The sequence alignment/map format and SAMtools H Li, B Handsaker, A Wysoker, T Fennell, J Ruan, N Homer, G Marth, ... bioinformatics 25 (16), 2078-2079, 2009 | 53785 | 2009 |
Fast and accurate short read alignment with Burrows–Wheeler transform H Li, R Durbin Bioinformatics 25 (14), 1754-1760, 2009 | 43949 | 2009 |
A global reference for human genetic variation GP Consortium Nature 526 (7571), 68-74, 2015 | 12857* | 2015 |
Fast and accurate long-read alignment with Burrows–Wheeler transform H Li, R Durbin Bioinformatics 26 (5), 589-595, 2010 | 11548 | 2010 |
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM H Li arXiv preprint arXiv:1303.3997, 2013 | 9970 | 2013 |
A map of human genome variation from population-scale sequencing 1000 Genomes Project Consortium Nature 467 (7319), 1061-1073, 2010 | 8717 | 2010 |
An integrated map of genetic variation from 1,092 human genomes 1000 Genomes Project Consortium Nature 491 (7422), 56-65, 2012 | 8213 | 2012 |
Minimap2: pairwise alignment for nucleotide sequences H Li Bioinformatics 34 (18), 3094-3100, 2018 | 7914 | 2018 |
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data H Li Bioinformatics 27 (21), 2987-2993, 2011 | 5772 | 2011 |
Accurate whole human genome sequencing using reversible terminator chemistry DR Bentley, S Balasubramanian, HP Swerdlow, GP Smith, J Milton, ... nature 456 (7218), 53-59, 2008 | 4985 | 2008 |
A draft sequence of the Neandertal genome RE Green, J Krause, AW Briggs, T Maricic, U Stenzel, M Kircher, ... science 328 (5979), 710-722, 2010 | 4893 | 2010 |
Twelve years of SAMtools and BCFtools P Danecek, JK Bonfield, J Liddle, J Marshall, V Ohan, MO Pollard, ... GigaScience 10 (2), giab008, 2021 | 4826* | 2021 |
Mapping short DNA sequencing reads and calling variants using mapping quality scores H Li, J Ruan, R Durbin Genome research 18 (11), 1851-1858, 2008 | 3488 | 2008 |
The complete genome sequence of a Neanderthal from the Altai Mountains K Prüfer, F Racimo, N Patterson, F Jay, S Sankararaman, S Sawyer, ... Nature 505 (7481), 43-49, 2014 | 2329 | 2014 |
Inference of human population history from individual whole-genome sequences H Li, R Durbin Nature 475 (7357), 493-496, 2011 | 2318 | 2011 |
Genetic history of an archaic hominin group from Denisova Cave in Siberia D Reich, RE Green, M Kircher, J Krause, N Patterson, EY Durand, B Viola, ... Nature 468 (7327), 1053-1060, 2010 | 2214 | 2010 |
A high-coverage genome sequence from an archaic Denisovan individual M Meyer, M Kircher, MT Gansauge, H Li, F Racimo, S Mallick, ... Science 338 (6104), 222-226, 2012 | 2101 | 2012 |
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm H Cheng, GT Concepcion, X Feng, H Zhang, H Li Nature methods 18 (2), 170-175, 2021 | 1902 | 2021 |
The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53, 2022 | 1701 | 2022 |
Ancient human genomes suggest three ancestral populations for present-day Europeans I Lazaridis, N Patterson, A Mittnik, G Renaud, S Mallick, K Kirsanow, ... Nature 513 (7518), 409-413, 2014 | 1486 | 2014 |
A draft sequence for the genome of the domesticated silkworm (Bombyx mori) Q Xia, Z Zhou, C Lu, D Cheng, F Dai, B Li, P Zhao, X Zha, T Cheng, ... Science 306 (5703), 1937-1940, 2004 | 1396 | 2004 |
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations S Mallick, H Li, M Lipson, I Mathieson, M Gymrek, F Racimo, M Zhao, ... Nature 538 (7624), 201-206, 2016 | 1382 | 2016 |
The sequence and de novo assembly of the giant panda genome R Li, W Fan, G Tian, H Zhu, L He, J Cai, Q Huang, Q Cai, B Li, Y Bai, ... Nature 463 (7279), 311-317, 2010 | 1372 | 2010 |
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates AJ Vilella, J Severin, A Ureta-Vidal, L Heng, R Durbin, E Birney Genome research 19 (2), 327-335, 2009 | 1269 | 2009 |
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome AM Wenger, P Peluso, WJ Rowell, PC Chang, RJ Hall, GT Concepcion, ... Nature biotechnology 37 (10), 1155-1162, 2019 | 1252 | 2019 |
A survey of sequence alignment algorithms for next-generation sequencing H Li, N Homer Briefings in bioinformatics 11 (5), 473-483, 2010 | 1232 | 2010 |
The diploid genome sequence of an Asian individual J Wang, W Wang, R Li, Y Li, G Tian, L Goodman, W Fan, J Zhang, J Li, ... Nature 456 (7218), 60-65, 2008 | 1144 | 2008 |
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences H Li Bioinformatics 32 (14), 2103-2110, 2016 | 1139 | 2016 |
Genome sequence of a 45,000-year-old modern human from western Siberia Q Fu, H Li, P Moorjani, F Jay, SM Slepchenko, AA Bondarev, ... Nature 514 (7523), 445-449, 2014 | 1133 | 2014 |
Fast and accurate long-read assembly with wtdbg2 J Ruan, H Li Nature methods 17 (2), 155-158, 2020 | 1021 | 2020 |
The genomes of Oryza sativa: a history of duplications J Yu, J Wang, W Lin, S Li, H Li, J Zhou, P Ni, W Dong, S Hu, C Zeng, ... PLoS Biol 3 (2), e38, 2005 | 1017 | 2005 |
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing PJ Campbell, PJ Stephens, ED Pleasance, S O'Meara, H Li, T Santarius, ... Nature genetics 40 (6), 722-729, 2008 | 975 | 2008 |
Great ape genetic diversity and population history J Prado-Martinez, PH Sudmant, JM Kidd, H Li, JL Kelley, ... Nature 499 (7459), 471-475, 2013 | 931 | 2013 |
Toward better understanding of artifacts in variant calling from high-coverage samples H Li Bioinformatics 30 (20), 2843-2851, 2014 | 907 | 2014 |
Efficient architecture-aware acceleration of BWA-MEM for multicore systems M Vasimuddin, S Misra, H Li, S Aluru 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS …, 2019 | 906 | 2019 |
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly VA Schneider, T Graves-Lindsay, K Howe, N Bouk, HC Chen, PA Kitts, ... Genome research 27 (5), 849-864, 2017 | 865 | 2017 |
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis TA Down, VK Rakyan, DJ Turner, P Flicek, H Li, E Kulesha, S Graef, ... Nature biotechnology 26 (7), 779-785, 2008 | 770 | 2008 |
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms GKS Wong, B Liu, J Wang, Y Zhang, X Yang, Z Zhang, Q Meng, J Zhou, ... Nature 432 (7018), 717-722, 2004 | 623 | 2004 |
TreeFam: a curated database of phylogenetic trees of animal gene families H Li, A Coghlan, J Ruan, LJ Coin, JK Heriche, L Osmotherly, R Li, T Liu, ... Nucleic acids research 34 (suppl_1), D572-D580, 2006 | 600 | 2006 |
Tabix: fast retrieval of sequence features from generic TAB-delimited files H Li Bioinformatics 27 (5), 718-719, 2011 | 589 | 2011 |
The date of interbreeding between Neandertals and modern humans S Sankararaman, N Patterson, H Li, S Pääbo, D Reich PLoS Genet 8 (10), e1002947, 2012 | 546 | 2012 |
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly H Li Bioinformatics 28 (14), 1838-1844, 2012 | 430 | 2012 |
TreeFam: 2008 update J Ruan, H Li, Z Chen, A Coghlan, LJM Coin, Y Guo, JK Heriche, Y Hu, ... Nucleic acids research 36 (suppl_1), D735-D740, 2007 | 371 | 2007 |
Three-dimensional genome structures of single diploid human cells L Tan, D Xing, CH Chang, H Li, XS Xie Science 361 (6405), 924-928, 2018 | 368 | 2018 |
A direct characterization of human mutation based on microsatellites JX Sun, A Helgason, G Masson, SS Ebenesersdóttir, H Li, S Mallick, ... Nature genetics 44 (10), 1161-1165, 2012 | 359 | 2012 |
Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI) C Chen, D Xing, L Tan, H Li, G Zhou, L Huang, XS Xie Science 356 (6334), 189-194, 2017 | 347 | 2017 |
Improving SNP discovery by base alignment quality H Li Bioinformatics 27 (8), 1157-1158, 2011 | 343 | 2011 |
New strategies to improve minimap2 alignment accuracy H Li Bioinformatics 37 (23), 4572-4574, 2021 | 310 | 2021 |
Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth E Palkopoulou, S Mallick, P Skoglund, J Enk, N Rohland, H Li, A Omrak, ... Current Biology 25 (10), 1395-1400, 2015 | 307 | 2015 |
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies B Pasaniuc, N Rohland, PJ McLaren, K Garimella, N Zaitlen, H Li, ... Nature genetics 44 (6), 631-635, 2012 | 289 | 2012 |
A draft human pangenome reference WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ... Nature 617 (7960), 312-324, 2023 | 275 | 2023 |
The design and construction of reference pangenome graphs with minigraph H Li, X Feng, C Chu Genome Biology 21 (1), 265, 2020 | 255 | 2020 |
The Human Pangenome Project: a global resource to map genomic diversity T Wang, L Antonacci-Fulton, K Howe, HA Lawson, JK Lucas, AM Phillippy, ... Nature 604 (7906), 437-446, 2022 | 233 | 2022 |
Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison C Li, P Ni, M Francki, A Hunter, Y Zhang, D Schibeci, H Li, A Tarr, J Wang, ... Functional & integrative genomics 4, 84-93, 2004 | 216 | 2004 |
BFC: correcting Illumina sequencing errors H Li Bioinformatics 31 (17), 2885-2887, 2015 | 215 | 2015 |
pIRS: Profile-based Illumina pair-end reads simulator X Hu, J Yuan, Y Shi, J Lu, B Liu, Z Li, Y Chen, D Mu, H Zhang, N Li, Z Yue, ... Bioinformatics 28 (11), 1533-1535, 2012 | 212 | 2012 |
No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans R Do, D Balick, H Li, I Adzhubei, S Sunyaev, D Reich Nature genetics 47 (2), 126-131, 2015 | 197 | 2015 |
HTSlib: C library for reading/writing high-throughput sequencing data JK Bonfield, J Marshall, P Danecek, H Li, V Ohan, A Whitwham, T Keane, ... GigaScience 10 (2), giab007, 2021 | 188 | 2021 |
Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects AA Regier, Y Farjoun, DE Larson, O Krasheninina, HM Kang, ... Nature communications 9 (1), 4038, 2018 | 185 | 2018 |
Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells M Daher, R Basar, E Gokdemir, N Baran, N Uprety, AK Nunez Cortes, ... Blood, The Journal of the American Society of Hematology 137 (5), 624-636, 2021 | 176 | 2021 |
Haplotype-resolved assembly of diploid genomes without parental data H Cheng, ED Jarvis, O Fedrigo, KP Koepfli, L Urban, NJ Gemmell, H Li Nature Biotechnology 40 (9), 1332-1335, 2022 | 166 | 2022 |
A synthetic-diploid benchmark for accurate variant-calling evaluation H Li, JM Bloom, Y Farjoun, M Fleharty, L Gauthier, B Neale, D MacArthur Nature methods 15 (8), 595, 2018 | 165 | 2018 |
The contribution of rare variation to prostate cancer heritability N Mancuso, N Rohland, KA Rand, A Tandon, A Allen, D Quinque, ... Nature genetics 48 (1), 30-35, 2016 | 161 | 2016 |
Chromosome-scale, haplotype-resolved assembly of human genomes S Garg, A Fungtammasan, A Carroll, M Chou, A Schmitt, X Zhou, S Mac, ... Nature Biotechnology 39 (3), 309-312, 2021 | 152* | 2021 |
SOAPindel: efficient identification of indels from short paired reads S Li, R Li, H Li, J Lu, Y Li, L Bolund, MH Schierup, J Wang Genome research 23 (1), 195-200, 2013 | 142 | 2013 |
Curated variation benchmarks for challenging medically relevant autosomal genes J Wagner, ND Olson, L Harris, J McDaniel, H Cheng, A Fungtammasan, ... Nature Biotechnology 40 (5), 672-680, 2022 | 113 | 2022 |
FermiKit: assembly-based variant calling for Illumina resequencing data H Li Bioinformatics 31 (22), 3694-3696, 2015 | 111 | 2015 |
Semi-automated assembly of high-quality diploid human reference genomes ED Jarvis, G Formenti, A Rhie, A Guarracino, C Yang, J Wood, A Tracey, ... Nature 611 (7936), 519-531, 2022 | 96 | 2022 |
The complete sequence of a human Y chromosome A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, ... Nature 621 (7978), 344-354, 2023 | 90 | 2023 |
Using population admixture to help complete maps of the human genome G Genovese, RE Handsaker, H Li, N Altemose, AM Lindgren, K Chambert, ... Nature genetics 45 (4), 406-414, 2013 | 89 | 2013 |
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags J Gorodkin, S Cirera, J Hedegaard, MJ Gilchrist, F Panitz, C Jørgensen, ... Genome biology 8, 1-16, 2007 | 83 | 2007 |
Fast construction of FM-index for long sequence reads H Li Bioinformatics 30 (22), 3274-3275, 2014 | 78 | 2014 |
Differential DNA methylation of vocal and facial anatomy genes in modern humans D Gokhman, M Nissim-Rafinia, L Agranat-Tamir, G Housman, ... Nature communications 11 (1), 1189, 2020 | 76 | 2020 |
Metagenome assembly of high-fidelity long reads with hifiasm-meta X Feng, H Cheng, D Portik, H Li Nature Methods 19 (6), 671-674, 2022 | 65 | 2022 |
Mapping the human reference genome’s missing sequence by three-way admixture in Latino genomes G Genovese, RE Handsaker, H Li, EE Kenny, SA McCarroll The American Journal of Human Genetics 93 (3), 411-421, 2013 | 61 | 2013 |
Protein-to-genome alignment with miniprot H Li Bioinformatics 39 (1), btad014, 2023 | 58 | 2023 |
Comprehensive identification of transposable element insertions using multiple sequencing technologies C Chu, R Borges-Monroy, VV Viswanadham, S Lee, H Li, EA Lee, PJ Park Nature Communications 12 (1), 3836, 2021 | 57 | 2021 |
Genome Graphs AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ... bioRxiv, 101378, 2017 | 55 | 2017 |
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA KE Holt, YY Teo, H Li, S Nair, G Dougan, J Wain, J Parkhill Bioinformatics 25 (16), 2074-2075, 2009 | 55 | 2009 |
Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands D Xing, L Tan, CH Chang, H Li, XS Xie Proceedings of the National Academy of Sciences 118 (8), e2013106118, 2021 | 54 | 2021 |
Snap: an integrated SNP annotation platform S Li, L Ma, H Li, S Vang, Y Hu, L Bolund, J Wang Nucleic acids research 35 (suppl_1), D707-D710, 2007 | 51 | 2007 |
Real-time mapping of nanopore raw signals H Zhang, H Li, C Jain, H Cheng, KF Au, H Li, S Aluru Bioinformatics 37 (Supplement_1), i477-i483, 2021 | 50 | 2021 |
BGT: efficient and flexible genotype query across many samples H Li Bioinformatics 32 (4), 590-592, 2015 | 49 | 2015 |
Pangenome graph construction from genome alignments with Minigraph-Cactus G Hickey, J Monlong, J Ebler, AM Novak, JM Eizenga, Y Gao, T Marschall, ... Nature Biotechnology, 1-11, 2023 | 46 | 2023 |
Fast alignment and preprocessing of chromatin profiles with Chromap H Zhang, L Song, X Wang, H Cheng, C Wang, C Meyer, T Liu, M Tang, ... Nature communications 12 (1), 6566, 2021 | 44 | 2021 |
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 … I Sudbery, J Stalker, JT Simpson, T Keane, AG Rust, ME Hurles, K Walter, ... Genome biology 10 (10), R112, 2009 | 42 | 2009 |
The anatomy of successful computational biology software S Altschul, B Demchak, R Durbin, R Gentleman, M Krzywinski, H Li, ... Nature biotechnology 31 (10), 894-897, 2013 | 40 | 2013 |
Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans S Luo, AY Jane, H Li, YS Song Life science alliance 2 (2), 2019 | 30 | 2019 |
Omics‐based profiling of carcinoma of the breast and matched regional lymph node metastasis J Li, P Gromov, I Gromova, JM Moreira, V Timmermans‐Wielenga, F Rank, ... Proteomics 8 (23‐24), 5038-5052, 2008 | 30 | 2008 |
A haplotype-aware de novo assembly of related individuals using pedigree sequence graph S Garg, J Aach, H Li, I Sebenius, R Durbin, G Church Bioinformatics 36 (8), 2385-2392, 2020 | 27 | 2020 |
Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres KT Tan, MK Slevin, M Meyerson, H Li Genome Biology 23 (1), 180, 2022 | 26 | 2022 |
Identifying centromeric satellites with dna-brnn H Li Bioinformatics 35 (21), 4408-4410, 2019 | 25 | 2019 |
Test data sets and evaluation of gene prediction programs on the rice genome H Li, JS Liu, Z Xu, J Jin, L Fang, L Gao, YD Li, ZX Xing, SG Gao, T Liu, ... Journal of computer science and technology 20, 446-453, 2005 | 24 | 2005 |
Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology J Ruan, L Jiang, Z Chong, Q Gong, H Li, C Li, Y Tao, C Zheng, W Zhai, ... BMC genomics 14, 1-9, 2013 | 23 | 2013 |
compleasm: a faster and more accurate reimplementation of BUSCO N Huang, H Li Bioinformatics 39 (10), btad595, 2023 | 19* | 2023 |
SAM/BAM format v1. 5 extensions for de novo assemblies PJA Cock, JK Bonfield, B Chevreux, H Li bioRxiv, 020024, 2015 | 19 | 2015 |
Mathematical notes on samtools algorithms H Li October, 2010 | 18 | 2010 |
Haplotype frequencies in a sub-region of chromosome 19q13. 3, related to risk and prognosis of cancer, differ dramatically between ethnic groups MH Schierup, T Mailund, H Li, J Wang, A Tjønneland, U Vogel, L Bolund, ... BMC Medical Genetics 10, 1-8, 2009 | 16 | 2009 |
SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing D Heller, M Vingron, G Church, H Li, S Garg BioRxiv, 2020.02. 25.964445, 2020 | 15 | 2020 |
Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies X Feng, H Li Molecular Biology and Evolution 38 (7), 2958-2966, 2021 | 13 | 2021 |