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1. Wang Y, Lu J*, Yu J, Gibbs RA, Fuli Yu* An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. In submission.

2. 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 In press.*Corresponding Author

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) PAPER BioTechniques Press

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 PDF

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 ABSTRACT PDF

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 PDF

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) PDF

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.ABSTRACT

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 PDF GENOME MEDICINE REPORT


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 PDF

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 PDF

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 PDF

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.

5. Momiao Xiong, Zhongming Zhao, Jonathan Arnold, and Fuli Yu. Next-Generation Sequencing, Editorial. Journal of Biomedicine and Biotechnology. LINK


1. The International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58 (2 September 2010)

2. The 1000 Genomes Consortium. A map of human genome variation from population scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

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 PDF.

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.PDF

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 PDF Supplemental Materials

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 PDF [Supplemental Materials]

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

Before 2009
1. The International HapMap Consortium. Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164):913-8. 2007

2. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature, 449(7164):851-61. 2007

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.

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.

5. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005.

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.

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.

8. The International HapMap Consortium. Integrating ethics and science in the International HapMap Project. Nature Reviews Genetics 5:465-475. 2004.

9. The International HapMap Consortium. The International HapMap Project. Nature 426:789-796. 2003.

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.


  1. November, 2010—Fuli Yu. Detecting Rare Genetic Variants in the Large-Scale 1000 Genomes Exome Resequencing Project. INVITED TALK Cold Spring Harbor Laboratory 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Long Island, NY
  2. September, 2010—Fuli Yu. Detecting Rare Genetic Variants in the Large-Scale 1000 Genomes Exome Resequencing Project. INVITED TALK Cambridge Healthtech Institute's Fourth Annual NGx: Evolution of Next-Generation Sequencing meeting, Providence, RI
  3. April, 2009—Fuli Yu. A SNP discovery method to assess variant allele probability in 2nd generation resequencing data, and examples for follow-up studies. INVITED TALK Fudan University, Shanghai, China.
  4. November, 2008—Fuli Yu. Empirical detection of recent selection at two brain-related genes: FOXP2 and AHI1. INVITED TALK Health science center at Houston, School of public health, The University of Texas.
  5. October, 2006—Fuli Yu. Empirical detection of natural selection at two brain-related genes (FOXP2 and AHI1) but failure to confirm evidence at ASPM. The American Society of Human Genetics 56th Annual Meeting, New Orleans, Louisiana.
  6. April, 2005—Fuli Yu. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene. The Annual Symposium of Society of Chinese Bioscientists in America (SCBA), Texas Chapter, Houston, Texas.
  7. January, 2005—Fuli Yu. The status of the BCM-HGSC HapMap Project, and positive selection of a pre-expansion CAG repeat of human Spinocerebellar Ataxia Type 2 gene. INVITED TALK. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China.
  8. December, 2004—Fuli Yu. The status of the BCM-HGSC HapMap Project. The Sixth Strategy Meeting of the International HapMap Project. Tokyo, Japan.
  9. February, 2004—Fuli Yu. The haplotype structure and linkage disequilibrium of human Chromosome 12. The 5th Annual Advances in Genome Biology and Technology (AGBT) and Automation in Mapping and DNA Sequencing (AMS) Meeting. Marco Island, Florida.

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