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@article{harrow2012gencode,
title={GENCODE: the reference human genome annotation for The ENCODE Project},
author={Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and others},
journal={Genome research},
volume={22},
number={9},
pages={1760--1774},
year={2012},
publisher={Cold Spring Harbor Lab}
}
@article{yandell2012beginner,
title={A beginner's guide to eukaryotic genome annotation},
author={Yandell, Mark and Ence, Daniel},
journal={Nature Reviews Genetics},
volume={13},
number={5},
pages={329--342},
year={2012},
publisher={Nature Publishing Group}
}
@article{kanehisa2015kegg,
title={KEGG as a reference resource for gene and protein annotation},
author={Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao},
journal={Nucleic acids research},
pages={gkv1070},
year={2015},
publisher={Oxford Univ Press}
}
@article{harrow2014vertebrate,
title={The vertebrate genome annotation browser 10 years on},
author={Harrow, Jennifer L and Steward, Charles A and Frankish, Adam and Gilbert, James G and Gonzalez, Jose M and Loveland, Jane E and Mudge, Jonathan and Sheppard, Dan and Thomas, Mark and Trevanion, Stephen and others},
journal={Nucleic acids research},
volume={42},
number={D1},
pages={D771--D779},
year={2014},
publisher={Oxford Univ Press}
}
@article{campbell2014genome,
title={Genome annotation and curation using MAKER and MAKER-P},
author={Campbell, Michael S and Holt, Carson and Moore, Barry and Yandell, Mark},
journal={Current Protocols in Bioinformatics},
pages={4--11},
year={2014},
publisher={Wiley Online Library}
}
@article{cantarel2008maker,
title={MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes},
author={Cantarel, Brandi L and Korf, Ian and Robb, Sofia MC and Parra, Genis and Ross, Eric and Moore, Barry and Holt, Carson and Alvarado, Alejandro S{\'a}nchez and Yandell, Mark},
journal={Genome research},
volume={18},
number={1},
pages={188--196},
year={2008},
publisher={Cold Spring Harbor Lab}
}
@article{rosenbloom2015ucsc,
title={The UCSC genome browser database: 2015 update},
author={Rosenbloom, Kate R and Armstrong, Joel and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Dreszer, Timothy R and Fujita, Pauline A and Guruvadoo, Luvina and Haeussler, Maximilian and others},
journal={Nucleic acids research},
volume={43},
number={D1},
pages={D670--D681},
year={2015},
publisher={Oxford Univ Press}
}
@article{nguyen2014comparative,
title={Comparative assembly hubs: web-accessible browsers for comparative genomics},
author={Nguyen, Ngan and Hickey, Glenn and Raney, Brian J and Armstrong, Joel and Clawson, Hiram and Zweig, Ann and Karolchik, Donna and Kent, William James and Haussler, David and Paten, Benedict},
journal={Bioinformatics},
volume={30},
number={23},
pages={3293--3301},
year={2014},
publisher={Oxford Univ Press}
}
@article{stanke2004augustus,
title={AUGUSTUS: a web server for gene finding in eukaryotes},
author={Stanke, Mario and Steinkamp, Rasmus and Waack, Stephan and Morgenstern, Burkhard},
journal={Nucleic acids research},
volume={32},
number={suppl 2},
pages={W309--W312},
year={2004},
publisher={Oxford Univ Press}
}
@article{vilella2009ensemblcompara,
title={EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates},
author={Vilella, Albert J and Severin, Jessica and Ureta-Vidal, Abel and Heng, Li and Durbin, Richard and Birney, Ewan},
journal={Genome research},
volume={19},
number={2},
pages={327--335},
year={2009},
publisher={Cold Spring Harbor Lab}
}
@article{stanke2008using,
title={Using native and syntenically mapped cDNA alignments to improve de novo gene finding},
author={Stanke, Mario and Diekhans, Mark and Baertsch, Robert and Haussler, David},
journal={Bioinformatics},
volume={24},
number={5},
pages={637--644},
year={2008},
publisher={Oxford Univ Press}
}
@article{konig2015simultaneous,
title={Simultaneous gene finding in multiple genomes},
author={K{\"o}nig, Stefanie and Romoth, Lars and Gerischer, Lizzy and Stanke, Mario},
journal={Bioinformatics},
volume={32},
number={21},
publisher={Oxford Univ Press},
year={2016},
}
@article{Aken01012016,
author = {Aken, Bronwen L. and Ayling, Sarah and Barrell, Daniel and Clarke, Laura and Curwen, Valery and Fairley, Susan and Fernandez Banet, Julio and Billis, Konstantinos and García Girón, Carlos and Hourlier, Thibaut and Howe, Kevin and Kähäri, Andreas and Kokocinski, Felix and Martin, Fergal J. and Murphy, Daniel N. and Nag, Rishi and Ruffier, Magali and Schuster, Michael and Tang, Y. Amy and Vogel, Jan-Hinnerk and White, Simon and Zadissa, Amonida and Flicek, Paul and Searle, Stephen M. J.},
title = {The Ensembl gene annotation system},
volume = {2016},
year = {2016},
doi = {10.1093/database/baw093},
abstract ={The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html},
URL = {http://database.oxfordjournals.org/content/2016/baw093.abstract},
eprint = {http://database.oxfordjournals.org/content/2016/baw093.full.pdf+html},
journal = {Database}
}
@article{paten2011cactus,
title={Cactus: Algorithms for genome multiple sequence alignment},
author={Paten, Benedict and Earl, Dent and Nguyen, Ngan and Diekhans, Mark and Zerbino, Daniel and Haussler, David},
journal={Genome research},
volume={21},
number={9},
pages={1512--1528},
year={2011},
publisher={Cold Spring Harbor Lab}
}
@article{hickey2013hal,
title={HAL: a hierarchical format for storing and analyzing multiple genome alignments},
author={Hickey, Glenn and Paten, Benedict and Earl, Dent and Zerbino, Daniel and Haussler, David},
journal={Bioinformatics},
pages={btt128},
year={2013},
publisher={Oxford Univ Press}
}
@article{hoff2015current,
title={Current methods for automated annotation of protein-coding genes},
author={Hoff, KJ and Stanke, M},
journal={Current Opinion in Insect Science},
volume={7},
pages={8--14},
year={2015},
publisher={Elsevier}
}
@article{dobin2013star,
title={STAR: ultrafast universal RNA-seq aligner},
author={Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R},
journal={Bioinformatics},
volume={29},
number={1},
pages={15--21},
year={2013},
publisher={Oxford Univ Press}
}
@article{gordon2016long,
title={Long-read sequence assembly of the gorilla genome},
author={Gordon, David and Huddleston, John and Chaisson, Mark JP and Hill, Christopher M and Kronenberg, Zev N and Munson, Katherine M and Malig, Maika and Raja, Archana and Fiddes, Ian and Hillier, LaDeana W and others},
journal={Science},
volume={352},
number={6281},
pages={aae0344},
year={2016},
publisher={American Association for the Advancement of Science}
}
@article{putnam2016chromosome,
title={Chromosome-scale shotgun assembly using an in vitro method for long-range linkage},
author={Putnam, Nicholas H and O'Connell, Brendan L and Stites, Jonathan C and Rice, Brandon J and Blanchette, Marco and Calef, Robert and Troll, Christopher J and Fields, Andrew and Hartley, Paul D and Sugnet, Charles W and others},
journal={Genome research},
volume={26},
number={3},
pages={342--350},
year={2016},
publisher={Cold Spring Harbor Lab}
}
@techreport{10xassembly,
title={CHROMIUM \textit{de novo} Assembly Solution},
URL={http://go.10xgenomics.com/l/172142/2016-08-10/3svkc/172142/8088/LIT00005_RevA_Chromium_De_Novo_Assembly_Solution_Application_Note2.pdf}
}
@article{haussler2009genome,
title={Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species},
author={Haussler, David and O'Brien, Stephen J and Ryder, Oliver A and Barker, F Keith and Clamp, Michele and Crawford, Andrew J and Hanner, Robert and Hanotte, Olivier and Johnson, Warren E and McGuire, Jimmy A and others},
journal={Journal of Heredity},
volume={100},
number={6},
pages={659--674},
year={2009}
}
@article{jarvis2014whole,
title={Whole-genome analyses resolve early branches in the tree of life of modern birds},
author={Jarvis, Erich D and Mirarab, Siavash and Aberer, Andre J and Li, Bo and Houde, Peter and Li, Cai and Ho, Simon YW and Faircloth, Brant C and Nabholz, Benoit and Howard, Jason T and others},
journal={Science},
volume={346},
number={6215},
pages={1320--1331},
year={2014},
publisher={American Association for the Advancement of Science}
}
@inproceedings{haussler1996generalized,
title={A generalized hidden Markov model for the recognition of human genes in DNA},
author={Haussler, David Kulp David and Eeckman, Martin G Reese Frank H},
booktitle={Proc. Int. Conf. on Intelligent Systems for Molecular Biology, St. Louis},
pages={134--142},
year={1996}
}
@article{sosinsky2000genomic,
title={The genomic structure of human olfactory receptor genes},
author={Sosinsky, Alona and Glusman, Gustavo and Lancet, Doron},
journal={Genomics},
volume={70},
number={1},
pages={49--61},
year={2000},
publisher={Elsevier}
}
@article{westerfield1998zebrafish,
title={Zebrafish informatics and the ZFIN database},
author={Westerfield, Monte and Doerry, Eckehard and Kirkpatrick, Arthur E and Douglas, Sarah A},
journal={Methods in cell biology},
volume={60},
pages={339--355},
year={1998},
publisher={Elsevier}
}
@article{stein2001wormbase,
title={WormBase: network access to the genome and biology of Caenorhabditis elegans},
author={Stein, Lincoln and Sternberg, Paul and Durbin, Richard and Thierry-Mieg, Jean and Spieth, John},
journal={Nucleic acids research},
volume={29},
number={1},
pages={82--86},
year={2001},
publisher={Oxford Univ Press}
}
@article{swarbreck2008arabidopsis,
title={The Arabidopsis Information Resource (TAIR): gene structure and function annotation},
author={Swarbreck, David and Wilks, Christopher and Lamesch, Philippe and Berardini, Tanya Z and Garcia-Hernandez, Margarita and Foerster, Hartmut and Li, Donghui and Meyer, Tom and Muller, Robert and Ploetz, Larry and others},
journal={Nucleic acids research},
volume={36},
number={suppl 1},
pages={D1009--D1014},
year={2008},
publisher={Oxford Univ Press}
}
@article{fushan2015gene,
title={Gene expression defines natural changes in mammalian lifespan},
author={Fushan, Alexey A and Turanov, Anton A and Lee, Sang-Goo and Kim, Eun Bae and Lobanov, Alexei V and Yim, Sun Hee and Buffenstein, Rochelle and Lee, Sang-Rae and Chang, Kyu-Tae and Rhee, Hwanseok and others},
journal={Aging cell},
volume={14},
number={3},
pages={352--365},
year={2015},
publisher={Wiley Online Library}
}
@article{cortez2014origins,
title={Origins and functional evolution of Y chromosomes across mammals},
author={Cortez, Diego and Marin, Ray and Toledo-Flores, Deborah and Froidevaux, Laure and Liechti, Ang{\'e}lica and Waters, Paul D and Gr{\"u}tzner, Frank and Kaessmann, Henrik},
journal={Nature},
volume={508},
number={7497},
pages={488--493},
year={2014},
publisher={Nature Publishing Group}
}
@article{liu2016identification,
title={Identification of distinct genes associated with seawater aspiration-induced acute lung injury by gene expression profile analysis},
author={Liu, Wei and Pan, Lei and Zhang, Minlong and Bo, Liyan and Li, Congcong and Liu, Qingqing and Wang, Li and Jin, Faguang},
journal={Molecular Medicine Reports},
volume={14},
number={4},
pages={3168--3178},
year={2016},
publisher={Spandidos Publications}
}
@article{brawand2011evolution,
title={The evolution of gene expression levels in mammalian organs},
author={Brawand, David and Soumillon, Magali and Necsulea, Anamaria and Julien, Philippe and Cs{\'a}rdi, G{\'a}bor and Harrigan, Patrick and Weier, Manuela and Liechti, Ang{\'e}lica and Aximu-Petri, Ayinuer and Kircher, Martin and others},
journal={Nature},
volume={478},
number={7369},
pages={343--348},
year={2011},
publisher={Nature Publishing Group}
}
@article{carelli2016life,
title={The life history of retrocopies illuminates the evolution of new mammalian genes},
author={Carelli, Francesco Nicola and Hayakawa, Takashi and Go, Yasuhiro and Imai, Hiroo and Warnefors, Maria and Kaessmann, Henrik},
journal={Genome research},
volume={26},
number={3},
pages={301--314},
year={2016},
publisher={Cold Spring Harbor Lab}
}
@article{pipes2013non,
title={The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics},
author={Pipes, Lenore and Li, Sheng and Bozinoski, Marjan and Palermo, Robert and Peng, Xinxia and Blood, Phillip and Kelly, Sara and Weiss, Jeffrey M and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and others},
journal={Nucleic acids research},
volume={41},
number={D1},
pages={D906--D914},
year={2013},
publisher={Oxford Univ Press}
}
@article{nuttle2016emergence,
title={Emergence of a Homo sapiens-specific gene family and chromosome 16p11. 2 CNV susceptibility},
author={Nuttle, Xander and Giannuzzi, Giuliana and Duyzend, Michael H and Schraiber, Joshua G and Narvaiza, I{\~n}igo and Sudmant, Peter H and Penn, Osnat and Chiatante, Giorgia and Malig, Maika and Huddleston, John and others},
journal={Nature},
year={2016},
publisher={Nature Research}
}
@article{diederichs2014four,
title={The four dimensions of noncoding RNA conservation},
author={Diederichs, Sven},
journal={Trends in genetics},
volume={30},
number={4},
pages={121--123},
year={2014},
publisher={Elsevier}
}
@article{marchetto2013differential,
title={Differential L1 regulation in pluripotent stem cells of humans and apes},
author={Marchetto, Maria CN and Narvaiza, I{\~n}igo and Denli, Ahmet M and Benner, Christopher and Lazzarini, Thomas A and Nathanson, Jason L and Paquola, Apu{\~a} CM and Desai, Keval N and Herai, Roberto H and Weitzman, Matthew D and others},
journal={Nature},
volume={503},
number={7477},
pages={525--529},
year={2013},
publisher={Nature Research}
}
@article {Lagarde105064,
author = {Lagarde, Julien and Uszczynska-Ratajczak, Barbara and Carbonell, Silvia and Davis, Carrie and Gingeras, Thomas R and Frankish, Adam and Harrow, Jennifer and Guigo, Roderic and Johnson, Rory},
title = {High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)},
year = {2017},
doi = {10.1101/105064},
publisher = {Cold Spring Harbor Labs Journals},
abstract = {Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, current reference gene collections remain far from complete: many genes models are fragmentary, while thousands more remain uncatalogued, particularly for long non coding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third generation long-read sequencing. We present an experimental re-annotation of the entire GENCODE intergenic lncRNA population in matched human and mouse tissues. CLS approximately doubles the annotated complexity of targeted loci, in terms of validated splice junctions and transcript models. The full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter- and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.},
URL = {http://biorxiv.org/content/early/2017/02/01/105064},
eprint = {http://biorxiv.org/content/early/2017/02/01/105064.full.pdf},
journal = {bioRxiv}
}
@article{chin2016phased,
title={Phased diploid genome assembly with single-molecule real-time sequencing},
author={Chin, Chen-Shan and Peluso, Paul and Sedlazeck, Fritz J and Nattestad, Maria and Concepcion, Gregory T and Clum, Alicia and Dunn, Christopher and O'Malley, Ronan and Figueroa-Balderas, Rosa and Morales-Cruz, Abraham and others},
journal={Nature Methods},
volume={13},
number={12},
pages={1050--1054},
year={2016},
publisher={Nature Research}
}
@article {Weisenfeld070425,
author = {Weisenfeld, Neil I and Kumar, Vijay and Shah, Preyas and Church, Deanna and Jaffe, David B},
title = {Direct determination of diploid genome sequences},
year = {2016},
doi = {10.1101/070425},
publisher = {Cold Spring Harbor Labs Journals},
abstract = {Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses and, in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed, free of reference bias, but nearly all were constructed by merging homologous loci into single {\textquoteleft}consensus{\textquoteright} sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing and one using thousands of clone pools. Here we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ~1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new {\textquoteleft}pushbutton{\textquoteright} algorithm, Supernova. Each computation took two days on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.},
URL = {http://biorxiv.org/content/early/2016/08/19/070425},
eprint = {http://biorxiv.org/content/early/2016/08/19/070425.full.pdf},
journal = {bioRxiv}
}
@article{rodriguez2012appris,
title={APPRIS: annotation of principal and alternative splice isoforms},
author={Rodriguez, Jose Manuel and Maietta, Paolo and Ezkurdia, Iakes and Pietrelli, Alessandro and Wesselink, Jan-Jaap and Lopez, Gonzalo and Valencia, Alfonso and Tress, Michael L},
journal={Nucleic acids research},
pages={gks1058},
year={2012},
publisher={Oxford Univ Press}
}
@article{popp2013organizing,
title={Organizing principles of mammalian nonsense-mediated mRNA decay},
author={Popp, Maximilian Wei-Lin and Maquat, Lynne E},
journal={Annual review of genetics},
volume={47},
pages={139--165},
year={2013},
publisher={Annual Reviews}
}
@article{huddleston2016discovery,
title={Discovery and genotyping of structural variation from long-read haploid genome sequence data},
author={Huddleston, John and Chaisson, Mark JP and Steinberg, Karyn Meltz and Warren, Wes and Hoekzema, Kendra and Gordon, David S and Graves-Lindsay, Tina A and Munson, Katherine M and Kronenberg, Zev N and Vives, Laura and others},
journal={Genome Research},
pages={gr--214007},
year={2016},
publisher={Cold Spring Harbor Lab}
}
@article{shi2009association,
title={Association of TRB3 gene Q84R polymorphism with type 2 diabetes mellitus in Chinese population},
author={Shi, Zhiyong and Liu, Jing and Guo, Qian and Ma, Xiaoqin and Shen, Linna and Xu, Sanni and Gao, Hongxia and Yuan, Xinjian and Zhang, Junling},
journal={Endocrine},
volume={35},
number={3},
pages={414--419},
year={2009},
publisher={Springer}
}
@article{10002010map,
title={A map of human genome variation from population-scale sequencing},
author={1000 Genomes Project Consortium and others},
journal={Nature},
volume={467},
number={7319},
pages={1061--1073},
year={2010},
publisher={Nature Publishing Group}
}
@article{li2011rsem,
title={RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome},
author={Li, Bo and Dewey, Colin N},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={323},
year={2011},
publisher={BioMed Central}
}
@article{gordon2015widespread,
title={Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing},
author={Gordon, Sean P and Tseng, Elizabeth and Salamov, Asaf and Zhang, Jiwei and Meng, Xiandong and Zhao, Zhiying and Kang, Dongwan and Underwood, Jason and Grigoriev, Igor V and Figueroa, Melania and others},
journal={PloS one},
volume={10},
number={7},
pages={e0132628},
year={2015},
publisher={Public Library of Science}
}
@article{haas2013novo,
title={De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity},
author={Haas, Brian J and Papanicolaou, Alexie and Yassour, Moran and Grabherr, Manfred and Blood, Philip D and Bowden, Joshua and Couger, Matthew Brian and Eccles, David and Li, Bo and Lieber, Matthias and others},
journal={Nature protocols},
volume={8},
number={8},
year={2013},
publisher={NIH Public Access}
}
@article{bray2015near,
title={Near-optimal RNA-Seq quantification},
author={Bray, Nicolas and Pimentel, Harold and Melsted, P{\'a}ll and Pachter, Lior},
journal={arXiv preprint arXiv:1505.02710},
year={2015}
}
@article{tyner2016ucsc,
title={The UCSC Genome Browser database: 2017 update},
author={Tyner, Cath and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Eisenhart, Christopher and Fischer, Clayton M and Gibson, David and Gonzalez, Jairo Navarro and Guruvadoo, Luvina and others},
journal={Nucleic acids research},
volume={45},
number={D1},
pages={D626--D634},
year={2016},
publisher={Oxford University Press}
}
@article{wolfe1993mammalian,
title={Mammalian gene evolution: nucleotide sequence divergence between mouse and rat},
author={Wolfe, Kenneth H and Sharp, Paul M},
journal={Journal of Molecular Evolution},
volume={37},
number={4},
pages={441--456},
year={1993},
publisher={Springer}
}
@article{clamp2007distinguishing,
title={Distinguishing protein-coding and noncoding genes in the human genome},
author={Clamp, Michele and Fry, Ben and Kamal, Mike and Xie, Xiaohui and Cuff, James and Lin, Michael F and Kellis, Manolis and Lindblad-Toh, Kerstin and Lander, Eric S},
journal={Proceedings of the National Academy of Sciences},
volume={104},
number={49},
pages={19428--19433},
year={2007},
publisher={National Acad Sciences}
}
@article{siepel2007targeted,
title={Targeted discovery of novel human exons by comparative genomics},
author={Siepel, Adam and Diekhans, Mark and Brejov{\'a}, Bro{\v{n}}a and Langton, Laura and Stevens, Michael and Comstock, Charles LG and Davis, Colleen and Ewing, Brent and Oommen, Shelly and Lau, Christopher and others},
journal={Genome research},
volume={17},
number={12},
pages={1763--1773},
year={2007},
publisher={Cold Spring Harbor Lab}
}
@article{lin2011phylocsf,
title={PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions},
author={Lin, Michael F and Jungreis, Irwin and Kellis, Manolis},
journal={Bioinformatics},
volume={27},
number={13},
pages={i275--i282},
year={2011},
publisher={Oxford University Press}
}
@article{dinger2008differentiating,
title={Differentiating protein-coding and noncoding RNA: challenges and ambiguities},
author={Dinger, Marcel E and Pang, Ken C and Mercer, Tim R and Mattick, John S},
journal={PLoS computational biology},
volume={4},
number={11},
pages={e1000176},
year={2008},
publisher={Public Library of Science}
}
@article{kent2003evolution,
title={Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes},
author={Kent, W James and Baertsch, Robert and Hinrichs, Angie and Miller, Webb and Haussler, David},
journal={Proceedings of the National Academy of Sciences},
volume={100},
number={20},
pages={11484--11489},
year={2003},
publisher={National Acad Sciences}
}
@article{blanchette2004aligning,
title={Aligning multiple genomic sequences with the threaded blockset aligner},
author={Blanchette, Mathieu and Kent, W James and Riemer, Cathy and Elnitski, Laura and Smit, Arian FA and Roskin, Krishna M and Baertsch, Robert and Rosenbloom, Kate and Clawson, Hiram and Green, Eric D and others},
journal={Genome research},
volume={14},
number={4},
pages={708--715},
year={2004},
publisher={Cold Spring Harbor Lab}
}
@article{earl2014alignathon,
title={Alignathon: a competitive assessment of whole-genome alignment methods},
author={Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Harris, Robert S and Fitzgerald, Stephen and Beal, Kathryn and Seledtsov, Igor and Molodtsov, Vladimir and Raney, Brian J and Clawson, Hiram and others},
journal={Genome research},
volume={24},
number={12},
pages={2077--2089},
year={2014},
publisher={Cold Spring Harbor Lab}
}
@article{miller200728,
title={28-way vertebrate alignment and conservation track in the UCSC Genome Browser},
author={Miller, Webb and Rosenbloom, Kate and Hardison, Ross C and Hou, Minmei and Taylor, James and Raney, Brian and Burhans, Richard and King, David C and Baertsch, Robert and Blankenberg, Daniel and others},
journal={Genome research},
volume={17},
number={12},
pages={1797--1808},
year={2007},
publisher={Cold Spring Harbor Lab}
}
@article {Jain128835,
author = {Jain, Miten and Koren, Sergey and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and Malla, Sunir and Marriott, Hannah and Miga, Karen H and Nieto, Tom and O{\textquoteright}Grady, Justin and Olsen, Hugh E and Pedersen, Brent S and Rhie, Arang and Richardson, Hollian and Quinlan, Aaron and Snutch, Terrance P and Tee, Louise and Paten, Benedict and Phillippy, Adam M. and Simpson, Jared T and Loman, Nicholas James and Loose, Matthew},
title = {Nanopore sequencing and assembly of a human genome with ultra-long reads},
year = {2017},
doi = {10.1101/128835},
publisher = {Cold Spring Harbor Labs Journals},
abstract = {Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However until recently nanopore sequencing has been mainly applied to small genomes, due to the limited output attainable. We present nanopore sequencing and assembly of the GM12878 Utah/Ceph human reference genome generated using the Oxford Nanopore MinION and R9.4 version chemistry. We generated 91.2 Gb of sequence data (~30x theoretical coverage) from 39 flowcells. De novo assembly yielded a highly complete and contiguous assembly (NG50 ~3Mb). We observed considerable variability in homopolymeric tract resolution between different basecallers. The data permitted sensitive detection of both large structural variants and epigenetic modifications. Further we developed a new approach exploiting the long-read capability of this system and found that adding an additional 5x-coverage of "ultra-long" reads (read N50 of 99.7kb) more than doubled the assembly contiguity. Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone. Portable de novo sequencing of human genomes may be important for rapid point-of-care diagnosis of rare genetic diseases and cancer, and monitoring of cancer progression. The complete dataset including raw signal is available as an Amazon Web Services Open Dataset at: https://github.com/nanopore-wgs-consortium/NA12878.},
URL = {http://www.biorxiv.org/content/early/2017/04/20/128835},
eprint = {http://www.biorxiv.org/content/early/2017/04/20/128835.full.pdf},
journal = {bioRxiv}
}
@article {Thybert158659,
author = {Thybert, David and Roller, Ma{\v s}a and Navarro, F{\'a}bio C. P. and Fiddes, Ian and Streeter, Ian and Feig, Christine and Martin-Galvez, David and Kolmogorov, Mikhail and Janou{\v s}ek, V{\'a}clav and Akanni, Wasiu and Aken, Bronwen and Aldridge, Sarah and Chakrapani, Varshith and Chow, William and Clarke, Laura and Cummins, Carla and Doran, Anthony and Dunn, Matthew and Goodstadt, Leo and Howe, Kerstin and Howell, Matthew and Josselin, Ambre-Aurore and Karn, Robert C. and Laukaitis, Christina M. and Jingtao, Lilue and Martin, Fergal and Muffato, Matthieu and Quail, Michael A. and Sisu, Cristina and Stanke, Mario and Stefflova, Klara and Van Oosterhout, Cock and Veyrunes, Frederic and Ward, Ben and Yang, Fengtang and Yazdanifar, Golbahar and Zadissa, Amonida and Adams, David and Brazma, Alvis and Gerstein, Mark and Paten, Benedict and Pham, Son and Keane, Thomas and Odom, Duncan T. and Flicek, Paul},
title = {Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes},
year = {2017},
doi = {10.1101/158659},
publisher = {Cold Spring Harbor Labs Journals},
abstract = {Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four- and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.},
URL = {http://www.biorxiv.org/content/early/2017/07/02/158659},
eprint = {http://www.biorxiv.org/content/early/2017/07/02/158659.full.pdf},
journal = {bioRxiv}
}
@article{zhu2007comparative,
title={Comparative genomics search for losses of long-established genes on the human lineage},
author={Zhu, Jingchun and Sanborn, J Zachary and Diekhans, Mark and Lowe, Craig B and Pringle, Tom H and Haussler, David},
journal={PLoS computational biology},
volume={3},
number={12},
pages={e247},
year={2007},
publisher={Public Library of Science}
}
@article{quinlan2010bedtools,
title={BEDTools: a flexible suite of utilities for comparing genomic features},
author={Quinlan, Aaron R and Hall, Ira M},
journal={Bioinformatics},
volume={26},
number={6},
pages={841--842},
year={2010},
publisher={Oxford University Press}
}
@article{wu2005gmap,
title={GMAP: a genomic mapping and alignment program for mRNA and EST sequences},
author={Wu, Thomas D and Watanabe, Colin K},
journal={Bioinformatics},
volume={21},
number={9},
pages={1859--1875},
year={2005},
publisher={Oxford University Press}
}
@article{vivian2017toil,
title={Toil enables reproducible, open source, big biomedical data analyses},
author={Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and others},
journal={Nature biotechnology},
volume={35},
number={4},
pages={314},
year={2017},
publisher={NIH Public Access}
}
@article{pruitt2006ncbi,
title={NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins},
author={Pruitt, Kim D and Tatusova, Tatiana and Maglott, Donna R},
journal={Nucleic acids research},
volume={35},
number={suppl\_1},
pages={D61--D65},
year={2006},
publisher={Oxford University Press}
}
@article{kent2002blat,
title={BLAT—the BLAST-like alignment tool},
author={Kent, W James},
journal={Genome research},
volume={12},
number={4},
pages={656--664},
year={2002},
publisher={Cold Spring Harbor Lab}
}
@article{stanke2006gene,
title={Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources},
author={Stanke, Mario and Sch{\"o}ffmann, Oliver and Morgenstern, Burkhard and Waack, Stephan},
journal={BMC bioinformatics},
volume={7},
number={1},
pages={62},
year={2006},
publisher={BioMed Central}
}
@article{tatusov1997genomic,
title={A genomic perspective on protein families},
author={Tatusov, Roman L and Koonin, Eugene V and Lipman, David J},
journal={Science},
volume={278},
number={5338},
pages={631--637},
year={1997},
publisher={American Association for the Advancement of Science}
}
@article{ashburner2000gene,
title={Gene Ontology: tool for the unification of biology},
author={Ashburner, Michael and Ball, Catherine A and Blake, Judith A and Botstein, David and Butler, Heather and Cherry, J Michael and Davis, Allan P and Dolinski, Kara and Dwight, Selina S and Eppig, Janan T and others},
journal={Nature genetics},
volume={25},
number={1},
pages={25},
year={2000},
publisher={NIH Public Access}
}
@article{kanehisa2000kegg,
title={KEGG: kyoto encyclopedia of genes and genomes},
author={Kanehisa, Minoru and Goto, Susumu},
journal={Nucleic acids research},
volume={28},
number={1},
pages={27--30},
year={2000},
publisher={Oxford University Press}
}
@article{marcotte1999detecting,
title={Detecting protein function and protein-protein interactions from genome sequences},
author={Marcotte, Edward M and Pellegrini, Matteo and Ng, Ho-Leung and Rice, Danny W and Yeates, Todd O and Eisenberg, David},
journal={Science},
volume={285},
number={5428},
pages={751--753},
year={1999},
publisher={American Association for the Advancement of Science}
}
@article{marti2007annolite,
title={The AnnoLite and AnnoLyze programs for comparative annotation of protein structures},
author={Marti-Renom, Marc A and Rossi, Andrea and Al-Shahrour, F{\'a}tima and Davis, Fred P and Pieper, Ursula and Dopazo, Joaqu{\'\i}n and Sali, Andrej},
journal={BMC bioinformatics},
volume={8},
number={4},
pages={S4},
year={2007},
publisher={BioMed Central}
}
@article{paten2008genome,
title={Genome-wide nucleotide-level mammalian ancestor reconstruction},
author={Paten, Benedict and Herrero, Javier and Fitzgerald, Stephen and Beal, Kathryn and Flicek, Paul and Holmes, Ian and Birney, Ewan},
journal={Genome research},
volume={18},
number={11},
pages={1829--1843},
year={2008},
publisher={Cold Spring Harbor Lab}
}
@article{zhang2014comparative,
title={Comparative genomics reveals insights into avian genome evolution and adaptation},
author={Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M and Lee, Chul and Storz, Jay F and Antunes, Agostinho and Greenwold, Matthew J and Meredith, Robert W and others},
journal={Science},
volume={346},
number={6215},
pages={1311--1320},
year={2014},
publisher={American Association for the Advancement of Science}
}
@article{klasberg2016computational,
title={Computational identification of novel genes: current and future perspectives},
author={Klasberg, Steffen and Bitard-Feildel, Tristan and Mallet, Ludovic},
journal={Bioinformatics and Biology insights},
volume={10},
pages={121},
year={2016},
publisher={Libertas Academica}
}
@article{van2007using,
title={Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences},
author={van Baren, Marijke J and Koebbe, Brian C and Brent, Michael R},
journal={Current Protocols in Bioinformatics},
pages={4--8},
year={2007},
publisher={Wiley Online Library}
}
@article{sharma2016coding,
title={Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation},
author={Sharma, Virag and Elghafari, Anas and Hiller, Michael},
journal={Nucleic acids research},
volume={44},
number={11},
pages={e103--e103},
year={2016},
publisher={Oxford University Press}
}
@article{paten2008enredo,
title={Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs},
author={Paten, Benedict and Herrero, Javier and Beal, Kathryn and Fitzgerald, Stephen and Birney, Ewan},
journal={Genome research},
volume={18},
number={11},
pages={1814--1828},
year={2008},
publisher={Cold Spring Harbor Lab}
}
@article{gross2007contrast,
title={CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction},
author={Gross, Samuel S and Do, Chuong B and Sirota, Marina and Batzoglou, Serafim},
journal={Genome biology},
volume={8},
number={12},
pages={R269},
year={2007},
publisher={BioMed Central}
}
@article{batzoglou2000human,
title={Human and mouse gene structure: comparative analysis and application to exon prediction},
author={Batzoglou, Serafim and Pachter, Lior and Mesirov, Jill P and Berger, Bonnie and Lander, Eric S},
journal={Genome research},
volume={10},
number={7},
pages={950--958},
year={2000},
publisher={Cold Spring Harbor Lab}
}
@article{roy2012cofactor,
title={COFACTOR: an accurate comparative algorithm for structure-based protein function annotation},
author={Roy, Ambrish and Yang, Jianyi and Zhang, Yang},
journal={Nucleic acids research},
volume={40},
number={W1},
pages={W471--W477},
year={2012},
publisher={Oxford University Press}
}
@article{mudge2015creating,
title={Creating reference gene annotation for the mouse C57BL6/J genome assembly},
author={Mudge, Jonathan M and Harrow, Jennifer},
journal={Mammalian Genome},
volume={26},
number={9-10},
pages={366--378},
year={2015},
publisher={Springer}
}
@article{o2015reference,
title={Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation},
author={O'Leary, Nuala A and Wright, Mathew W and Brister, J Rodney and Ciufo, Stacy and Haddad, Diana and McVeigh, Rich and Rajput, Bhanu and Robbertse, Barbara and Smith-White, Brian and Ako-Adjei, Danso and others},
journal={Nucleic acids research},
volume={44},
number={D1},
pages={D733--D745},
year={2015},
publisher={Oxford University Press}
}
@article{paten2008sequence,
title={Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment},
author={Paten, Benedict and Herrero, Javier and Beal, Kathryn and Birney, Ewan},
journal={Bioinformatics},
volume={25},
number={3},
pages={295--301},
year={2008},
publisher={Oxford University Press}
}
@article{bateman2004pfam,
title={The Pfam protein families database},
author={Bateman, Alex and Coin, Lachlan and Durbin, Richard and Finn, Robert D and Hollich, Volker and Griffiths-Jones, Sam and Khanna, Ajay and Marshall, Mhairi and Moxon, Simon and Sonnhammer, Erik LL and others},
journal={Nucleic acids research},
volume={32},
number={suppl\_1},
pages={D138--D141},
year={2004},
publisher={Oxford University Press}
}
@article{zdobnov2001interproscan,
title={InterProScan--an integration platform for the signature-recognition methods in InterPro},
author={Zdobnov, Evgeni M and Apweiler, Rolf},
journal={Bioinformatics},
volume={17},
number={9},
pages={847--848},
year={2001},
publisher={Oxford University Press}
}
@article{lukashin1998genemark,
title={GeneMark. hmm: new solutions for gene finding},
author={Lukashin, Alexander V and Borodovsky, Mark},
journal={Nucleic acids research},
volume={26},
number={4},
pages={1107--1115},
year={1998},
publisher={Oxford University Press}
}
@article{letovsky1998gdb,
title={GDB: the human genome database},
author={Letovsky, Stanley I and Cottingham, Robert W and Porter, Christopher J and Li, Peter WD},
journal={Nucleic Acids Research},
volume={26},
number={1},
pages={94--99},
year={1998},
publisher={Oxford University Press}
}
@article{encode2004encode,
title={The ENCODE (ENCyclopedia of DNA elements) project},
author={ENCODE Project Consortium and others},
journal={Science},
volume={306},
number={5696},
pages={636--640},
year={2004},
publisher={American Association for the Advancement of Science}
}
@article{sherry2001dbsnp,
title={dbSNP: the NCBI database of genetic variation},
author={Sherry, Stephen T and Ward, M-H and Kholodov, M and Baker, J and Phan, Lon and Smigielski, Elizabeth M and Sirotkin, Karl},
journal={Nucleic acids research},
volume={29},
number={1},
pages={308--311},
year={2001},
publisher={Oxford University Press}
}
@article{alexandersson2003slam,
title={SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model},
author={Alexandersson, Marina and Cawley, Simon and Pachter, Lior},
journal={Genome Research},
volume={13},
number={3},
pages={496--502},
year={2003},
publisher={Cold Spring Harbor Lab}
}
@article{korf2001integrating,
title={Integrating genomic homology into gene structure prediction},
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