Computational pan-genomics: status, promises and challenges
暂无分享,去创建一个
Ying Zhang | Eleazar Eskin | Knut Reinert | Francesca Chiaromonte | Paul Medvedev | Benedict Paten | Veli Mäkinen | Victor Guryev | Tobias Marschall | Nadia Pisanti | Rayan Chikhi | Eric-Wubbo Lameijer | Ole Schulz-Trieglaff | Pierre Peterlongo | Carl Shneider | Manja Marz | Fabio Vandin | Can Alkan | Thomas Abeel | Kai Ye | Pieter B. T. Neerincx | Adam M. Novak | Erik Garrison | Louis Dijkstra | Alexander Schönhuth | Bas E Dutilh | Mohammed El-Kebir | Daniel Valenzuela | Gunnar W Klau | Valentina Boeva | Paul Kersey | Corinna Ernst | Matthias Schlesner | Eric Rivals | Siavash Sheikhizadeh | Sandra Smit | Cornelia M Van Duijn | Jasmijn A Baaijens | Sven Rahmann | Jiayin Wang | Benjamin Langmead | Ali Ghaffaari | Adam M Novak | David Porubsky | Robin Cijvat | Erwin Datema | Marcel Martin | Pieter Neerincx | Klaasjan Ouwens | Ben Raphael | Jeroen de Ridder | Lodewyk Wessels | Jan O Korbel | Tobias Manja Thomas Louis Bas E Ali Paul Wigard P Veli Ad Marschall Marz Abeel Dijkstra Dutilh Ghaff | Wigard P Kloosterman | Paul I W De Bakker | Raoul J P Bonnal | Francesca D Ciccarelli | Evan E Eichler | John C Mu | Dick de Ridder | Ashley D Sanders | E. Eichler | K. Reinert | C. Alkan | B. Langmead | E. Eskin | J. Korbel | P. D. de Bakker | K. Ye | B. Paten | P. Kersey | Fabio Vandin | W. Kloosterman | M. Schlesner | Erik K. Garrison | T. Marschall | C. V. van Duijn | F. Chiaromonte | L. Wessels | R. Chikhi | V. Mäkinen | Eric Rivals | V. Guryev | A. Sanders | D. Porubsky | J. Mu | Eric-Wubbo Lameijer | S. Smit | F. Ciccarelli | P. Peterlongo | M. Marz | T. Abeel | V. Boeva | Marcel Martin | D. de Ridder | E. Datema | N. Pisanti | B. Dutilh | S. Rahmann | A. Schönhuth | Jiayin Wang | G. Klau | Ole Schulz-Trieglaff | M. El-Kebir | R. Bonnal | The Icgctcga Pan-Cancer Analysis of Whole Genomes Consortium | J. Baaijens | J. de Ridder | C. Ernst | Ying Zhang | L. Dijkstra | K. Ouwens | Robin Cijvat | C. Shneider | Ali Ghaffaari | Daniel Valenzuela | P. Medvedev | B. Raphael | Siavash Sheikhizadeh
[1] D. G. MacArthur,et al. Guidelines for investigating causality of sequence variants in human disease , 2014, Nature.
[2] Gil McVean,et al. Improved genome inference in the MHC using a population reference graph , 2014, Nature Genetics.
[3] Jens Roat Kultima,et al. An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.
[4] Michael C. Schatz,et al. SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips , 2014, Bioinform..
[5] Dmitry Pushkarev,et al. Whole-genome haplotyping using long reads and statistical methods , 2014, Nature Biotechnology.
[6] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[7] Andrew C. Adey,et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions , 2013, Nature Biotechnology.
[8] Bas E. Dutilh,et al. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic , 2015, Front. Microbiol..
[9] Timothy D Read,et al. Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology , 2014, Genome Medicine.
[10] N. McGranahan,et al. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. , 2015, Cancer cell.
[11] K. Polyak,et al. Intra-tumour heterogeneity: a looking glass for cancer? , 2012, Nature Reviews Cancer.
[12] Gonzalo Navarro,et al. Compressed full-text indexes , 2007, CSUR.
[13] Kendra N. Pesko,et al. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification , 2012, Nucleic acids research.
[14] Jens Stoye,et al. Bloom Filter Trie - A Data Structure for Pan-Genome Storage , 2015, WABI.
[15] A. Magi,et al. Detection of Genomic Structural Variants from Next-Generation Sequencing Data , 2015, Front. Bioeng. Biotechnol..
[16] Joshua S. Paul,et al. Genotype and SNP calling from next-generation sequencing data , 2011, Nature Reviews Genetics.
[17] Alexander Schönhuth,et al. Discovering motifs that induce sequencing errors , 2013, BMC Bioinformatics.
[18] K. Metzner,et al. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data , 2012, Front. Microbio..
[19] James Y. Zou. Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.
[20] Joachim Denzler,et al. Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research , 2014, DATA.
[21] Hanlee P. Ji,et al. Haplotyping germline and cancer genomes using high-throughput linked-read sequencing , 2015, Nature Biotechnology.
[22] N. Loman,et al. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. , 2013, JAMA.
[23] Robert A Edwards,et al. Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions , 2014, BMC Genomics.
[24] Michael C. Heinold,et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing , 2015, Nature Communications.
[25] Jonathan Crabtree,et al. Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic , 2014, mBio.
[26] G. McVean,et al. De novo assembly and genotyping of variants using colored de Bruijn graphs , 2011, Nature Genetics.
[27] Szymon Grabowski,et al. Indexes of Large Genome Collections on a PC , 2014, PloS one.
[28] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[29] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[30] Enno Ohlebusch,et al. Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis , 2015, CPM.
[31] T. Williams,et al. An archaeal origin of eukaryotes supports only two primary domains of life , 2013, Nature.
[32] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .
[33] B. Barrell,et al. Life with 6000 Genes , 1996, Science.
[34] S. Koren,et al. Assembly algorithms for next-generation sequencing data. , 2010, Genomics.
[35] Richard J. Hall,et al. MinION nanopore sequencing of an influenza genome , 2015, Front. Microbiol..
[36] Leo van Iersel,et al. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads , 2015, J. Comput. Biol..
[37] Jun Wang,et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. , 2014, The Plant journal : for cell and molecular biology.
[38] Gos Micklem,et al. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes , 2015, Genome Biology.
[39] Andrew Menzies,et al. Analysis of the Genetic Phylogeny of Multifocal Prostate Cancer Identifies Multiple Independent Clonal Expansions in Neoplastic and Morphologically Normal Prostate Tissue , 2015, Nature Genetics.
[40] R. Gibbs,et al. Comparative primate genomics: emerging patterns of genome content and dynamics , 2014, Nature Reviews Genetics.
[41] David Heckerman,et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control , 2013, eLife.
[42] Volodymyr Kuleshov,et al. Probabilistic single-individual haplotyping , 2014, Bioinform..
[43] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[44] R. Fleischmann,et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.
[45] M. Olivier. A haplotype map of the human genome , 2003, Nature.
[46] N. Carter,et al. Estimation of rearrangement phylogeny for cancer genomes. , 2012, Genome research.
[47] M. Olivier. A haplotype map of the human genome. , 2003, Nature.
[48] C. Nusbaum,et al. Comprehensive variation discovery in single human genomes , 2014, Nature Genetics.
[49] Sven Rahmann,et al. PanCake: A Data Structure for Pangenomes , 2013, GCB.
[50] Jan O. Korbel,et al. Data analysis: Create a cloud commons , 2015, Nature.
[51] Gustavo Glusman,et al. Whole-genome haplotyping approaches and genomic medicine , 2014, Genome Medicine.
[52] N. Warthmann,et al. Simultaneous alignment of short reads against multiple genomes , 2009, Genome Biology.
[53] Victor V. Solovyev,et al. The Ctenophore Genome and the Evolutionary Origins of Neural Systems , 2014, Nature.
[54] Katherine H. Huang,et al. Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.
[55] Michele Morgante,et al. Transposable elements and the plant pan-genomes. , 2007, Current opinion in plant biology.
[56] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .
[57] Sorin Istrail,et al. Haplotype assembly in polyploid genomes and identical by descent shared tracts , 2013, Bioinform..
[58] Hilary S. Leeds,et al. Data use under the NIH GWAS Data Sharing Policy and future directions , 2014, Nature Genetics.
[59] Julian Parkhill,et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic , 2013, Genome research.
[60] Robert P. Davey,et al. Population genomics of domestic and wild yeasts , 2008, Nature.
[61] Bas E. Dutilh,et al. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly , 2009, Bioinform..
[62] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[63] Knut Reinert,et al. Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop , 2014, Bioinform..
[64] F. Rohwer,et al. Metagenomics and future perspectives in virus discovery , 2012, Current Opinion in Virology.
[65] P. Ashton,et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island , 2014, Nature Biotechnology.
[66] C. Greenman. Estimation of Rearrangement Phylogeny in Cancer , 2012 .
[67] E. Domingo,et al. Quasispecies Theory in Virology , 2002, Journal of Virology.
[68] Matthew W. Snyder,et al. Haplotype-resolved genome sequencing: experimental methods and applications , 2015, Nature Reviews Genetics.
[69] G. McVean,et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.
[70] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[71] Doolittle Wf. Phylogenetic Classification and the Universal Tree , 1999 .
[72] Knut Reinert,et al. Genome alignment with graph data structures: a comparison , 2014, BMC Bioinformatics.
[73] Pieter B. T. Neerincx,et al. Supplementary Information Whole-genome sequence variation , population structure and demographic history of the Dutch population , 2022 .
[74] Dan M. Bolser,et al. Ensembl Genomes 2016: more genomes, more complexity , 2015, Nucleic Acids Res..
[75] Dick de Ridder,et al. PanTools: representation, storage and exploration of pan-genomic data , 2016, Bioinform..
[76] Kevin Y. Yip,et al. Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays , 2015, Genetics.
[77] David Haussler,et al. Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.
[78] Derrick E. Wood,et al. Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.
[79] Sebastian Deorowicz,et al. KMC 2: Fast and resource-frugal k-mer counting , 2014, Bioinform..
[80] Nikolay Vyahhi,et al. Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes , 2013, WABI.
[81] Geoffrey J. Barton,et al. Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..
[82] L. Orgel,et al. Phylogenetic Classification and the Universal Tree , 1999 .
[83] Yongjun Zhao,et al. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution , 2012, Nature Methods.
[84] Veli Mäkinen,et al. Indexing Graphs for Path Queries with Applications in Genome Research , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[85] Lisa Zeigler Allen,et al. Single Virus Genomics: A New Tool for Virus Discovery , 2011, PloS one.
[86] Mark J. P. Chaisson,et al. Resolving the complexity of the human genome using single-molecule sequencing , 2014, Nature.
[87] David Haussler,et al. Comparative assembly hubs: Web-accessible browsers for comparative genomics , 2013, Bioinform..
[88] Aaron R. Quinlan,et al. Efficient genotype compression and analysis of large genetic variation datasets , 2015, Nature Methods.
[89] Haixu Tang,et al. De novo repeat classification and fragment assembly , 2004, RECOMB.
[90] Nicholas Eriksson,et al. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data , 2011, BMC Bioinformatics.
[91] Bonnie Berger,et al. HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data , 2014, PLoS Comput. Biol..
[92] Dominique Lavenier,et al. DSK: k-mer counting with very low memory usage , 2013, Bioinform..
[93] Rob J. L. Willems,et al. Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages , 2014, PLoS genetics.
[94] B. Browning,et al. Haplotype phasing: existing methods and new developments , 2011, Nature Reviews Genetics.
[95] J. Marchini,et al. Genotype imputation for genome-wide association studies , 2010, Nature Reviews Genetics.
[96] R. Mott,et al. The 1001 Genomes Project for Arabidopsis thaliana , 2009, Genome Biology.
[97] David Penny,et al. The Origin of Land Plants: A Phylogenomic Perspective , 2015, Evolutionary bioinformatics online.
[98] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[99] Haixu Tang,et al. Splicing graphs and EST assembly problem , 2002, ISMB.
[100] M. Stephens,et al. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. , 2003, Genetics.
[101] David Haussler,et al. Building a Pan-Genome Reference for a Population , 2015, J. Comput. Biol..
[102] Justin Zobel,et al. Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.
[103] Annelot M. Dekker,et al. Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis , 2017 .
[104] Jaideep P. Sundaram,et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[105] Roberto Grossi,et al. Mobilomics in Saccharomyces cerevisiae strains , 2013, BMC Bioinformatics.
[106] A. Halpern,et al. The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples , 2008, PloS one.
[107] David Heckerman,et al. Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1 , 2012, Journal of Virology.
[108] Stefan Engelen,et al. Genome assembly using Nanopore-guided long and error-free DNA reads , 2015, BMC Genomics.
[109] F Sigaux. [Cancer genome or the development of molecular portraits of tumors]. , 2000, Bulletin de l'Academie nationale de medecine.
[110] David Haussler,et al. Cactus Graphs for Genome Comparisons , 2010, RECOMB.
[111] Kay Nieselt,et al. Pan-Tetris: an interactive visualisation for Pan-genomes , 2015, BMC Bioinformatics.
[112] M. Stratton,et al. The cancer genome , 2009, Nature.
[113] Simon J. Puglisi,et al. Searching and Indexing Genomic Databases via Kernelization , 2014, bioRxiv.
[114] Kay Nieselt,et al. GenomeRing: alignment visualization based on SuperGenome coordinates , 2012, Bioinform..
[115] Enno Ohlebusch,et al. Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform , 2016, Bioinform..
[116] Qiang Feng,et al. A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.
[117] C. Dekker,et al. DNA sequencing with nanopores , 2012, Nature Biotechnology.
[118] R. Edwards,et al. Viral metagenomics , 2005, Nature Reviews Microbiology.
[119] Bas E. Dutilh,et al. Assessment of phylogenomic and orthology approaches for phylogenetic inference , 2007, Bioinform..
[120] A. Fujiyama,et al. A map of rice genome variation reveals the origin of cultivated rice , 2012, Nature.
[121] Pui-Yan Kwok,et al. Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome , 2013, PloS one.
[122] B. Snel,et al. Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.
[123] Faraz Hach,et al. Robustness of Massively Parallel Sequencing Platforms , 2015, PloS one.
[124] Heng Li,et al. A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..
[125] Richard Durbin,et al. Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT) , 2014, Bioinform..
[126]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[127]
Veli Mäkinen,et al.
Indexing Finite Language Representation of Population Genotypes
,
2010,
WABI.
[128]
Jun Yu,et al.
A Brief Review of Software Tools for Pangenomics
,
2015,
Genom. Proteom. Bioinform..
[129]
Pierre Peterlongo,et al.
Read Mapping on de Bruijn graph
,
2015,
ArXiv.
[130]
Luigi Cattivelli,et al.
Emerging Knowledge from Genome Sequencing of Crop Species
,
2012,
Molecular Biotechnology.
[131]
P. Bork,et al.
Patterns and ecological drivers of ocean viral communities
,
2015,
Science.
[132]
Paola Bonizzoni,et al.
HapCol: accurate and memory-efficient haplotype assembly from long reads
,
2016,
Bioinform..
[133]
J. Chen,et al.
Genome-wide genetic changes during modern breeding of maize
,
2012,
Nature Genetics.
[134]
Pierre Peterlongo,et al.
Read mapping on de Bruijn graphs
,
2015,
BMC Bioinformatics.
[135]
David Haussler,et al.
Building a Pangenome Reference for a Population
,
2014,
RECOMB.
[136]
T Laver,et al.
Assessing the performance of the Oxford Nanopore Technologies MinION
,
2015,
Biomolecular detection and quantification.
[137]
M. Daugherty,et al.
Rules of engagement: molecular insights from host-virus arms races.
,
2012,
Annual review of genetics.
[138]
Bradley P. Coe,et al.
Genome structural variation discovery and genotyping
,
2011,
Nature Reviews Genetics.
[139]
D. Huson,et al.
A Survey of Combinatorial Methods for Phylogenetic Networks
,
2010,
Genome biology and evolution.
[140]
R. Edwards,et al.
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
,
2013,
Briefings in functional genomics.
[141]
Cédric Notredame,et al.
Recent Evolutions of Multiple Sequence Alignment Algorithms
,
2007,
PLoS Comput. Biol..
[142]
V. Bansal,et al.
The importance of phase information for human genomics
,
2011,
Nature Reviews Genetics.
[143]
Gabor T. Marth,et al.
A global reference for human genetic variation
,
2015,
Nature.
[144]
Alexander Schönhuth,et al.
Viral Quasispecies Assembly via Maximal Clique Enumeration
,
2014,
PLoS Comput. Biol..
[145]
David R. Riley,et al.
Ten years of pan-genome analyses.
,
2015,
Current opinion in microbiology.
[146]
Jun Li,et al.
Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum
,
2013,
Nature Communications.
[147]
Gonzalo Navarro,et al.
Storage and Retrieval of Individual Genomes
,
2009,
RECOMB.
[148]
Gonzalo Navarro,et al.
Storage and Retrieval of Highly Repetitive Sequence Collections
,
2010,
J. Comput. Biol..
[149]
Lin Huang,et al.
Short read alignment with populations of genomes
,
2013,
Bioinform..
[150]
Dominique Lavenier,et al.
GATB: Genome Assembly & Analysis Tool Box
,
2014,
Bioinform..
[151]
E. Birney,et al.
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
,
2008,
Genome research.
[152]
N. Lennon,et al.
Characterizing and measuring bias in sequence data
,
2013,
Genome Biology.
[153]
Paul Medvedev,et al.
On the representation of de Bruijn graphs
,
2014,
RECOMB.
[154]
David C. Schwartz,et al.
High-resolution human genome structure by single-molecule analysis
,
2010,
Proceedings of the National Academy of Sciences.
[155]
S. Tringe,et al.
Tackling soil diversity with the assembly of large, complex metagenomes
,
2014,
Proceedings of the National Academy of Sciences.
[156]
I. Dubchak,et al.
Visualizing genomes: techniques and challenges
,
2010,
Nature Methods.
[157]
D. Mccormick.
Sequence the Human Genome
,
1986,
Bio/Technology.
[158]
B. Snel,et al.
Genome trees and the nature of genome evolution.
,
2005,
Annual review of microbiology.
[159]
Páll Melsted,et al.
Efficient counting of k-mers in DNA sequences using a bloom filter
,
2011,
BMC Bioinformatics.
[160]
S. Lewis,et al.
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream
,
2015,
Genome biology and evolution.
[161]
Jeffrey T Leek,et al.
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
,
2016,
Nature Protocols.
[162]
Maurits J. J. Dijkstra,et al.
Multiple Sequence Alignment.
,
2017,
Methods in molecular biology.