article
PubMed
CAS
Google Scholar
Wilson Sayres MA, Venditti C, Pagel M, Makova KD: Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes. Evolution. 2011, 65 (10): 2800-2815. 10.1111/j.1558-5646.2011.01337.x.
Article
PubMed
Google Scholar
Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH, Antonarakis SE, Program N: Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A. 2007, 104 (51): 20443-20448. 10.1073/pnas.0705658104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jamieson BG: Reproductive Biology and Phylogeny of Birds. 2007, CRC Press, London
Google Scholar
International Chicken Genome Sequencing C: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004, 432 (7018): 695-716. 10.1038/nature03154.
Article
Google Scholar
Zhou Q, Bachtrog D: Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science. 2012, 337 (6092): 341-345. 10.1126/science.1225385.
Article
PubMed
CAS
PubMed Central
Google Scholar
Singh ND, Davis JC, Petrov DA: X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Genetics. 2005, 171 (1): 145-155. 10.1534/genetics.105.043497.
Article
PubMed
CAS
PubMed Central
Google Scholar
Charlesworth B: The effect of life-history and mode of inheritance on neutral genetic variability. Genet Res. 2001, 77 (2): 153-166. 10.1017/S0016672301004979.
Article
PubMed
CAS
Google Scholar
Webster MT, Axelsson E, Ellegren H: Strong regional biases in nucleotide substitution in the chicken genome. Mol Biol Evol. 2006, 23 (6): 1203-1216. 10.1093/molbev/msk008.
Article
PubMed
CAS
Google Scholar
Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X: Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res. 2011, 18 (6): 499-512. 10.1093/dnares/dsr035.
Article
PubMed
CAS
PubMed Central
Google Scholar
Grath S, Parsch J: Rate of amino acid substitution is influenced by the degree and conservation of male-biased transcription over 50 myr of Drosophila evolution. Genome Biol Evol. 2012, 4 (3): 346-359. 10.1093/gbe/evs012.
Article
PubMed
PubMed Central
Google Scholar
Vicoso B, Emerson JJ, Zektser Y, Mahajan S, Bachtrog D: Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biol 2013, 11(8):e1001643.,
Sackton TB, Corbett-Detig RB, Nagaraju J, Vaishna L, Arunkumar KP, Hartl DL: Positve selection drives faster-Z evolution in silkmoths. Evolution. 2014, 68 (8): 2331-2342.
PubMed
PubMed Central
Google Scholar
Dunn PO, Whittingham LA, Pitcher TE: Mating systems, sperm competition, and the evolution of sexual dimorphism in birds. Evolution. 2001, 55 (1): 161-175. 10.1111/j.0014-3820.2001.tb01281.x.
Article
PubMed
CAS
Google Scholar
Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, Sinclair AH: The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature. 2009, 461 (7261): 267-271. 10.1038/nature08298.
Article
PubMed
CAS
Google Scholar
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, et al: The genome of a songbird. Nature. 2010, 464 (7289): 757-762. 10.1038/nature08819.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stenberg P, Larsson J: Buffering and the evolution of chromosome-wide gene regulation. Chromosoma. 2011, 120 (3): 213-225. 10.1007/s00412-011-0319-8.
Article
PubMed
PubMed Central
Google Scholar
Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T: Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 2009, 324 (5934): 1561-1564. 10.1126/science.1171243.
Article
PubMed
CAS
Google Scholar
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24 (8): 1586-1591. 10.1093/molbev/msm088.
Article
PubMed
CAS
Google Scholar
Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T: Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symposia on Quantitative Biology. 1987, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 863-867.
Google Scholar
McNab BK: Ecological factors affect the level and scaling of avian BMR. Comp Biochem Physiol A Mol Integr Physiol. 2009, 152 (1): 22-45. 10.1016/j.cbpa.2008.08.021.
Article
PubMed
Google Scholar
Calhim S, Birkhead TR: Testes size in birds: quality versus quantity—assumptions, errors, and estimates. Behav Ecol. 2007, 18 (1): 271-275. 10.1093/beheco/arl076.
Article
Google Scholar
Pagel M: Inferring the historical patterns of biological evolution. Nature. 1999, 401 (6756): 877-884. 10.1038/44766.
Article
PubMed
CAS
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Giga Sci 2012, 1(1):18.,
Charlesworth D, Charlesworth B, Marais G: Steps in the evolution of heteromorphic sex chromosomes. Heredity. 2005, 95 (2): 118-128. 10.1038/sj.hdy.6800697.
Article
PubMed
CAS
Google Scholar
Vicario S, Moriyama EN, Powell JR: Codon usage in twelve species of Drosophila. BMC Evol Biol 2007, 7:226.,
Qiu S, Bergero R, Zeng K, Charlesworth D: Patterns of codon usage bias in Silene latifolia. Mol Biol Evol. 2011, 28 (1): 771-780. 10.1093/molbev/msq251.
Article
PubMed
CAS
Google Scholar
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Odeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, et al: Comparative genomics reveals insights into avian genome evolution and adaptation. Science 2014, in press.,
Talavera G, Castresana J: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007, 56 (4): 564-577. 10.1080/10635150701472164.
Article
PubMed
CAS
Google Scholar
Axelsson E, Hultin-Rosenberg L, Brandstrom M, Zwahlen M, Clayton DF, Ellegren H: Natural selection in avian protein-coding genes expressed in brain. Mol Ecol. 2008, 17 (12): 3008-3017. 10.1111/j.1365-294X.2008.03795.x.
Article
PubMed
CAS
Google Scholar
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27 (3): 431-432. 10.1093/bioinformatics/btq675.
Article
PubMed
CAS
PubMed Central
Google Scholar
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012, 9 (4): 357-359. 10.1038/nmeth.1923.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J: SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009, 19 (6): 1124-1132. 10.1101/gr.088013.108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012, 6 (2): 80-92. 10.4161/fly.19695.
Article
PubMed
CAS
PubMed Central
Google Scholar
Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grutzner F, Bergmann S, Nielsen R, Paabo S, Kaessmann H: The evolution of gene expression levels in mammalian organs. Nature. 2011, 478 (7369): 343-348. 10.1038/nature10532.
Article
PubMed
CAS
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25 (9): 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed
CAS
PubMed Central
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010, 28 (5): 511-515. 10.1038/nbt.1621.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J: SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014, 30 (12): 1660-1666. 10.1093/bioinformatics/btu077.
Article
PubMed
CAS
Google Scholar