徐書華 ，男 ， 中國科學(xué)院上海生命科學(xué)研究院計算生物學(xué)研究所研究員，博導(dǎo)，PI 。

教育及工作經(jīng)歷：

2011.07—至今 中科院-馬普計算生物學(xué)研究所馬普青年科學(xué)家小組組長。

2010.12—至今 中科院-馬普計算生物學(xué)研究所研究員、博士生導(dǎo)師。

2009.12—至今 中科院-馬普計算生物學(xué)研究所研究組長(PI)。

2008.12—2009.11 中科院-馬普計算生物學(xué)研究所副研究員。

2006.07—2008.11 中科院-馬普計算生物學(xué)研究所助理研究員。

2003.9—2006.7 復(fù)旦大學(xué)生命科學(xué)學(xué)院博士。

1996.9—2003.7 湖北大學(xué)生命科學(xué)學(xué)院學(xué)士、碩士。

學(xué)術(shù)兼職：

資料更新中……

主講課程：

計算生物學(xué)

培養(yǎng)研究生情況：

在讀博士生5人，碩士生2人。已畢業(yè)博士生1人，碩士生6人。

    目前指導(dǎo)7名在讀博士研究生。一名博士生靳文菲（與復(fù)旦大學(xué)金力教授共同指導(dǎo)）已于2011年底順利答辯正式畢業(yè)。靳文菲在讀期間發(fā)表多篇論文，其中第一作者論文分別發(fā)表在領(lǐng)域著名核心期刊Genome Research和Human Molecular Genetics. 另一名在讀博士生樓海一已有1篇第一作者論文發(fā)表在PLoS One.此外，一名實(shí)習(xí)生陽雄在其實(shí)習(xí)期間在PLoS One發(fā)表1篇第一作者論文。

研究方向：

群體基因組學(xué)（Population Genomics）是連接人類進(jìn)化歷史和藥物遺傳學(xué)以及基因治療的橋梁。我們通過在群體水平進(jìn)行大規(guī)模基因組學(xué)研究，了解遺傳變異在群體內(nèi)以及群體間的分布模式，以及弄清影響其分布模式的各種因素，并試圖闡明遺傳變異在群體和基因組水平的動態(tài)演化機(jī)制。同時，通過對基因組范圍大量遺傳變異的研究，揭示其一般性質(zhì)；尋找到那些偏離基因組一般性質(zhì)的遺傳變異，建立起遺傳變異與環(huán)境及致病因素的關(guān)聯(lián)；并最終闡明遺傳變異與表型變異以及與內(nèi)外環(huán)境相互作用的關(guān)系和機(jī)制。

群體基因組學(xué)課題組（Population Genomics Group, PGG）致力于以下兩個方面的研究：

1、群體基因組結(jié)構(gòu)研究

研究內(nèi)容主要包括利用遺傳多態(tài)性（如STR，SNP，CNV）數(shù)據(jù)研究群體在在基因組的分布模式以及基因組水平的連鎖不平衡、重組以及基因轉(zhuǎn)換模式；同時研究遺傳多態(tài)性在群體中的保存機(jī)制。

2、現(xiàn)代人群的遺傳結(jié)構(gòu)研究

現(xiàn)代人“走出非洲”、向全球各地探險式地遷徙，其間經(jīng)歷了各種新的地理環(huán)境、氣候變化、戰(zhàn)爭等多種因素導(dǎo)致的人口增減、遺傳多樣性劇烈波動的事件；到目前遍布地球的現(xiàn)代人群形成是一個群體分化、隔離、接觸、交流和融合的復(fù)雜過程；最終不可避免地造成了我們現(xiàn)在看到的不同人群之間的遺傳差異。全面解析現(xiàn)代人群的精細(xì)遺傳結(jié)構(gòu)、量化各人群的遺傳差異，重新審視群體、個體以及染色體片段的遺傳親緣關(guān)系，一方面有助于深入了解人群的起源、遷徙和融合的歷史；另一方面充分了解人群遺傳結(jié)構(gòu)及其對復(fù)雜疾病基因定位研究的影響程度，是合理實(shí)驗(yàn)設(shè)計的前提，也是保證基因定位研究結(jié)果可靠的必要條件，對尋找致病遺傳因素的基因定位研究具有重要價值。

現(xiàn)代人群遺傳結(jié)構(gòu)研究是我們的一個長期研究方向，目前我們主要利用全基因組DNA芯片分型數(shù)據(jù)，應(yīng)用和發(fā)展計算生物學(xué)方法進(jìn)行相關(guān)研究，部分前期研究成果已經(jīng)在Science（2009）、AJHG（2009）等雜志發(fā)表。

3、混合人群的歷史和復(fù)雜性狀基因定位研究

人類歷史上的基因交流和民族融合是人類群體遺傳學(xué)和現(xiàn)代人類學(xué)研究中的一個永久性命題。在生物學(xué)研究發(fā)展到現(xiàn)在的后基因組時代，人群融合又成為人類群體基因組學(xué)研究的重要內(nèi)容。一方面，人們可以從基因組水平全面而細(xì)致地研究人群融合的歷史；另一方面，人群融合的一個重要遺傳學(xué)效應(yīng)是染色體不同遺傳座位上的等位基因之間的關(guān)聯(lián)程度（連鎖不平衡）得到增強(qiáng)，利用混合人群這一特殊遺傳學(xué)特征進(jìn)行基因定位的策略稱為“混合作圖”（Admixture mapping）。由人群融合產(chǎn)生的混合人群在尋找致病遺傳因素的基因定位研究中具有特殊的價值。

我們將長期致力于混合人群的歷史和基因定位策略研究，部分前期相關(guān)工作發(fā)表在AJHG（2008）、MBE（2007、2009）等專業(yè)期刊上。

4、利用混合人群的特征進(jìn)行allele-allele以及gene-gene交互作用研究

由于人群歷史、遺傳漂變、功能限制以及自然選擇的原因，人類基因組中相當(dāng)部分的遺傳多態(tài)性在不同的人群中丟失或固定下來，使得很多基因組區(qū)域的allele-allele以及gene-gene交互作用研究很難在一般人群中進(jìn)行。而近期混合人群由于同時攜帶了固定在不同人群中的等位基因，而且能在個體水平觀察到不同等位基因組合所對應(yīng)的表型，因而成為研究這類allele-allele以及gene-gene交互作用的絕佳載體。我們正在致力于發(fā)展針對性的方法，以期在全基因組水平大規(guī)模、系統(tǒng)地研究混合人群中的allele-allele以及gene-gene交互作用。

5、現(xiàn)代人群對環(huán)境的適應(yīng)及自然選擇研究

適應(yīng)與自然選擇研究在進(jìn)化遺傳學(xué)和群體遺傳學(xué)中有非常悠久的歷史，目前我們主要針對兩類人群、進(jìn)行兩個層面的研究。一類是適應(yīng)特定環(huán)境，尤其是極端環(huán)境的人群（如適應(yīng)高原缺氧環(huán)境的藏族人群）；一類是具有特殊遺傳結(jié)構(gòu)特征的混合人群（如新疆維吾爾族、美國黑人等）。在基因組水平和表達(dá)組水平兩個層面利用組學(xué)數(shù)據(jù)、應(yīng)用和發(fā)展基于群體基因組學(xué)的方法，檢測和發(fā)現(xiàn)與環(huán)境適應(yīng)相關(guān)的遺傳因素。

1、2008 上海生科院優(yōu)秀青年人才領(lǐng)域前沿項(xiàng)目　 構(gòu)建混合人群的基因定位圖譜　

資料更新中……

科研成果：

資料更新中……

發(fā)表論文：

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. 遺傳混合、重組與人類遷移歷史及環(huán)境適應(yīng)研究 徐書華 中國遺傳學(xué)會第九次全國會員代表大會暨學(xué)術(shù)研討會論文摘要匯編（2009-2013） 2013-09-18 中國會議

39. 現(xiàn)代人類混血的群體基因組學(xué)研究 徐書華 科學(xué) 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. 亞洲人群的基因組多樣性、遷移歷史與環(huán)境適應(yīng)研究 徐書華; 金力 中國的遺傳學(xué)研究——遺傳學(xué)進(jìn)步推動中國西部經(jīng)濟(jì)與社會發(fā)展——2011年中國遺傳學(xué)會大會論文摘要匯編 2011-08-09 中國會議

        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.  

榮譽(yù)獎勵：

1. 上海市科技啟明星（2011.11）。

2. 教育部自然科學(xué)獎（一等）（第二完成人）（2011.11）。

3. 全國優(yōu)秀博士論文（2011.8）。

4. 入選中國科學(xué)院青年創(chuàng)新促進(jìn)會（2011）。

5. 復(fù)旦大學(xué)優(yōu)秀博士論文（2010.1）。

6. 上海市優(yōu)秀博士論文（2009.12）。

7. 中國科學(xué)院盧嘉錫青年人才獎（2009-2014）。

8. 賽諾菲-安萬特（法國）－上海生科院優(yōu)秀青年人才獎（2009）。

9. 明治乳業(yè)（日本）生命科學(xué)獎（2009）。

本報訊（記者黃辛）中科院上海生科院計算生物學(xué)研究所徐書華研究組在最新研究中，首次揭示了漢族人與日本人之間在轉(zhuǎn)錄水平方面的差異，并估計了遺傳變異對人群基因表達(dá)譜差異的貢獻(xiàn)率。有關(guān)專家認(rèn)為，該研究有助于理解基因表達(dá)與遺傳變異之間的聯(lián)系，并為闡明近緣人群之間表型差異的分子機(jī)制提供線索。相關(guān)研究成果近日在線發(fā)表于《醫(yī)學(xué)遺傳學(xué)雜志》。

中國漢族人和日本人有共同的遺傳起源，在外表形態(tài)上也存在很高的相似度。但是人們普遍的印象是，漢族人和日本人在外表上的差異似乎能被人眼識別出來。那么，從生物學(xué)的角度，漢族人與日本人之間究竟存在怎樣的性狀差異？有多少差異是由于環(huán)境差異導(dǎo)致的？有多少差異是由于遺傳因素影響而產(chǎn)生的？

徐書華表示，要回答這些問題并不容易。一個主要的困難在于對視覺可見的最終表型如何度量和量化，而這一點(diǎn)在近緣人群中尤其具有挑戰(zhàn)性。因此，研究組決定從可以大規(guī)模量化的一種中間表型——基因表達(dá)譜入手，對漢族人和日本人的全基因組表達(dá)譜芯片數(shù)據(jù)進(jìn)行系統(tǒng)、細(xì)致的分析。

通過比較分析，研究人員鑒定出在兩個人群之間存在高度表達(dá)差異的基因，發(fā)現(xiàn)其中某些差異表達(dá)基因與人體血液和生化特性有關(guān)，還有一些基因與人體身高以及某些疾病相關(guān)。

此外，研究人員還進(jìn)一步估計了遺傳變異對基因表達(dá)差異的貢獻(xiàn)率，結(jié)果顯示，對于在漢族人和日本人之間存在顯著差異的基因表達(dá)，單個遺傳變異的貢獻(xiàn)在7%到43%之間。這些研究結(jié)果表明，漢族人和日本人的差異，不僅僅是地理、語言和文化等方面的區(qū)別，更是在生物學(xué)上存在的系統(tǒng)性差異，這些差異有可能通過自然科學(xué)研究手段精確量化并客觀描述。

據(jù)悉，該研究工作得到了國家自然科學(xué)基金委員會、中國科學(xué)院、上海市科委、德國馬普學(xué)會、香港王寬誠教育基金會等機(jī)構(gòu)的資助。

《中國科學(xué)報》 (2013-06-20 第1版 要聞)