ZN
Zemin Ning
GenomeGenome, HumanGenomicsEvolution, MolecularSoftwareAlgorithmsGenetic VariationHaplotypesSequence Analysis, DNADNA Transposable Elements
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
68 papers in the corpus · 2001–2026Pre-divergence hybridization and adaptive introgression shaped the genetic architecture of East Asian domestic pigs.42584836 · Wang, Yuzhan, Kong, Yuan, Cui, Qiqian et al.2026 · 0 citationsScience China. Life sciences. 2026;69(11):4075-4090
The Vertebrate Genomes Project Phase I: A global reference genome resource.42395566 · Formenti, Giulio, Absolon, Dominic E, Abueg, Linelle Ann L et al.2026 · 10 citationsbioRxiv : the preprint server for biology. 2026
Highly accurate ab initio gene annotation with ANNEVO.41820667 · Zhang, Pengyu, Xu, Tun, Wang, Songbo et al.2026 · 33 citationsNature methods. 2026;23(4):740-748
A scalable platform for EPSC-Induced MSC extracellular vesicles with therapeutic potential.40765003 · Gong, Shixin, Li, Nan, Peng, Qinqing et al.2025 · 22 citationsStem cell research & therapy. 2025;16(1):426
Haplotype-phased genome assemblies and annotation of the northern white-cheeked gibbon (Nomascus leucogenys).39587154 · Luo, Zhonglai, Jiang, Libo, Xu, Jianing et al.2024 · 0 citationsScientific data. 2024;11(1):1279
The Bioinformatic Applications of Hi-C and Linked Reads.38905513 · Jiang, Libo, Quail, Michael A, Fraser-Govil, Jack et al.2024 · 3 citationsGenomics, proteomics & bioinformatics. 2024;22(4)
A haplotype-resolved genome reveals the genetic basis of spine formation in Atelerix albiventris.38950858 · Jiang, Libo, Xu, Jianing, Zhu, Mengyuan et al.2024 · 2 citationsJournal of genetics and genomics = Yi chuan xue bao. 2024;51(12):1529-1532
Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas.38232733 · Ijaz, Jannat, Harry, Edward, Raine, Keiran et al.2024 · 14 citationsCell genomics. 2024;4(2):100484
Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule.37783803 · Bruzos, Alicia L, Santamarina, Martín, García-Souto, Daniel et al.2023 · 23 citationsNature cancer. 2023;4(11):1575-1591
Editorial: Challenges and progressions in herbal genomics.37746010 · Cao, Yinghao, Ning, Zemin, Zhao, Yiqiang2023 · 1 citationFrontiers in plant science. 2023;14:1273769
Genomics of cold adaptations in the Antarctic notothenioid fish radiation.37296119 · Bista, Iliana, Wood, Jonathan M D, Desvignes, Thomas et al.2023 · 94 citationsNature communications. 2023;14(1):3412
The evolution of two transmissible cancers in Tasmanian devils.37079675 · Stammnitz, Maximilian R, Gori, Kevin, Kwon, Young Mi et al.2023 · 66 citationsScience (New York, N.Y.). 2023;380(6642):283-293
Author Correction: A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.35768458 · Catania, Theresa, Li, Yi, Winzer, Thilo et al.2022 · 0 citationsNature communications. 2022;13(1):3755
A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.35672295 · Catania, Theresa, Li, Yi, Winzer, Thilo et al.2022 · 20 citationsNature communications. 2022;13(1):3150
Genome sequence assembly evaluation using long-range sequencing data10.1101/2022.05.10.491304v3 · Guan, D., McCarthy, S., Wood, J. et al.2022 · 3 citationsbioRxiv
Efficient iterative Hi-C scaffolder based on N-best neighbors.34837944 · Guan, Dengfeng, McCarthy, Shane A, Ning, Zemin et al.2021 · 19 citationsBMC bioinformatics. 2021;22(1):569
Incipient diploidization of the medicinal plant Perilla within 10,000 years.34535649 · Zhang, Yujun, Shen, Qi, Leng, Liang et al.2021 · 96 citationsNature communications. 2021;12(1):5508
Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies.34352039 · Alenquer, Marta, Ferreira, Filipe, Lousa, Diana et al.2021 · 99 citationsPLoS pathogens. 2021;17(8):e1009772
A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop.33960539 · Ma, Xiao, Vaistij, Fabián E, Li, Yi et al.2021 · 58 citationsThe Plant journal : for cell and molecular biology. 2021;107(2):613-628
Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 binding10.1101/2021.04.22.441007v2 · Alenquer, M., Ferreira, F., Lousa, D. et al.2021 · 8 citationsbioRxiv
Towards complete and error-free genome assemblies of all vertebrate species.33911273 · Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier et al.2022 · 3,205 citationsNature. 2021;592(7856):737-746
The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861).33195818 · Bista, Iliana, McCarthy, Shane A, Wood, Jonathan et al.2025 · 22 citationsWellcome open research. 2020;5:148
scanPAV: a pipeline for extracting presence-absence variations in genome pairs.29608694 · Giordano, Francesca, Stammnitz, Maximilian R, Murchison, Elizabeth P et al.2019 · 27 citationsBioinformatics (Oxford, England). 2018;34(17):3022-3024
The opium poppy genome and morphinan production.30166436 · Guo, Li, Winzer, Thilo, Yang, Xiaofei et al.2018 · 343 citationsScience (New York, N.Y.). 2018;362(6412):343-347
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.29634948 · Stammnitz, Maximilian R, Coorens, Tim H H, Gori, Kevin C et al.2019 · 107 citationsCancer cell. 2018;33(4):607-619.e15
Split-Read Indel and Structural Variant Calling Using PINDEL.30039366 · Ye, Kai, Guo, Li, Yang, Xiaofei et al.2019 · 32 citationsMethods in molecular biology (Clifton, N.J.). 2018;1833:95-105
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.28638050 · Giordano, Francesca, Aigrain, Louise, Quail, Michael A et al.2019 · 147 citationsScientific reports. 2017;7(1):3935
Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas.28096377 · Hu, Yibo, Wu, Qi, Ma, Shuai et al.2018 · 264 citationsProceedings of the National Academy of Sciences of the United States of America. 2017;114(5):1081-1086
Oxford Nanopore MinION Sequencing and Genome Assembly.27646134 · Lu, Hengyun, Giordano, Francesca, Ning, Zemin2017 · 935 citationsGenomics, proteomics & bioinformatics. 2016;14(5):265-279
Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.27121471 · McKerrell, Thomas, Moreno, Thaidy, Ponstingl, Hannes et al.2017 · 59 citationsBlood. 2016;128(1):e1-9
Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza.27018390 · Xu, Haibin, Song, Jingyuan, Luo, Hongmei et al.2018 · 347 citationsMolecular plant. 2016;9(6):949-52
Erratum: The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.26220136 · Wang, Yaping, Lu, Ying, Zhang, Yong et al.2015 · 27 citationsNature genetics. 2015;47(8):962
The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.25938946 · Wang, Yaping, Lu, Ying, Zhang, Yong et al.2015 · 435 citationsNature genetics. 2015;47(6):625-31
A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.25485836 · Rad, Roland, Rad, Lena, Wang, Wei et al.2015 · 80 citationsNature genetics. 2015;47(1):47-56
Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage.24458646 · Murchison, Elizabeth P, Wedge, David C, Alexandrov, Ludmil B et al.2014 · 187 citationsScience (New York, N.Y.). 2014;343(6169):437-440
Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs.24182360 · Ye, Kai, Beekman, Marian, Lameijer, Eric-Wubbo et al.2014 · 41 citationsTwin research and human genetics : the official journal of the International Society for Twin Studies. 2013;16(6):1026-32
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
The zebrafish reference genome sequence and its relationship to the human genome.23594743 · Howe, Kerstin, Clark, Matthew D, Torroja, Carlos F et al.2013 · 5,095 citationsNature. 2013;496(7446):498-503
The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).23435089 · Peng, Zhenhua, Lu, Ying, Li, Lubin et al.2013 · 592 citationsNature genetics. 2013;45(4):456-61, 461e1-2
The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.23358416 · Li, Meng Amy, Pettitt, Stephen J, Eckert, Sabine et al.2013 · 91 citationsMolecular and cellular biology. 2013;33(7):1317-30
Genetic basis of Y-linked hearing impairment.23352258 · Wang, Qiuju, Xue, Yali, Zhang, Yujun et al.2013 · 27 citationsAmerican journal of human genetics. 2013;92(2):301-6
Next-generation sequencing and large genome assemblies.22676195 · Henson, Joseph, Tischler, German, Ning, Zemin2012 · 134 citationsPharmacogenomics. 2012;13(8):901-15
Expansion of CORE-SINEs in the genome of the Tasmanian devil.22559330 · Nilsson, Maria A, Janke, Axel, Murchison, Elizabeth P et al.2012 · 10 citationsBMC genomics. 2012;13:172
Insights into hominid evolution from the gorilla genome sequence.22398555 · Scally, Aylwyn, Dutheil, Julien Y, Hillier, LaDeana W et al.2012 · 754 citationsNature. 2012;483(7388):169-75
Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.22341448 · Murchison, Elizabeth P, Schulz-Trieglaff, Ole B, Ning, Zemin et al.2012 · 326 citationsCell. 2012;148(4):780-91
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.22219203 · Zhang, Yanju, Lameijer, Eric-Wubbo, 't Hoen, Peter A C et al.2012 · 32 citationsBioinformatics (Oxford, England). 2012;28(4):479-86
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.22057783 · Hu, Min, Ayub, Qasim, Guerra-Assunção, José Afonso et al.2012 · 9 citationsHuman genetics. 2012;131(5):665-74
Mobilization of giant piggyBac transposons in the mouse genome.21948799 · Li, Meng Amy, Turner, Daniel J, Ning, Zemin et al.2012 · 174 citationsNucleic acids research. 2011;39(22):e148
Assemblathon 1: a competitive assessment of de novo short read assembly methods.21926179 · Earl, Dent, Bradnam, Keith, St John, John et al.2012 · 507 citationsGenome research. 2011;21(12):2224-41
PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.21264334 · Long, Quan, Jeffares, Daniel C, Zhang, Qingrun et al.2011 · 44 citationsPloS one. 2011;6(1):e15292
Career total: 99 works. 68 are in this corpus.Showing the 50 most recent.
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