Sanger Institute, Genome Research Limited

People

Ning, Zemin
Dr Zemin Ning
Group Leader

Zemin oversees the activities of the group. He interacts with both internal and external collaborators on various projects, while providing technical guidance and support for the group members.  He is also actively involved in algorithm development and code programming.

Key Projects, Collaborations, Tools & Data

The group is currently involved in a numbe of projects: (1) Platform evaluation and applications of Oxford Nanopore sequencing data with focus on genome assembly and CNV detections;   (2)  NGS Assembler Phusion2: De novo assembly pipeline for NGS data;  (3) Detection of segmental duplications from k-mer distribution statistics;  (4) Cross_genome: genome scaffolding using cross species synteny. 

Partners and Funders

Internal Partners
External Partners and Funders

Publications

  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

    Ye K, Schulz MH, Long Q, Apweiler R and Ning Z

    Bioinformatics (Oxford, England) 2009;25;21;2865-71

  • SSAHA: a fast search method for large DNA databases.

    Ning Z, Cox AJ and Mullikin JC

    Genome research 2001;11;10;1725-9

  • The phusion assembler.

    Mullikin JC and Ning Z

    Genome research 2003;13;1;81-90

  • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.

    Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M and Turner DJ

    Nature methods 2009;6;4;291-5

  • Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

    Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ et al.

    Cell 2012;148;4;780-91

  • The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.

    Wang Y, Lu Y, Zhang Y, Ning Z, Li Y et al.

    Nature genetics 2015;47;6;625-31

  • The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).

    Peng Z, Lu Y, Li L, Zhao Q, Feng Q et al.

    Nature genetics 2013;45;4;456-61, 461e1-2

  • Next-generation sequencing and large genome assemblies.

    Henson J, Tischler G and Ning Z

    Pharmacogenomics 2012;13;8;901-15

  • Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza.

    Xu H, Song J, Luo H, Zhang Y, Li Q et al.

    Molecular plant 2016

  • The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.

    Wang Y, Lu Y, Zhang Y, Ning Z, Li Y et al.

    Nature genetics 2015;47;6;625-31

  • A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.

    Rad R, Rad L, Wang W, Strong A, Ponstingl H et al.

    Nature genetics 2015;47;1;47-56

  • Detecting Break Points of Insertions and Deletions from Paired-end Short Reads

    Kai Ye and Zemin Ning

    Next-generation Sequencing: Current Technologies and Applications 2014

  • Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage.

    Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I et al.

    Science (New York, N.Y.) 2014;343;6169;437-40

  • Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs.

    Ye K, Beekman M, Lameijer EW, Zhang Y, Moed MH et al.

    Twin research and human genetics : the official journal of the International Society for Twin Studies 2013;16;6;1026-32

  • Systematic evaluation of spliced alignment programs for RNA-seq data.

    Engström PG, Steijger T, Sipos B, Grant GR, Kahles A et al.

    Nature methods 2013;10;12;1185-91

  • The zebrafish reference genome sequence and its relationship to the human genome.

    Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C et al.

    Nature 2013;496;7446;498-503

  • The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).

    Peng Z, Lu Y, Li L, Zhao Q, Feng Q et al.

    Nature 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.

    Li MA, Pettitt SJ, Eckert S, Ning Z, Rice S et al.

    Molecular and cellular biology 2013;33;7;1317-30

  • Genetic basis of Y-linked hearing impairment.

    Wang Q, Xue Y, Zhang Y, Long Q, Asan et al.

    American journal of human genetics 2013;92;2;301-6

  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

    Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M et al.

    GigaScience 2013;2;1;10

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

  • Next-generation sequencing and large genome assemblies.

    Henson J, Tischler G and Ning Z

    Pharmacogenomics 2012;13;8;901-15

  • Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.

    Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z et al.

    Human genetics 2012;131;5;665-74

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

  • Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

    Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ et al.

    Cell 2012;148;4;780-91

  • PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

    Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, Slagboom PE and Ye K

    Bioinformatics (Oxford, England) 2012;28;4;479-86

  • Expansion of CORE-SINEs in the genome of the Tasmanian devil.

    Nilsson MA, Janke A, Murchison EP, Ning Z and Hallström BM

    BMC genomics 2012;13;172

  • Assemblathon 1: a competitive assessment of de novo short read assembly methods.

    Earl D, Bradnam K, St John J, Darling A, Lin D et al.

    Genome research 2011;21;12;2224-41

  • Mobilization of giant piggyBac transposons in the mouse genome.

    Li MA, Turner DJ, Ning Z, Yusa K, Liang Q et al.

    Nucleic acids research 2011;39;22;e148

  • PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.

    Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V et al.

    PloS one 2011;6;1;e15292

  • International network of cancer genome projects.

    International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD et al.

    Nature 2010;464;7291;993-8

  • A comprehensive catalogue of somatic mutations from a human cancer genome.

    Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ et al.

    Nature 2010;463;7278;191-6

  • Out of the sequencer and into the wiki as we face new challenges in genome informatics.

    Ning Z and Montgomery SB

    Genome biology 2010;11;10;308

  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

    Ye K, Schulz MH, Long Q, Apweiler R and Ning Z

    Bioinformatics (Oxford, England) 2009;25;21;2865-71

  • HI: haplotype improver using paired-end short reads.

    Long Q, MacArthur D, Ning Z and Tyler-Smith C

    Bioinformatics (Oxford, England) 2009;25;18;2436-7

  • The genome of the blood fluke Schistosoma mansoni.

    Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP et al.

    Nature 2009;460;7253;352-8

  • The Schistosoma japonicum genome reveals features of host-parasite interplay.

    Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium

    Nature 2009;460;7253;345-51

  • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.

    Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M and Turner DJ

    Nature methods 2009;6;4;291-5

  • Assessing the gene space in draft genomes.

    Parra G, Bradnam K, Ning Z, Keane T and Korf I

    Nucleic acids research 2009;37;1;289-97

  • Accurate whole human genome sequencing using reversible terminator chemistry.

    Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J et al.

    Nature 2008;456;7218;53-9

  • Finishing the finished human chromosome 22 sequence.

    Cole CG, McCann OT, Collins JE, Oliver K, Willey D et al.

    Genome biology 2008;9;5;R78

  • Initial sequencing and comparative analysis of the mouse genome.

    Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J et al.

    Nature 2002;420;6915;520-62