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Heng Li
Heng Li
Dana-Farber Cancer Institute & Harvard University
Verified email at jimmy.harvard.edu - Homepage
Title
Cited by
Cited by
Year
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
537852009
Fast and accurate short read alignment with Burrows–Wheeler transform
H Li, R Durbin
Bioinformatics 25 (14), 1754-1760, 2009
439492009
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
115482010
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
H Li
arXiv preprint arXiv:1303.3997, 2013
99702013
A map of human genome variation from population-scale sequencing
1000 Genomes Project Consortium
Nature 467 (7319), 1061-1073, 2010
87172010
An integrated map of genetic variation from 1,092 human genomes
1000 Genomes Project Consortium
Nature 491 (7422), 56-65, 2012
82132012
Minimap2: pairwise alignment for nucleotide sequences
H Li
Bioinformatics 34 (18), 3094-3100, 2018
79142018
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
57722011
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
49852008
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
48932010
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
34882008
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
23292014
Inference of human population history from individual whole-genome sequences
H Li, R Durbin
Nature 475 (7357), 493-496, 2011
23182011
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
22142010
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
21012012
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
19022021
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
17012022
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
14862014
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
13962004
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
13822016
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
13722010
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
12692009
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
12522019
A survey of sequence alignment algorithms for next-generation sequencing
H Li, N Homer
Briefings in bioinformatics 11 (5), 473-483, 2010
12322010
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
11442008
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
H Li
Bioinformatics 32 (14), 2103-2110, 2016
11392016
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
11332014
Fast and accurate long-read assembly with wtdbg2
J Ruan, H Li
Nature methods 17 (2), 155-158, 2020
10212020
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
10172005
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
9752008
Great ape genetic diversity and population history
J Prado-Martinez, PH Sudmant, JM Kidd, H Li, JL Kelley, ...
Nature 499 (7459), 471-475, 2013
9312013
Toward better understanding of artifacts in variant calling from high-coverage samples
H Li
Bioinformatics 30 (20), 2843-2851, 2014
9072014
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
9062019
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
8652017
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
7702008
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
6232004
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
6002006
Tabix: fast retrieval of sequence features from generic TAB-delimited files
H Li
Bioinformatics 27 (5), 718-719, 2011
5892011
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
5462012
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
H Li
Bioinformatics 28 (14), 1838-1844, 2012
4302012
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
3712007
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
3682018
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
3592012
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
3472017
Improving SNP discovery by base alignment quality
H Li
Bioinformatics 27 (8), 1157-1158, 2011
3432011
New strategies to improve minimap2 alignment accuracy
H Li
Bioinformatics 37 (23), 4572-4574, 2021
3102021
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
3072015
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
2892012
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
2752023
The design and construction of reference pangenome graphs with minigraph
H Li, X Feng, C Chu
Genome Biology 21 (1), 265, 2020
2552020
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
2332022
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
2162004
BFC: correcting Illumina sequencing errors
H Li
Bioinformatics 31 (17), 2885-2887, 2015
2152015
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
2122012
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
1972015
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
1882021
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
1852018
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
1762021
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
1662022
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
1652018
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
1612016
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
1422013
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
1132022
FermiKit: assembly-based variant calling for Illumina resequencing data
H Li
Bioinformatics 31 (22), 3694-3696, 2015
1112015
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
962022
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
902023
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
892013
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
832007
Fast construction of FM-index for long sequence reads
H Li
Bioinformatics 30 (22), 3274-3275, 2014
782014
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
762020
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
652022
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
612013
Protein-to-genome alignment with miniprot
H Li
Bioinformatics 39 (1), btad014, 2023
582023
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
572021
Genome Graphs
AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ...
bioRxiv, 101378, 2017
552017
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
552009
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
542021
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
512007
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
502021
BGT: efficient and flexible genotype query across many samples
H Li
Bioinformatics 32 (4), 590-592, 2015
492015
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
462023
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
442021
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
422009
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
402013
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
302019
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
302008
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
272020
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
262022
Identifying centromeric satellites with dna-brnn
H Li
Bioinformatics 35 (21), 4408-4410, 2019
252019
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
242005
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
232013
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
192015
Mathematical notes on samtools algorithms
H Li
October, 2010
182010
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
162009
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
152020
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
132021
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