徐书华——中科院上海生科院计算生物学研究所研究员

徐书华 ，男 ， 中国科学院上海生命科学研究院计算生物学研究所研究员，博导，PI 。

教育及工作经历：

2011.07—至今 中科院-马普计算生物学研究所马普青年科学家小组组长。

2010.12—至今 中科院-马普计算生物学研究所研究员、博士生导师。

2009.12—至今 中科院-马普计算生物学研究所研究组长(PI)。

2008.12—2009.11 中科院-马普计算生物学研究所副研究员。

2006.07—2008.11 中科院-马普计算生物学研究所助理研究员。

2003.9—2006.7 复旦大学生命科学学院博士。

1996.9—2003.7 湖北大学生命科学学院学士、硕士。

学术兼职：

资料更新中……

主讲课程：

计算生物学

培养研究生情况：

在读博士生5人，硕士生2人。已毕业博士生1人，硕士生6人。

    目前指导7名在读博士研究生。一名博士生靳文菲（与复旦大学金力教授共同指导）已于2011年底顺利答辩正式毕业。靳文菲在读期间发表多篇论文，其中第一作者论文分别发表在领域著名核心期刊Genome Research和Human Molecular Genetics. 另一名在读博士生楼海一已有1篇第一作者论文发表在PLoS One.此外，一名实习生阳雄在其实习期间在PLoS One发表1篇第一作者论文。

研究方向：

群体基因组学（Population Genomics）是连接人类进化历史和药物遗传学以及基因治疗的桥梁。我们通过在群体水平进行大规模基因组学研究，了解遗传变异在群体内以及群体间的分布模式，以及弄清影响其分布模式的各种因素，并试图阐明遗传变异在群体和基因组水平的动态演化机制。同时，通过对基因组范围大量遗传变异的研究，揭示其一般性质；寻找到那些偏离基因组一般性质的遗传变异，建立起遗传变异与环境及致病因素的关联；并最终阐明遗传变异与表型变异以及与内外环境相互作用的关系和机制。

群体基因组学课题组（Population Genomics Group, PGG）致力于以下两个方面的研究：

1、群体基因组结构研究

研究内容主要包括利用遗传多态性（如STR，SNP，CNV）数据研究群体在在基因组的分布模式以及基因组水平的连锁不平衡、重组以及基因转换模式；同时研究遗传多态性在群体中的保存机制。

2、现代人群的遗传结构研究

现代人“走出非洲”、向全球各地探险式地迁徙，其间经历了各种新的地理环境、气候变化、战争等多种因素导致的人口增减、遗传多样性剧烈波动的事件；到目前遍布地球的现代人群形成是一个群体分化、隔离、接触、交流和融合的复杂过程；最终不可避免地造成了我们现在看到的不同人群之间的遗传差异。全面解析现代人群的精细遗传结构、量化各人群的遗传差异，重新审视群体、个体以及染色体片段的遗传亲缘关系，一方面有助于深入了解人群的起源、迁徙和融合的历史；另一方面充分了解人群遗传结构及其对复杂疾病基因定位研究的影响程度，是合理实验设计的前提，也是保证基因定位研究结果可靠的必要条件，对寻找致病遗传因素的基因定位研究具有重要价值。

现代人群遗传结构研究是我们的一个长期研究方向，目前我们主要利用全基因组DNA芯片分型数据，应用和发展计算生物学方法进行相关研究，部分前期研究成果已经在Science（2009）、AJHG（2009）等杂志发表。

3、混合人群的历史和复杂性状基因定位研究

人类历史上的基因交流和民族融合是人类群体遗传学和现代人类学研究中的一个永久性命题。在生物学研究发展到现在的后基因组时代，人群融合又成为人类群体基因组学研究的重要内容。一方面，人们可以从基因组水平全面而细致地研究人群融合的历史；另一方面，人群融合的一个重要遗传学效应是染色体不同遗传座位上的等位基因之间的关联程度（连锁不平衡）得到增强，利用混合人群这一特殊遗传学特征进行基因定位的策略称为“混合作图”（Admixture mapping）。由人群融合产生的混合人群在寻找致病遗传因素的基因定位研究中具有特殊的价值。

我们将长期致力于混合人群的历史和基因定位策略研究，部分前期相关工作发表在AJHG（2008）、MBE（2007、2009）等专业期刊上。

4、利用混合人群的特征进行allele-allele以及gene-gene交互作用研究

由于人群历史、遗传漂变、功能限制以及自然选择的原因，人类基因组中相当部分的遗传多态性在不同的人群中丢失或固定下来，使得很多基因组区域的allele-allele以及gene-gene交互作用研究很难在一般人群中进行。而近期混合人群由于同时携带了固定在不同人群中的等位基因，而且能在个体水平观察到不同等位基因组合所对应的表型，因而成为研究这类allele-allele以及gene-gene交互作用的绝佳载体。我们正在致力于发展针对性的方法，以期在全基因组水平大规模、系统地研究混合人群中的allele-allele以及gene-gene交互作用。

5、现代人群对环境的适应及自然选择研究

适应与自然选择研究在进化遗传学和群体遗传学中有非常悠久的历史，目前我们主要针对两类人群、进行两个层面的研究。一类是适应特定环境，尤其是极端环境的人群（如适应高原缺氧环境的藏族人群）；一类是具有特殊遗传结构特征的混合人群（如新疆维吾尔族、美国黑人等）。在基因组水平和表达组水平两个层面利用组学数据、应用和发展基于群体基因组学的方法，检测和发现与环境适应相关的遗传因素。

1、2008 上海生科院优秀青年人才领域前沿项目　 构建混合人群的基因定位图谱　

资料更新中……

科研成果：

资料更新中……

发表论文：

2015

1.Xia Liu, Bo Zhao, Hua-Jun Zheng, Yan Hu, Gang Lu, Chang-Qing Yang, Jie-Dan Chen, Jun-Jian Chen, Dian-Yang Chen, Liang Zhang, Yan Zhou, Ling-Jian Wang, Wang-Zhen Guo, Yu-Lin Bai, Ju-Xin Ruan, Xiao-Xia Shangguan, Ying-Bo Mao, Chun-Min Shan, Jian-Ping Jiang, Yong-Qiang Zhu, Lei Jin, Hui Kang, Shu-Ting Chen, Xu-Lin He, Rui Wang, Yue-Zhu Wang, Jie Chen, Li-Jun Wang, Shu-Ting Yu, Bi-Yun Wang, Jia Wei, Si-Chao Song, Xin-Yan Lu, Zheng-Chao Gao, Wen-Yi Gu, Xiao Deng, Dan Ma, Sen Wang, Wen-Hua Liang, Lei Fang, Cai-Ping Cai, Xie-Fei Zhu, Bao-Liang Zhou, Z. Jeffrey Chen, Shu-Hua Xu, Yu-Gao Zhang*, Sheng-Yue Wang, Tian-Zhen Zhang*, Guo-Ping Zhao & Xiao-Ya Chen*. 2015. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Scientific Reports. 5:14139.

2.Xumin Ni, Wei Guo, Kai Yuan, Xiong Yang, Zhiming Ma, Shuhua Xu, Shihua Zhang*. 2015. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

3.Zhuoma Basang, Boyang Wang, Lei Li, La Yang, Lan Liu, Chaoying Cui, Gongga Lanzi, Nima Yuzhen, Ji Duo, Hongxiang Zheng, Yi Wang, Shuhua Xu, Li Jin*, Xiaofeng Wang*. 2015. HIF2A Variants Were Associated with Different Levels of High-Altitude Hypoxia among Native Tibetans. PLoS One. 10(9):e0137956.

4.Lian Deng, Boon-Peng Hoh, Dongsheng Lu, Woei-Yuh Saw, Rick Twee-Hee Ong, Anuradhani Kasturiratne, H. Janaka de Silva, Bin Alwi Zilfalil, Norihiro Kato, Ananda R. Wickremasinghe, Yik-Ying Teo & Shuhua Xu*. 2015. Dissecting the genetic structure and admixture of four geographical Malay populations. Scientific Reports. 5:14375.

5.Boon-Peng Hoh*, Lian Deng, Mat Jusoh Julia-Ashazila, Zakaria Zuraihan, Ma’amor Nur-Hasnah, Ab Rajab Nur-Shafawati, Wan Isa Hatin, Ismail Endom, Bin Alwi Zilfalil, Yusoff Khalid and Shuhua Xu*. 2015. Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies. Human Genomics. 9:16.

6.Haiyi Lou, Yan Lu, Dongsheng Lu, Ruiqing Fu, Xiaoji Wang, Qidi Feng, Sijie Wu, Yajun Yang, Shilin Li, Longli Kang, Yaqun Guan, Boon-Peng Hoh, Yeun-Jun Chung, Li Jin, Bing Su, Shuhua Xu*. 2015. A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence. Am.J.Hum.Genet. 97(1):54-66.

7.Pankaj Jha, Dongsheng Lu, Shuhua Xu*. 2015. Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data. PLoS One. 10(6):e0129023

8.Chao Zhang, Jing Li, Dongsheng Lu, Kai Yuan, Yuan Yuan, Shuhua Xu*. 2015. Differential Natural Selection of Human Zinc Transporter Genes between African and Non-African Populations. Scientific Reports. 5:9658.

9.Pankaj Jha, Dongsheng Lu, Yuan Yuan, Shuhua Xu*. 2015. Signature of positive selection of PTK6 gene in East Asian populations: a cross talk for Helicobacter pylori invasion and gastric cancer endemicity. Molecular Genetics and Genomics. 290(5):1741-1752.

10.Haiyi Lou, Shilin Li, Wenfei Jin, Ruiqing Fu, Dongsheng Lu, Xinwei Pan, Huaigu Zhou, Yuan Ping, Li Jin and Shuhua Xu*. 2015. Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups. European Journal of Human Genetics. 23:536-542.

11.Pengfei Qin, Ying Zhou, Haiyi Lou, Dongsheng Lu, Xiong Yang, Yuchen Wang, Li Jin, Yeun-Jun Chung, Shuhua Xu*. 2015. Quantitating and Dating Recent Gene Flow between European and East Asian Populations. Scientific Reports. 5:9500.

12.Xuanyao Liu, Yushimah Yunus, Dongsheng Lu, Farhang Aghakhanian, Woei-Yuh Saw, Lian Deng, Mohammad Ali, Xu Wang, Fadzilah Ghazali, Thuhairah Abdul Rahman, Shahrul Azlin Shaari, Mohd Zaki Salleh, Maude E. Phipps, Rick Twee-Hee Ong, Shuhua Xu, Yik-Ying Teo, Boon-Peng Hoh*. 2015. Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet. 134(4):375-392.

13.Yuan Yuan, Lei Tian, Dongsheng Lu, Shuhua Xu*. 2015. Analysis of Genome-Wide RNA-Sequencing Data Suggests Age of the CEPH/Utah (CEU) Lymphoblastoid Cell Lines Systematically Biases Gene Expression Profiles. Scientific Reports. 5:7960. 

 14. Yungang He, Minxian Wang, Xin Huang, Ran Li, Hongyang Xu, Shuhua Xu, Li Jin. A probabilistic method for testing and estimating selection differences between populations. Genome Res 2015,pii: gr.192336.115

2014

15.Qiliang Ding, Ya Hu, Shuhua Xu, Chuanchao Wang, Hui Li, Ruyue Zhang, Shi Yan, Jiucun Wang, Li Jin*. 2014. Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans. Molecular Biology and Evolution. 31(8):1994-2003.

16.Jing Guo, Jingze Tan, Yajun Yang, Hang Zhou, Sile Hu, Agu Hashan, Nurmamat Bahaxar, Shuhua Xu, Timothy D. Weaver, Li Jin, Mark Stoneking, Kun Tang*. 2014. Variation and signatures of selection on the human face. J.Hum.Evol. 75:143-152.
 

17.Liang Peng; Qiang Zhao, Qibin Li, Miaoxin Li, Caixia Li,Tingting Xu,Xiangyi Jing, Xiang Zhu, Ye Wang, Fucheng Li, Ruihong Liu, Cheng Zhong, Qihao Pan, Binghui Zeng, Qijun Liao, Bin Hu, Zhao-xia Hu, Yang-su Huang, Pak Sham, Jinsong Liu, Shuhua Xu, Jun Wang, Zhi-liang Gao, Yiming Wang. 2014. The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B. Hepatology. 61(4):1251-1260.

18.Wan Isa Hatin, Ab Rajab Nur-Shafawati, Ali Etemad, Wenfei Jin, Pengfei Qin,Shuhua Xu, Li Jin,Soon-Guan Tan, Pornprot Limprasert, Merican Amir Feisal, Mohammed Rizman-Idid, Bin Alwi Zilfalil* and The HUGO Pan-Asian SNP Consortium. 2014. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. The HUGO Journal. 8:5.

19.Xiong Yang, Suzanne Al-Bustan, Qidi Feng, Wei Guo, Zhiming Ma, Makia Marafie, Sindhu Jacob, Fahd Al-Mulla and Shuhua Xu*. 2014. The influence of admixture and consanguinity on population genetic diversity in Middle East. Journal of Human Genetics. 59:615-622.

20.Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhi-Ming Ma* andShuhua Xu*. 2014. A new method for modeling coalescent processes with recombination. BMC Bioinformatics. 15:273.

21.Jing Li, Haiyi Lou, Xiong Yang, Dongsheng Lu, Shilin Li, Li Jin, Xinwei Pan, Wenjun Yang, Manshu Song, Dolikun Mamatyusupu, Shuhua Xu*. 2014. Genetic architectures of ADME genes in five Eurasian admixed populations and implications for drug safety and efficacy. Journal of Medical Genetics. 51(9):614-22.

22.Lian Deng, Boon Peng Hoh, Dongsheng Lu, Ruiqing Fu, Maude E. Phipps, Shilin Li, Ab Rajab Nur‑Shafawati, Wan Isa Hatin, Endom Ismail, Siti Shuhada Mokhtar, Li Jin, Bin Alwi Zilfalil, Christian R. Marshall, Stephen W. Scherer, Fahd Al‑Mulla, Shuhua Xu*. 2014. The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. Hum Genet. 133(9):1169-1185 

23.Jing Li, Xingzhen Lao, Chao Zhang, Lei Tian, Dongsheng Lu and Shuhua Xu*. 2014. Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics. BMC Genetics. 15:52

24.Pengfei Qin, Zhiqiang Li, Wenfei Jin, Dongsheng Lu, Haiyi Lou, Jiawei Shen, Li Jin*, Yongyong Shi* and Shuhua Xu*. 2014. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. European Journal of Human Genetics. 22:248-253

25.Wenfei Jin, Ran Li, Ying Zhou and Shuhua Xu*. 2014. Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping. European Journal of Human Genetics. 22:930-937

2013

       26.Yang Liu, Liangliang Zhang, Shuhua Xu, Landian Hu, Laurence D. Hurst, Xiangyin Kong*. 2013. Identification of Two Maternal Transmission Ratio Distortion Loci in Pedigrees of the Framingham Heart Study. Scientific Reports. 3. Article No. 2147.

27.Erli Wang, Shuna Sun, Bin Qiao, Wenyuan Duan, Guoying Huang, Yu An, Shuhua Xu, Yufang Zheng, Zhixi Su, Xun Gu, Li Jin*, Hongyan Wang*. 2013. Identification of Functional Mutations in GATA4 in Patients with Congenital Heart Disease. PLoS One. 8(4): e62138

28.Qiliang Ding, Ya Hu, Shuhua Xu. Jiucun Wang, Li Jin*. 2013. Neanderthal Introgression at Chromosome 3p21.31 was Under Positive Natural Selection in East Asians. Molecular Biology and Evolution. 31(3):683-95.

29.Jun Rong*, Shuhua Xu, Patrick G. Meirmans and Klaas Vrieling. 2013. Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression. Annals of Botany. 112(7):1361-1370

30.Dongsheng Lu and Shuhua Xu*. 2013. Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia. Frontiers in Genetics. 4:1-9. Article No. 127.

31.Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Nur-Shafawati Rajab, Norhazrini Hasan, Syed Hassan Syed Abdul Aziz, Noorizan Abdul Majid, Bin Alwi Zilfalil. 2013. Gastric precancerous lesions are associated with gene variants in Helicobacter pylori -susceptible ethnic Malays. World Journal of Gastroenterology. 19(23):3615-3622

32.Yuan Yuan, Ling Yang, Meng Shi, Dongsheng Lu, Haiyi Lou, Yi-Ping Phoebe Chen, Li Jin, Shuhua Xu*. 2013. Identification of well-differentiated gene expressions between Han Chinese and Japanese using genome-wide microarray data analysis. Journal of Medical Genetics. 50:534-542

33.Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Mahendra Raj Sundramoorthy, Noorizan Abdul Majid, Keng Ee Choo, Zilfalil Alwi, David Y Graham. 2013. Toward understanding the low prevalence of Helicobacter pylori (H. pylori) in Malays: Genetic variants differ among H. pylori negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians. Journal of Digestive Diseases. 14:196-202

34.Wei Qian, Lian Deng, Dongsheng Lu, Shuhua Xu*. 2013. Genome-Wide Landscapes of Human Local Adaptation in Asia. PLoS One. 8(1):e54224.

35.Shuhua Xu*. 2013. Admixture population genomics of modern human. Science (KEXUE). 65(1):14-18

36. Jin W, Li R, Zhou Y, Xu S. Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping. Eur J Hum Genet 2013,doi: 10.1038/ejhg.2013.265 

37. Qin P, Li Z, Jin W, Lu D, Lou H, Shen J, Jin L, Shi Y, Xu S. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Eur J Hum Genet 2013,doi: 10.1038/ejhg.2013.111. 

38. 遗传混合、重组与人类迁移历史及环境适应研究 徐书华 中国遗传学会第九次全国会员代表大会暨学术研讨会论文摘要汇编（2009-2013） 2013-09-18 中国会议

39. 现代人类混血的群体基因组学研究 徐书华 科学 2013-01-25

2012

40.Wenfei Jin, Sijia Wang, Haifeng Wang, Li Jin, Shuhua Xu*. 2012. Exploring Population Admixture Dynamics Using Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments. Am.J.Hum.Genet. 91(5):849-862.

41.Shuhua Xu*. 2012. Human Population Admixture in Asia. Genomics & Informatics 10(2):133-144.

42.Shuhua Xu*, Wenfei Jin. 2012. Population Genetics in the Genomic Era (Book Chapter in Population Genetics, Book edited by Dr. Stuart Raleigh, University of Northampton, UK), InTech, Rijeka, Croatia (ISBN 979-953-307-446-6). Page: 137-168.

43.Shuhua Xu* and Mark Stoneking. 2012. Reply to Denham and Donohue: Asian-Papuan genetic admixture is in excellent agreement with Austronesian dispersal in eastern Indonesia. PNAS. 109:39.

44.Sathiya Maran, Yeong Yeh Lee*, Shuhua Xu, Nur-Shafawati Rajab, Norhazrini Hasan, Nazri Mustaffa, Noorizan Abdul Majid and Zilfalil Alwi. 2012. Deleted in Colorectal Cancer (DCC) Gene Polymorphism is Associated with H. pylori Infection among Susceptible Malays from the North-Eastern Region of Peninsular Malaysia. Hepato-Gastroenterology. 60(121):124-128.

45.Hui-Qi Qu*, Quan Li, Shuhua Xu, Joseph B. McCormick, Susan P. Fisher-Hoch, Momiao Xiong, Jin Qian, and Li Jin*. 2012. Ancestry Informative Marker Set for Han Chinese Population. G3: Genes, Genomes, Genetics. 2(3):339-41.

46.Yungang He*, Wei R. Wang, Shuhua Xu, Li Jin, and The HUGO Pan-Asian SNP Consortium. 2012. Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data. Scientific Reports. 2:355.

47.Shuhua Xu*, Irina Pugach, Mark Stoneking, Manfred Kayser, Li Jin, and The HUGO Pan-Asian SNP Consortium. 2012. Genetic Dating Indicates that the Asian-Papuan Admixture Through Eastern Indonesia Corresponds to the Austronesian Expansion. PNAS. 109(12):4574-4579.

48.Wenfei Jin, Pengfei Qin, Haiyi Lou, Li Jin*, Shuhua Xu*. 2012. A Systematic Characterization of Genes Underlying both Complex and Mendelian Diseases. Hum.Mol.Genet. 21(7):1611-1624. 

49.Wenfei Jin, Shuhua Xu*, Haifeng Wang, Yongguo Li, Yiping Shen, Bailin Wu, Li Jin*. 2012. Genome-Wide Detection of Natural Selection in African Americans Pre-and Post-Admixture. Genome Res. 22(3):519-527.

2011

 50.Xiong Yang, Shuhua Xu*, The HUGO Pan-Asian SNP Consortium. 2011. Identification of Close Relatives in the HUGO Pan-Asian SNP Database. PLoS One 6(12):e29502.

51.Haiyi Lou, Shilin Li, Yajun Yang, Longli Kang, Xin Zhang, Wenfei Jin, Bailin Wu , Li Jin*, Shuhua Xu*. 2011. A Map of Copy Number Variations in Chinese Populations. PLoS One 6(11):e27341.

52.Shuhua Xu*, Li Jin. 2011. Chromosome-Wide Haplotype Sharing: A Measure Integrating Recombination Information to Reconstruct the Phylogeny of Human Populations. Ann.Hum.Genet. 75(6):694-706.

53.Shuhua Xu*, Shilin Li, Yajun Yang, Jingze Tan, Haiyi Lou, Wenfei Jin, Ling Yang, Xuedong Pan, Jiucun Wang, Yiping Shen, Bailin Wu, Hongyan Wang, Li Jin*. 2011. A Genome-Wide Search for Signals of High Altitude Adaptation in Tibetans. Mol.Biol.Evol. 28(2):1003-1011.

54.Chumpol Ngamphiw, Anunchai Assawamakin, Shuhua Xu, Philip J. Shaw, Jin Ok Yang, Ho Ghang, Jong Bhak, Edison Liu, Sissades Tongsima*, The HUGO Pan-Asian SNP Consortium. 2011. PanSNPdb: The Pan-Asian SNP Genotyping Database. PLoS One 6(6):e21451.

55.Pankaj Jha, Swapnil Sinha, Kanika Kanchan, Tabish Qidwai, Ankita Narang, Prashant Kumar Singh, Sudhanshu S. Pati, Sanjib Mohanty, Saroj K. Mishra, Surya K. Sharma, Shally Awasthi, Vimala Venkatesh, Sanjeev Jain, Analabha Basu, Shuhua Xu, Indian Genome Variation ConsortiumMitali Mukerji, Saman Habib. 2011. Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria. Infection, Genetics and Evolution 12:142-148 (10.1016/j.meegid.2011.11.001).

56.Xiaoyun Cai, Zhendong Qin, Bo Wen, Shuhua Xu, Yi Wang, Yan Lu, Lanhai Wei, Chuanchao Wang, Shilin Li, Xingqiu Huang, Li Jin, Hui Li*, the Genographic Consortium. 2011. Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes. PLoS One 6(8):e24282.

57.Wan Isa Hatin, Ab Rajab Nur-Shafawati, Mohd-Khairi Zahri, Shuhua Xu, Li Jin, Soon-Guan Tan, Mohammed Rizman-Idid, Bin Alwi Zilfalil, The HUGO Pan-Asian SNP Consortium. 2011. Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups. PLoS One 6(4):e18312.

58.Frederick Delfin, Jazelyn M Salvador, Gayvelline C Calacal, Henry B Perdigon, Kristina A Tabbada, Lilian P Villamor, Saturnina C Halos, Ellen Gunnarsdo´ ttir, Sean Myles, David A Hughes, Shuhua Xu, Li Jin, Oscar Lao, Manfred Kayser, Matthew E Hurles, Mark Stoneking and Maria Corazon A De Ungria*. 2011. The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. Eur.J.Hum.Genet. 19:224-230.

59.Wenfei Jin, Shuhua Xu*, Haifeng Wang, Yongguo Li, Yiping Shen, Bailin Wu, Li Jin*. 2011. Genome-Wide Detection of Natural Selection in African Americans Pre-and Post-Admixture. Genome Research (doi:10.1101/gr.124784.111).

60.Wenfei Jin, Pengfei Qin, Haiyi Lou, Li Jin*, Shuhua Xu*. 2011. A Systematic Characterization of Genes Underlying both Complex and Mendelian Diseases. Hum.Mol.Genet. (doi:10.1093/hmg/DDR599). 

       61. 亚洲人群的基因组多样性、迁移历史与环境适应研究 徐书华; 金力 中国的遗传学研究——遗传学进步推动中国西部经济与社会发展——2011年中国遗传学会大会论文摘要汇编 2011-08-09 中国会议

        2010

62.Shuhua Xu*, Sanchit Guputa and Li Jin*. 2010. PEAS V1.0: A Package for Elementary Analysis of SNP Data. Mol.Ecol.Res. 10:1085-1088.

63.Shuhua Xu, Daoroong Kangwanpong, Mark Seielstad, Metawee Srikummool, Jatupol Kampuansai, Li Jin*. The HUGO Pan-Asian SNP Consortium. 2010. Genetic Evidence Supports Linguistic Affinity of Mlabri — a Hunter-Gatherer Group in Thailand. BMC Genet. 11:18.

       2009

64.The HUGO Pan-Asian SNP Consortium (Co-corresponding author). 2009. Mapping Genetic Diversity in Asia. Science 326: 1541-1545.

65.Shuhua Xu, Xianyong Yin, Shilin Li, Wenfei Jin, Haiyi Lou, Ling Yang, Xiaohong Gong, Hongyan Wang, Yiping shen, Xuedong Pan, Yungang He, Yajun Yang, Yi Wang, Wenqing Fu, Yu An, Jiucun Wang, Jingze Tan, Ji Qian, Xiaoli Chen, Xin Zhang, Yangfei Sun, Xuejun Zhang, Bailin Wu, Li Jin. 2009. Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies. Am.J.Hum.Genet. 85:762-774.

66.Shuhua Xu and Li Jin, 2009. Response to Li et al., Am.J.Hum.Genet. 85:937-939.

67.Shuhua Xu, Wenfei Jin, Li Jin. 2009. Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Mol.Biol.Evol. 26:2197-2206.

68.Shuhua Xu, Li Jin. 2009. Computational Biology—Review and Prospects. Science (KEXUE). 61(4):34-37.

69.Yungang He, Shuhua Xu, Chuan Jia, Li Jin. 2009. A design of multi-source samples as a shared control for association studies in genetically stratified populations. Cell Research 19:913-915.

      2008

70.Shuhua Xu, Li Jin. 2008. A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery. Am.J.Hum.Genet. 83:322-336.

71.Shuhua Xu, Wei Huang, Ji Qian, Li Jin. 2008. Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy. Am.J.Hum.Genet. 82:883-894.

72.Fuzhong Xue, Yi Wang, Shuhua Xu, Feng Zhang, Bo Wen, Xuesen Wu, Ming Lu, Ranjan Deka, Ji Qian, and Li Jin. 2008. A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages. Eur.J.Hum.Genet. 16:705-717

      2007

73.Shuhua Xu, Wei Huang, Haifeng Wang, Yungang He, Ying Wang, Yi Wang, Ji Qian, Momiao Xiong, Li Jin. 2007. Dissecting Linkage Disequilibrium in African American Genomes: Roles of Markers and Individuals. Mol.Biol.Evol. 24:2049-2058.  

荣誉奖励：

1. 上海市科技启明星（2011.11）。

2. 教育部自然科学奖（一等）（第二完成人）（2011.11）。

3. 全国优秀博士论文（2011.8）。

4. 入选中国科学院青年创新促进会（2011）。

5. 复旦大学优秀博士论文（2010.1）。

6. 上海市优秀博士论文（2009.12）。

7. 中国科学院卢嘉锡青年人才奖（2009-2014）。

8. 赛诺菲-安万特（法国）－上海生科院优秀青年人才奖（2009）。

9. 明治乳业（日本）生命科学奖（2009）。

本报讯（记者黄辛）中科院上海生科院计算生物学研究所徐书华研究组在最新研究中，首次揭示了汉族人与日本人之间在转录水平方面的差异，并估计了遗传变异对人群基因表达谱差异的贡献率。有关专家认为，该研究有助于理解基因表达与遗传变异之间的联系，并为阐明近缘人群之间表型差异的分子机制提供线索。相关研究成果近日在线发表于《医学遗传学杂志》。

中国汉族人和日本人有共同的遗传起源，在外表形态上也存在很高的相似度。但是人们普遍的印象是，汉族人和日本人在外表上的差异似乎能被人眼识别出来。那么，从生物学的角度，汉族人与日本人之间究竟存在怎样的性状差异？有多少差异是由于环境差异导致的？有多少差异是由于遗传因素影响而产生的？

徐书华表示，要回答这些问题并不容易。一个主要的困难在于对视觉可见的最终表型如何度量和量化，而这一点在近缘人群中尤其具有挑战性。因此，研究组决定从可以大规模量化的一种中间表型——基因表达谱入手，对汉族人和日本人的全基因组表达谱芯片数据进行系统、细致的分析。

通过比较分析，研究人员鉴定出在两个人群之间存在高度表达差异的基因，发现其中某些差异表达基因与人体血液和生化特性有关，还有一些基因与人体身高以及某些疾病相关。

此外，研究人员还进一步估计了遗传变异对基因表达差异的贡献率，结果显示，对于在汉族人和日本人之间存在显著差异的基因表达，单个遗传变异的贡献在7%到43%之间。这些研究结果表明，汉族人和日本人的差异，不仅仅是地理、语言和文化等方面的区别，更是在生物学上存在的系统性差异，这些差异有可能通过自然科学研究手段精确量化并客观描述。

据悉，该研究工作得到了国家自然科学基金委员会、中国科学院、上海市科委、德国马普学会、香港王宽诚教育基金会等机构的资助。

《中国科学报》 (2013-06-20 第1版 要闻)