Difference between revisions of "Fuli:Publications"

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'''See up-to-date Publications of Fuli's Group on [http://scholar.google.com/citations?user=1Z8SOakAAAAJ&hl=en Google Scholars Profile of Fuli Yu]'''
1. CHARGE ASSOCIATION PAPER. '''''Nature Genetics''''' In press.  <BR>
2. CHARGE SELECTION PAPER. In submission. <BR>
3. FIG PAPER. '''''Science''''' In press. <BR>
4. Lotta LA, Tuana G, Yu J, Martinelli I, Wang M, '''''Fuli Yu''''', Passamonti SM, Pappalardo E, Valsecchi C, Scherer SE, Hale W, Muzny DM, Randi G, Rosendaal FR, Gibbs RA, Peyvandi F. Next-generation sequencing study finds an excess of rare, coding single nucleotide variants of ADAMTS13 in patients with deep vein thrombosis. ''''' Journal of Thrombosis and Haemostasis'''''  (2013) [http://onlinelibrary.wiley.com/doi/10.1111/jth.12291/abstract ABSTRACT] <BR>
5. Line SRP, Liu X, Souza APd and '''''Fuli Yu''''' Translational signatures and mRNA levels are highly correlated in human stably expressed genes. '''''BMC Genomics''''' (2013) [http://www.biomedcentral.com/content/pdf/1471-2164-14-268.pdf PDF] <BR>
6. Wang Y, Lu J*, Yu J, Gibbs RA, '''''Fuli Yu'''''* An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. '''''Genome Research''''' (2013) *Corresponding Author[http://genome.cshlp.org/content/early/2013/03/13/gr.146084.112.abstract ABSTRACT] [http://sourceforge.net/projects/snptools/ SOFTWARE]<BR>
7. Wang Q, Song J, Gibbs RA,Boerwinkle E, Dong JF*, '''''Fuli Yu'''''* Characterizing Polymorphisms and Allelic Diversity of von Willebrand Factor Gene in the 1000 Genomes.''''' Journal of Thrombosis and Haemostasis''''' (2013) .*Corresponding Author [http://onlinelibrary.wiley.com/doi/10.1111/jth.12093/abstract ABSTRACT] <BR>
1. '''''1000 Genomes Project Consortium'''''. An integrated map of genetic variation from 1,092 human genomes (i.e. 1000 Genome Phase 1 Paper) '''''Nature''''' (2012) [ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/paper/ PAPER] [http://www.biotechniques.com/news/1000-Genomes-Project-Publishes-Variation-Maps/biotechniques-336769.html BioTechniques Press]<BR>
2. Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C,  Milosavljevic A* and '''''Fuli Yu'''''*. Atlas2 Cloud: a framework for personal genome analysis in the cloud. '''''BMC Genomics''''' (2012).*''Corresponding Author'' [http://www.biomedcentral.com/content/pdf/1471-2164-13-S6-S19.pdf PDF]<BR>
3. Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Coarfa C, Milosavljevic A*, and '''''Fuli Yu'''''*. Enabling Atlas2 Personal Genome Analysis on the Cloud. Conference paper at ''''' (2011) IEEE International Workshop on Genomic Signal Processing and Statistics''''', *''Corresponding Author'' [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6169458&tag=1 ABSTRACT]  [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6169458 PDF]<BR>
4. Lu J*, Wang Y, Gibbs RA, '''''Fuli Yu'''''*. Characterizing Linkage Disequilibrium and Evaluating Imputation Power of Human Genomic Insertion-deletion Polymorphisms. '''''Genome Biology''''' (2012)*''Corresponding Author'' [http://genomebiology.com/content/pdf/gb-2012-13-2-r15.pdf PDF]<BR>
5. Lotta LA, Wang M, Yu J, Martinelli IM, '''''Fuli Yu''''', Passamonti SM, Consonni D, Pappalardo E, Menegatti M, Scherer SE, Lewis LL, Akbar H, Wu Y, Muzny DM, Mannucci PM, Gibbs RA and Peyvandi F. Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of hemostatic genes. '''''BMC Medical Genomics'''''  (2012) [http://www.biomedcentral.com/1755-8794/5/7/abstract PDF]<BR>
6. Campos M, Buchanan A, '''''Fuli Yu''''' (co-first author), Barbalic M, Xiao Y, Chambless LE, Wu KK, Folsom AR, Boerwinkle E, Dong J. Influence of single nucleotide polymorphisms in factor VIII and von Willebrand factor genes on factor VIII activity: the ARIC study. '''''Blood''''' 2012.[http://bloodjournal.hematologylibrary.org/content/early/2012/01/04/blood-2011-10-383661.short?rss=1 ABSTRACT]<BR>
7. Danny Challis, Jin Yu (co-first author), Uday Evani, Andrew R. Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A. Gibbs, '''''Fuli Yu'''''*,An integrative variant analysis suite for whole exome next-generation sequencing data. '''''BMC Bioinformatics''''' 2012  *''Corresponding Author'' [http://www.biomedcentral.com/1471-2105/13/8/abstract PDF] [http://genomemedicine.com/content/4/1/7/abstract GENOME MEDICINE REPORT] [http://sourceforge.net/projects/atlas2/ SOFTWARE]<BR>
1.Gabor T. Marth, '''''Fuli Yu'''''‡, Amit R. Indap‡, Kiran Garimella‡, Simon Gravel‡, Wen Fung Leong‡,
Chris Tyler-Smith‡, Matthew Bainbridge, Tom Blackwell, Xiangqun Zheng-Bradley, Yuan Chen,
Danny Challis, Laura Clarke, Edward V. Ball, Kristian Cibulskis, David N. Cooper, Bob Fulton,
Chris Hartl, Dan Koboldt, Donna Muzny, Richard Smith, Carrie Sougnez, Chip Stewart, Alistair
Ward, Jin Yu, Yali Xue, David Altshuler, Carlos D. Bustamante, Andrew G. Clark, Mark Daly,
Mark DePristo, Paul Flicek, Stacey Gabrie, Elaine Mardis, Aarno Palotie, Richard Gibbs, and
the 1000 Genomes Project. The functional spectrum of low-frequency coding variation. ‡ ''Equal Contribution'' '''''Genome Biology''''' 2011, 12:R84 [http://genomebiology.com/content/pdf/gb-2011-12-9-r84.pdf PDF] <BR>
2. Simon Gravel, Brenna M. Henn, Ryan N. Gutenkunst, Amit R. Indap, Gabor T. Marth, Andrew G. Clark, '''''Fuli Yu''''', Richard A. Gibbs, The 1000 Genomes Project, and Carlos D. Bustamante. Demographic history and rare allele sharing among human populations. '''''Proc Natl Acad Sci USA''''' 2011 Jul 19;108(29):11983-11988. Epub 2011 Jul 5  [http://www.pnas.org.ezproxyhost.library.tmc.edu/content/108/29/11983.full.pdf+html PDF]<BR>
3.Gloria L Fawcett, Muthuswamy Raveendran, David Rio Deiros, David Chen, '''''Fuli Yu''''', Ronald Alan Harris, Yanru Ren, Donna M Muzny, Jeffrey G Reid, David A Wheeler, Kimberly C Worley, Steven E Shelton, Ned H Kalin, Aleksandar Milosavljevic, Richard Gibbs and Jeffrey Rogers. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). '''''BMC Genomics'''''. 2011 [http://www.biomedcentral.com/content/pdf/1471-2164-12-311.pdf PDF]<BR>
4. Marco Campos, Wei Sun, '''''Fuli Yu''''' (co-first author), Maja Barbalic, Weihong Tang, Woody Chambless, Christie Ballantyne, Aaron Folsom, Eric Boerwinkle, Jing-fei Dong. Genetic Determinants of Plasma von Willebrand Factor Antigen Levels: A Target Gene SNP and Haplotype Analysis of ARIC Cohort. 2011 '''''Blood''''' May 12;117(19):5224-30. Epub 2011 Feb 22. <BR>
5. Momiao Xiong, Zhongming Zhao, Jonathan Arnold, and '''''Fuli Yu'''''. Next-Generation Sequencing,  Editorial. '''''Journal of Biomedicine and Biotechnology'''''. [http://www.hindawi.com/journals/jbb/2010/370710/ LINK] <BR>
1. '''''The International HapMap 3 Consortium'''''. Integrating common and rare genetic variation in diverse human populations. '''''Nature''''' 467, 52-58 (2 September 2010)<BR>
2. '''''The 1000 Genomes Consortium'''''. A map of human genome variation from population scale sequencing. '''''Nature'''''. 2010 Oct 28;467(7319):1061-73.<BR>
3. Jinchuan Xing, W. Scott Watkins, Ya Hu, Chad D. Huff, Aniko Sabo, Donna M. Muzny, Michael J. Bamshad, Richard A. Gibbs, Lynn B. Jorde, and '''''Fuli Yu'''''*. Inference of human expansion in Eurasia and genetic diversity in India. '''''Genome Biol.''''' 2010 Nov 24;11(11):R113. *''Corresponding Author'' [http://genomebiology.com/content/pdf/gb-2010-11-11-r113.pdf PDF].<BR>
4. Cristian Coarfa, '''''Fuli Yu''''', Zuozhou Chen, Christopher A. Miller, R. Alan Harris, Aleksandar Milosavljevic. Pash 3.0: A versatile software package for read mapping, sequence comparison and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. '''''BMC Bioinformatics''''' 2010 Nov 23;11:572.[http://www.biomedcentral.com/content/pdf/1471-2105-11-572.pdf PDF]<BR>
1. Yufeng Shen, Zhengzheng Wan, Cristian Coarfa, Rafal Drabek, Lei Chen, Elizabeth A. Ostrowski, Yue Liu, George M. Weinstock, David A. Wheeler, Richard A. Gibbs and '''''Fuli Yu'''''*. A SNP discovery method to assess variant allele probability in next generation resequencing data. '''''Genome Research''''' In press. 2009 *''Corresponding Author'' [http://genome.cshlp.org/content/early/2009/12/16/gr.096388.109.full.pdf+html PDF] [[Supplemental Materials]]<BR>
2. '''''Fuli Yu'''''*, Alon Keinan, Hua Chen, Russell J. Ferland, Robert S. Hill, Andre A. Mignault, Christopher A. Walsh and David Reich. Detecting natural selection by empirical comparison to random regions of the genome. '''''Human Molecular Genetics''''', 2009, Vol. 18, No. 24 4853–4867  *''Corresponding Author''  [http://hmg.oxfordjournals.org/cgi/reprint/18/24/4853 PDF]  [[http://hmg.oxfordjournals.org/cgi/data/ddp457/DC1/1 Supplemental Materials]]<BR>
3. Florez JC, Price AL, Campbell D, Riba L, Parra MV, '''''Fuli Yu''''', Duque C, Saxena R, Gallego N, Tello-Ruiz M, Franco L, Rodríguez-Torres M, Villegas A, Bedoya G, Aguilar-Salinas CA, Tusié-Luna MT, Ruiz-Linares A, Reich D. Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. '''''Diabetologia''''''52(8):1528-36, 2009 <BR>
'''Before 2009'''<BR>
1. '''''The International HapMap Consortium.''''' Genome-wide detection and characterization of positive selection in human populations. '''''Nature''''', 449(7164):913-8. 2007 <BR>
2. '''''The International HapMap Consortium.''''' A second generation human haplotype map of over 3.1 million SNPs. '''''Nature''''', 449(7164):851-61. 2007 <BR>
3. Alkes L. Price, Nick Patterson, '''''Fuli Yu''''', David R. Cox … and David Reich. A genomewide admixture map for Latino populations. '''''American Journal of Human Genetics''''', 80(6):1024-1036. 2007. <BR>
4. '''''Fuli Yu''''', R. Sean Hill, Eric T. Wang, Andre A. Mignault … and David Reich. Comment on “Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens”. '''''Science''''', 316(5823):370. 2007. <BR>
5. '''''The International HapMap Consortium.''''' A haplotype map of the human genome. '''''Nature''''' 437, 1299-1320. 2005. <BR>
6. '''''Fuli Yu''''', Pardis C. Sabeti, Paul Hardenbol, Qing Fu … and Richard A. Gibbs. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene. '''''PLoS Genetics''''' 1(3):e41. 2005. <BR>
7. Paul Hardenbol, '''''Fuli Yu''''', John Belmont, Jennifer Barrett … and Richard Gibbs. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. '''''Genome Research''''' 15:269-275. 2005. <BR>
[[http://openwetware.org/wiki/Fuli%27s_Lab home page]]
8. '''''The International HapMap Consortium.''''' Integrating ethics and science in the International HapMap Project. '''''Nature Reviews Genetics''''' 5:465-475. 2004. <BR>
9. '''''The International HapMap Consortium.''''' The International HapMap Project. '''''Nature''''' 426:789-796. 2003. <BR>
10. M. Maheshwari, J. Belmont, S. Fernbach, T. Ho, L. Molinari, I. Yakub, '''''Fuli Yu''''' … and Richard Gibbs. PTPN11 mutations in Noonan syndrome type I: detection of recurrent mutations in exon 3 and 13. '''''Human Mutation''''' 20:298-304. 2002. <BR>

Latest revision as of 09:10, 22 October 2015


See up-to-date Publications of Fuli's Group on Google Scholars Profile of Fuli Yu

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