Harvard Catalyst Profiles

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Heng Li, Ph.D.

Title
Institution
Department
Address
Profile Picture

Biography
education and training
Wellcome Trust Sanger Institute, Cambridge, UK09/2009Bioinformatics
Institute of Theoretical Physics, Beijing, ChinaPhD08/2006Theoretical Biophysics
Nanjing University, Nanjing, ChinaBSc08/2001Physics
awards and honors
2014 - 2018
Highly Cited Researcher (top 1%)
2012
Benjamin Franklin Award for contributions in Open Source Bioinformatics
2009 - 2010
Newcomb Cleveland Prize for the Most Outstanding Paper published in Science

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
Most Recent  |  List All
  1. U01HG010961 (LI, HENG) Mar 1, 2020 - Feb 28, 2023
    NIH
    The construction and utility of reference pan-genome graphs
    Role: Principal Investigator
  2. R01HG010040 (LI, HENG) May 1, 2018 - Feb 28, 2022
    NIH
    Advanced computational methods in analyzing high-throughput sequencing data
    Role: Principal Investigator
  3. U01CA226196 (LI, HENG) Apr 6, 2018 - Mar 31, 2021
    NIH
    Bioinformatics Technology to Characterize Tumor Infiltrating Immune Repertoires
    Role: Principal Investigator

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Li H. Identifying centromeric satellites with dna-brnn. Bioinformatics. 2019 11 01; 35(21):4408-4410. PMID: 30989183.
    Citations: 4     Fields:    Translation:HumansCells
  2. Regier AA, Farjoun Y, Larson DE, Krasheninina O, Kang HM, Howrigan DP, Chen BJ, Kher M, Banks E, Ames DC, English AC, Li H, Xing J, Zhang Y, Matise T, Abecasis GR, Salerno W, Zody MC, Neale BM, Hall IM. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun. 2018 10 02; 9(1):4038. PMID: 30279509.
    Citations: 64     Fields:    Translation:Humans
  3. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 09 15; 34(18):3094-3100. PMID: 29750242.
    Citations: 1978     Fields:    Translation:Cells
  4. Tan L, Xing D, Chang CH, Li H, Xie XS. Three-dimensional genome structures of single diploid human cells. Science. 2018 08 31; 361(6405):924-928. PMID: 30166492; PMCID: PMC6360088.
    Citations: 129     Fields:    Translation:HumansCells
  5. Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D. A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods. 2018 08; 15(8):595-597. PMID: 30013044; PMCID: PMC6341484.
    Citations: 48     Fields:    Translation:HumansCells
  6. Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science. 2017 04 14; 356(6334):189-194. PMID: 28408603.
    Citations: 123     Fields:    Translation:HumansCells
  7. Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017 05; 27(5):849-864. PMID: 28396521; PMCID: PMC5411779.
    Citations: 255     Fields:    Translation:Humans
  8. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13; 538(7624):201-206. PMID: 27654912; PMCID: PMC5161557.
    Citations: 428     Fields:    Translation:HumansAnimals
  9. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016 07 15; 32(14):2103-10. PMID: 27153593.
    Citations: 393     Fields:    Translation:HumansAnimalsCells
  10. Mancuso N, Rohland N, Rand KA, Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman CA, Pasaniuc B, Reich D. The contribution of rare variation to prostate cancer heritability. Nat Genet. 2016 Jan; 48(1):30-5. PMID: 26569126; PMCID: PMC7534691.
    Citations: 68     Fields:    Translation:Humans
  11. Li H. BGT: efficient and flexible genotype query across many samples. Bioinformatics. 2016 Feb 15; 32(4):590-2. PMID: 26500154.
    Citations: 14     Fields:    Translation:Humans
  12. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 01; 526(7571):68-74. PMID: 26432245; PMCID: PMC4750478.
    Citations: 5257     Fields:    Translation:Humans
  13. Li H. FermiKit: assembly-based variant calling for Illumina resequencing data. Bioinformatics. 2015 Nov 15; 31(22):3694-6. PMID: 26220959.
    Citations: 40     Fields:    Translation:HumansCells
  14. Li H. BFC: correcting Illumina sequencing errors. Bioinformatics. 2015 Sep 01; 31(17):2885-7. PMID: 25953801.
    Citations: 76     Fields:    Translation:Humans
  15. Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D, Dalén L. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol. 2015 May 18; 25(10):1395-400. PMID: 25913407; PMCID: PMC4439331.
    Citations: 80     Fields:    Translation:Animals
  16. Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nat Genet. 2015 Feb; 47(2):126-31. PMID: 25581429; PMCID: PMC4310772.
    Citations: 81     Fields:    Translation:HumansAnimals
  17. Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PL, Aximu-Petri A, Prüfer K, de Filippo C, Meyer M, Zwyns N, Salazar-García DC, Kuzmin YV, Keates SG, Kosintsev PA, Razhev DI, Richards MP, Peristov NV, Lachmann M, Douka K, Higham TF, Slatkin M, Hublin JJ, Reich D, Kelso J, Viola TB, Pääbo S. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature. 2014 Oct 23; 514(7523):445-9. PMID: 25341783.
    Citations: 293     Fields:    Translation:HumansAnimalsCells
  18. Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kucinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014 Sep 18; 513(7518):409-13. PMID: 25230663; PMCID: PMC4170574.
    Citations: 440     Fields:    Translation:Humans
  19. Li H. Fast construction of FM-index for long sequence reads. Bioinformatics. 2014 Nov 15; 30(22):3274-5. PMID: 25107872.
    Citations: 15     Fields:    
  20. Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014 Oct 15; 30(20):2843-51. PMID: 24974202.
    Citations: 358     Fields:    Translation:HumansCells
  21. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014 Jan 02; 505(7481):43-9. PMID: 24352235; PMCID: PMC4031459.
    Citations: 618     Fields:    Translation:HumansAnimals
  22. Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI. Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology. BMC Genomics. 2013 Oct 17; 14:711. PMID: 24134808.
    Citations: 9     Fields:    Translation:Animals
  23. Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The anatomy of successful computational biology software. Nat Biotechnol. 2013 Oct; 31(10):894-7. PMID: 24104757.
    Citations: 10     Fields:    
  24. Genovese G, Handsaker RE, Li H, Kenny EE, McCarroll SA. Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes. Am J Hum Genet. 2013 Sep 05; 93(3):411-21. PMID: 23932108; PMCID: PMC3971454.
    Citations: 21     Fields:    Translation:HumansCells
  25. Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA. Using population admixture to help complete maps of the human genome. Nat Genet. 2013 Apr; 45(4):406-14, 414e1-2. PMID: 23435088.
    Citations: 41     Fields:    Translation:HumansCells
  26. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 01; 491(7422):56-65. PMID: 23128226; PMCID: PMC3498066.
    Citations: 4052     Fields:    Translation:HumansCells
  27. Sankararaman S, Patterson N, Li H, Pääbo S, Reich D. The date of interbreeding between Neandertals and modern humans. PLoS Genet. 2012; 8(10):e1002947. PMID: 23055938; PMCID: PMC3464203.
    Citations: 117     Fields:    Translation:HumansAnimals
  28. Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J. SOAPindel: efficient identification of indels from short paired reads. Genome Res. 2013 Jan; 23(1):195-200. PMID: 22972939.
    Citations: 61     Fields:    Translation:Humans
  29. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12; 338(6104):222-6. PMID: 22936568.
    Citations: 622     Fields:    Translation:HumansAnimalsCells
  30. Sun JX, Helgason A, Masson G, Ebenesersdóttir SS, Li H, Mallick S, Gnerre S, Patterson N, Kong A, Reich D, Stefansson K. A direct characterization of human mutation based on microsatellites. Nat Genet. 2012 Oct; 44(10):1161-5. PMID: 22922873.
    Citations: 128     Fields:    Translation:HumansCells
  31. Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PI, Reich D, Price AL. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet. 2012 May 20; 44(6):631-5. PMID: 22610117.
    Citations: 125     Fields:    Translation:Humans
  32. Li H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics. 2012 Jul 15; 28(14):1838-44. PMID: 22569178.
    Citations: 152     Fields:    Translation:Humans
  33. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W. pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics. 2012 Jun 01; 28(11):1533-5. PMID: 22508794.
    Citations: 83     Fields:    Translation:Humans
  34. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 01; 27(21):2987-93. PMID: 21903627.
    Citations: 2082     Fields:    Translation:Humans
  35. Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011 Jul 13; 475(7357):493-6. PMID: 21753753.
    Citations: 770     Fields:    Translation:Humans
  36. Li H. Improving SNP discovery by base alignment quality. Bioinformatics. 2011 Apr 15; 27(8):1157-8. PMID: 21320865.
    Citations: 135     Fields:    Translation:Cells
  37. Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011 Mar 01; 27(5):718-9. PMID: 21208982.
    Citations: 221     Fields:    
  38. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23; 468(7327):1053-60. PMID: 21179161.
    Citations: 444     Fields:    Translation:HumansAnimals
  39. Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott J, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK. Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics. 2010 Dec; 8(4):211-28. PMID: 21382590.
    Citations: 7     Fields:    Translation:Animals
  40. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28; 467(7319):1061-73. PMID: 20981092; PMCID: PMC3042601.
    Citations: 4080     Fields:    Translation:HumansCells
  41. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010 Sep; 11(5):473-83. PMID: 20460430.
    Citations: 252     Fields:    Translation:HumansCells
  42. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010 May 07; 328(5979):710-722. PMID: 20448178; PMCID: PMC5100745.
    Citations: 1110     Fields:    Translation:HumansAnimalsCells
  43. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010 Mar 01; 26(5):589-95. PMID: 20080505.
    Citations: 4665     Fields:    Translation:HumansCells
  44. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J. The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21; 463(7279):311-7. PMID: 20010809.
    Citations: 520     Fields:    Translation:HumansAnimalsCells
  45. Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD, Li H, Ning Z, Nadeau JH, Croniger CM, Durbin R, Adams DJ. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol. 2009; 10(10):R112. PMID: 19825173.
    Citations: 23     Fields:    Translation:AnimalsCells
  46. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15; 25(16):2078-9. PMID: 19505943; PMCID: PMC2723002.
    Citations: 21517     Fields:    Translation:Cells
  47. Holt KE, Teo YY, Li H, Nair S, Dougan G, Wain J, Parkhill J. Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics. 2009 Aug 15; 25(16):2074-5. PMID: 19497932.
    Citations: 23     Fields:    Translation:Cells
  48. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15; 25(14):1754-60. PMID: 19451168.
    Citations: 17713     Fields:    
  49. Schierup MH, Mailund T, Li H, Wang J, Tjønneland A, Vogel U, Bolund L, Nexø BA. Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. BMC Med Genet. 2009 Mar 03; 10:20. PMID: 19257887; PMCID: PMC2654437.
    Citations: 7     Fields:    Translation:HumansCells
  50. Li J, Gromov P, Gromova I, Moreira JM, Timmermans-Wielenga V, Rank F, Wang K, Li S, Li H, Wiuf C, Yang H, Zhang X, Bolund L, Celis JE. Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics. 2008 Dec; 8(23-24):5038-52. PMID: 19003862.
    Citations: 12     Fields:    Translation:Humans
  51. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 2009 Feb; 19(2):327-35. PMID: 19029536.
    Citations: 615     Fields:    Translation:HumansAnimals
  52. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J. The diploid genome sequence of an Asian individual. Nature. 2008 Nov 06; 456(7218):60-5. PMID: 18987735; PMCID: PMC2716080.
    Citations: 485     Fields:    Translation:HumansAnimalsCells
  53. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 06; 456(7218):53-9. PMID: 18987734; PMCID: PMC2581791.
    Citations: 1554     Fields:    Translation:HumansCells
  54. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov; 18(11):1851-8. PMID: 18714091.
    Citations: 1329     Fields:    Translation:HumansCells
  55. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008 Jul; 26(7):779-85. PMID: 18612301.
    Citations: 287     Fields:    Translation:Cells
  56. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008 Jun; 40(6):722-9. PMID: 18438408.
    Citations: 396     Fields:    Translation:HumansCells
  57. Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R. TreeFam: 2008 Update. Nucleic Acids Res. 2008 Jan; 36(Database issue):D735-40. PMID: 18056084.
    Citations: 184     Fields:    Translation:Animals
  58. Li H, Guan L, Liu T, Guo Y, Zheng WM, Wong GK, Wang J. A cross-species alignment tool (CAT). BMC Bioinformatics. 2007 Sep 19; 8:349. PMID: 17880681.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  59. Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 2007; 8(4):R45. PMID: 17407547; PMCID: PMC1895994.
    Citations: 41     Fields:    Translation:Animals
  60. Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. Snap: an integrated SNP annotation platform. Nucleic Acids Res. 2007 Jan; 35(Database issue):D707-10. PMID: 17135198; PMCID: PMC1751554.
    Citations: 21     Fields:    Translation:Humans
  61. Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D572-80. PMID: 16381935; PMCID: PMC1347480.
    Citations: 268     Fields:    Translation:HumansAnimals
  62. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H. The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 2005 Feb; 3(2):e38. PMID: 15685292; PMCID: PMC546038.
    Citations: 380     Fields:    Translation:AnimalsCells
  63. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Li G, Su J, Wang X, Li G, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Xu J, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li C, Li D, Sun Y, Zhang Z, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Li J, Ye J, Chen H, Zhou Y, Liu B, Wang J, Ye J, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Li S, Wang J, Wong GK, Yang H. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science. 2004 Dec 10; 306(5703):1937-40. PMID: 15591204.
    Citations: 374     Fields:    Translation:AnimalsCells
  64. Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature. 2004 Dec 09; 432(7018):717-22. PMID: 15592405; PMCID: PMC2263125.
    Citations: 147     Fields:    Translation:HumansAnimalsCells
  65. Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GK. Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature. 2004 Oct 14; 431(7010):1 p following 757; discussion following 757. PMID: 15495343.
    Citations: 85     Fields:    Translation:HumansAnimalsCells
  66. Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R. Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Funct Integr Genomics. 2004 May; 4(2):84-93. PMID: 14770301.
    Citations: 42     Fields:    Translation:AnimalsCells
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