PubRank

Yingrui Li

Author PubWeight™ 497.08‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 SOAP: short oligonucleotide alignment program. Bioinformatics 2008 68.13
2 The diploid genome sequence of an Asian individual. Nature 2008 46.29
3 De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2009 45.91
4 A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010 43.63
5 SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009 39.47
6 SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012 20.89
7 SNP detection for massively parallel whole-genome resequencing. Genome Res 2009 15.96
8 The sequence and de novo assembly of the giant panda genome. Nature 2009 15.76
9 Mapping copy number variation by population-scale genome sequencing. Nature 2011 12.55
10 A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012 12.25
11 A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012 11.68
12 Sequencing of 50 human exomes reveals adaptation to high altitude. Science 2010 11.27
13 Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011 8.38
14 The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011 8.23
15 The genome of the cucumber, Cucumis sativus L. Nat Genet 2009 8.19
16 Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010 7.51
17 Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011 7.11
18 Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet 2011 5.73
19 Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 2012 5.62
20 Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012 5.58
21 Building the sequence map of the human pan-genome. Nat Biotechnol 2009 5.53
22 The oyster genome reveals stress adaptation and complexity of shell formation. Nature 2012 5.30
23 Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 2012 5.16
24 Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 2011 4.84
25 Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013 4.11
26 Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet 2012 4.07
27 Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 2012 4.03
28 Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet 2013 3.87
29 Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet 2011 3.66
30 Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn 2012 3.54
31 Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 2013 3.40
32 Whole-genome sequence of Schistosoma haematobium. Nat Genet 2012 2.91
33 Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 2012 2.82
34 Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 2009 2.68
35 Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet 2011 2.52
36 Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet 2013 2.47
37 SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 2012 2.37
38 Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol 2011 2.37
39 Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 2012 2.22
40 Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 2010 2.17
41 Ascaris suum draft genome. Nature 2011 2.16
42 Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res 2013 2.12
43 Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol 2010 2.06
44 Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 2010 2.03
45 Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 2011 1.93
46 Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A 2014 1.91
47 SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 2012 1.89
48 COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics 2012 1.83
49 SOAPindel: efficient identification of indels from short paired reads. Genome Res 2012 1.59
50 Whole exome sequencing of insulinoma reveals recurrent T372R mutations in YY1. Nat Commun 2013 1.57
51 Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 2011 1.54
52 SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol 2013 1.47
53 Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies. BMC Med Genomics 2012 1.45
54 Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet 2013 1.43
55 SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. PLoS One 2013 1.39
56 Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol 2014 1.38
57 An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun 2012 1.28
58 Extensive X-linked adaptive evolution in central chimpanzees. Proc Natl Acad Sci U S A 2012 1.23
59 The YH database: the first Asian diploid genome database. Nucleic Acids Res 2009 1.22
60 A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenat Diagn 2013 1.22
61 A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing. PLoS One 2013 1.15
62 The sequence and analysis of a Chinese pig genome. Gigascience 2012 1.15
63 Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet 2013 1.06
64 Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biol 2013 1.06
65 Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. PLoS Genet 2013 1.04
66 HIVID: an efficient method to detect HBV integration using low coverage sequencing. Genomics 2013 1.02
67 Diverse modes of genomic alteration in hepatocellular carcinoma. Genome Biol 2014 0.99
68 Faster human genome sequencing. Nat Biotechnol 2009 0.99
69 An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinformatics 2012 0.94
70 Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol 2014 0.94
71 Whole-genome sequencing of matched primary and metastatic hepatocellular carcinomas. BMC Med Genomics 2014 0.93
72 Exome sequencing and linkage analysis identified tenascin-C (TNC) as a novel causative gene in nonsyndromic hearing loss. PLoS One 2013 0.90
73 MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). BMC Bioinformatics 2015 0.89
74 Whole-genome sequences of DA and F344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer. Genetics 2013 0.87
75 Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics 2014 0.86
76 A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Hum Mutat 2013 0.84
77 An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing. PLoS One 2013 0.84
78 A population model for genotyping indels from next-generation sequence data. Nucleic Acids Res 2012 0.81
79 Whole-exome sequencing identifies a polymorphism in the BMP5 gene associated with SSRI treatment response in major depression. J Psychopharmacol 2013 0.79
80 Integrative analysis of two cell lines derived from a non-small-lung cancer patient--a panomics approach. Pac Symp Biocomput 2014 0.79
81 YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data. BMC Bioinformatics 2013 0.75
82 Corrigendum: Lanosterol reverses protein aggregation in cataracts. Nature 2015 0.75