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Songtao Gui, Ph.D.

  • Researcher in population genetics, pan-genomics and graph genome;

  • Trying to solve the \( V_{Geno} \sim V_{Pheno} \) problem using multi-omics evidences;

  • Developing tools and databases related to omics-analyses;

Contacts

songtaogui@sina.com Blog GitHub Twitter ORCID GoogleScholar

Skills

  • Programming Languages: Bash; Perl; R; Julia; Python(Read&Edit); Rust(Trying);

  • Systems: Linux(Debian, Ubuntu, Red Hat); Windows; HPC cluster(CentOS7-based)

  • Bioinformatics:

    • State-of-art NGS/omics-seq analyses: DNA/RNA-seq(Illumina, PB-SMRT/RSII, ONT), ChIP/HiC/WGS/ATAC etc.

    • Downstream analyses: Population Genetics, Phylogenetics, Genomics, Epigenetics etc.

    • Visualisation: R/ggplot-x, Julia/Makie, AdobeIllustrator, Photoshop etc.

    • DIY pipelines when necessary: Pan-genomic, SV calling, GWAS and post-GWAS etc.

    • Web development: more a designer than a developer, dealing with data more than code

  • Biological:

    • Evolutionary > Functional: tends to understand questions through large data supports

    • Theoretical > Practical: embracing cooperations for making bioinfo-data practical

Research/Work Experience

 
 
 
 
 

Professor(tenure track)

SDAU

Jan 2023 – Now Tai'an
Responsibilities include:

  • Pan-genomics and multi-omics integration based Crop improvements

  • Wheat genomics and population genetics

  • Crop domestication and adaptation

 
 
 
 
 

PostDoc

Huazhong Agricultural University; Supervisor: Prof. Jianbing Yan

Jan 2018 – Dec 2022 Wuhan
Responsibilities include:

  • Study the pan-genomics of Zea

  • Study the genomics and genetic variations in Zea

  • Construct and maintain the Zea multi-omics database Zeamap

 
 
 
 
 

Developer(concurrent post)

BGI Genomics

Dec 2018 – Dec 2019 Shenzhen
Cooperate with/Lead a group of 5 members to develop the Zeamap database.
 
 
 
 
 

PhD candidate

Wuhan University; Mentor: Prof. Yi Ding

Sep 2012 – Dec 2017 Wuhan
Responsibilities include:

  • Construct the genetic linkage map of Nelumbo nucifera

  • Study the genome of Nelumbo nucifera and comparative genomics among eudicots

  • Study the organelle genomes of Nelumbo nucifera

  • Study the CenH3 and centromere of Nelumbo nucifera

  • Identify DNA fingerprints for Rice germplasms

Interests & Education

Interests

  • Population genetics
  • Graph genomics
  • Cool codes in julia
  • Ping-Pong
  • Cat

Education

  • PostDoc in Crop Breeding, 2018-2022

    Huazhong Agricultural University

  • PhD in Genetics, 2012-2017

    Wuhan University

  • BSc in Biological Science, 2008-2012

    Shandong Normal University

Foundings/Achievements

  • 2021-2023, National Natural Science Foundation of China, 32000396; Founding (240,000RMB)

  • 2022, Hubei Postdoctoral Innovation and Entrepreneurship Competition, Winner's Price

  • 2020, 1st National Crop Science Postdoctoral Academic Forum, Outstanding Award;

  • 2019-2021, College of Plant Science, HZAU, Outstanding Postdoctoral funding;

  • 2017, 7th Hubei Congress of Plant Biology, 1st reporter award;

  • 2016, 2016 National Congress of Plant Biology, 3rd poster award;

  • 2016, National Scholarship for PhD. students;

Bibliography

#: Co-first authors; *: Correspondence

Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication

article sequencing pangenome single-cell domestication physiology
GUI SONGTAO, Martinez-Rivas Juan Felix, Wen Weiwei, Meng Minghui, Yan Jianbing, Usadel Björn, Fernie R. Alisdair
Publication year: 2022
The Plant Journal, n/a

A pan-Zea genome map for enhancing maize improvement

article Zea pan-genome structural variation GAB
GUI SONGTAO, Wei Wenjie, Chenglin Jiang, Luo Jingyun, Wu Shenshen, Li Wenqiang, Wang Yuebin, Li Shuyan, Yang Ning, Li Qing, Fernie R. Alisdair, Yan Jianbing*
Publication year: 2022
Genome Biology, 178, 23

Genome sequencing reveals evidence of adaptive variation in the genus Zea

article Zea WGS adaptation selection
Chen Lu#, Luo Jingyun#, Jin Minliang#, Yang Ning#*, Liu Xiangguo, Peng Yong, Li Wenqiang, Philips Alyssa, Cameron Brenda, Bernal Julio, Rubén Rellán-Álvarez, Sawers JH Ruairidh, Qing Liu, Yin Yuejia, Ye Xinnan, Yan Jiali, Zhang Qinghua, Zhang Xiaoting, Wu Shenshen, GUI SONGTAO, Wei Wenjie, Wang Yuebin, Luo Yun, Jiang Chengling, Deng Min, Jin Min, Jian Liumei, Yu Yanhui, Zhang Maolin, Yang Xiaohong, Hufford B. Matthew, Fernie R. Alisdair, Warburton L. Marilyn, Ross-Ibarra Jeffrey*, Yan Jianbing*
Publication year: 2022
Nature Genetics, 1-10

A Heavy Metal Transporter Gene ZmHMA3a Promises Safe Agricultural Production on Cadmium-Polluted Arable Land

article Zea GWAS Heavy metal ZmHMA3a
Chen Yuanyuan#, Chao Zhen-Fei#, Jin Min, Wang Ya-Ling, Li Yaoyao, Wu Jia-Chen, Xiao Yingjie, Peng Yong, Lv Qiao-Yan, GUI SONGTAO, Wang Xiaqing, Han Mei-Ling, Fernie R. Alisdair, Chao Dai-Yin*, Yan Jianbing*
Publication year: 2022
Journal of Genetics and Genomics, S1673852722002156

Three Types of Genes Underlying the Gametophyte Factor1 Locus Cause Unilateral Cross Incompatibility in Maize

article Zea Unilateral Cross Incompatibility ga1
Wang Yuebin#, Li Wenqiang#, Wang Luxi, Yan Jiali, Lu Gang, Yang Ning, Xu Jieting, Wang Yuqing, GUI SONGTAO, Chen Gengshen, Li Shuyan, Wu Chengxiu, Guo Tingting, Xiao Yingjie, Warburton L. Marilyn, Fernie R. Alisdair, Dresselhaus Thomas, Yan Jianbing*
Publication year: 2022
Nature Communications, 4498, 13

The Transcription Factor GATA10 Regulates Fertility Conversion of a Two‐line Hybrid Tms5 Mutant Rice via the Modulation of Ub_L40 Expression

article rice TF-GATA10 atac-seq
Jin Jing, GUI SONGTAO, Li Qian, Wang Ying, Zhang Hongyuan, Zhu Zhixuan, Chen Hao, Sun Yueyang, Zou Yu, Huang Xingguo, Ding Yi*
Publication year: 2020
Journal of Integrative Plant Biology, 1034--1056, 62

ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era

article maize database multi-omics Integration
GUI SONGTAO, Yang Linfeng, Li Jianbo, Luo Jingyun, Xu Xiaokai, Yuan Jianyu, Chen Lu, Li Wenqiang, Yang Xin, Wu Shenshen, Li Shuyan, Wang Yuebin, Zhu Yabing, Gao Qiang, Yang Ning, Yan Jianbing*
Publication year: 2020
iScience, 101241, 23

Genome Assembly of a Tropical Maize Inbred Line Provides Insights into Structural Variation and Crop Improvement

article maize genome assembly structural variation crop improvement
Yang Ning#, Liu Jie#, Gao Qiang#, GUI SONGTAO, Chen Lu, Yang Linfeng, Huang Juan, Deng Tianquan, Luo Jingyun, He Lijuan, Wang Yuebin, Xu Pengwei, Peng Yong, Shi Zhuoxing, Lan Liu, Ma Zhiyun, Yang Xin, Zhang Qianqian, Bai Mingzhou, Li San, Li Wenqiang, Liu Lei, Jackson David, Yan Jianbing*
Publication year: 2019
Nature Genetics, 1052--1059, 51

Improving Nelumbo Nucifera Genome Assemblies Using High‐resolution Genetic Maps and BioNano Genome Mapping Reveals Ancient Chromosome Rearrangements

article Nelumbo nucifera genetic map bionano ancient chromosome rearrangements
GUI SONGTAO, Peng Jing, Wang Xiaolei, Wu Zhihua, Cao Rui, Salse Jérôme, Zhang Hongyuan, Zhu Zhixuan, Xia Qiuju, Quan Zhiwu, Shu Liping, Ke Wedong, Ding Yi*
Publication year: 2018
The Plant Journal, 721--734, 94

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna Unguiculata

article RAD sequencing genetic map vigna unguiculata
Pan Lei, Wang Nian, Wu Zhihua, Guo Rui, Yu Xiaolu, Zheng Yu, Xia Qiuju, GUI SONGTAO, Chen Chanyou*
Publication year: 2017
Frontiers in Plant Science, 1544, 8

The NnCenH3 Protein and Centromeric DNA Sequence Profiles of Nelumbo Nucifera Gaertn. (Sacred Lotus) Reveal the DNA Structures and Dynamics of Centromeres in Basal Eudicots

article Nelumbo nucifera centromeric DNA centromeric protein
Zhu Zhixuan, GUI SONGTAO, Jin Jing, Yi Rong, Wu Zhihua, Qian Qian, Ding Yi*
Publication year: 2016
The Plant Journal, 568--582, 87

Development and Characterization of Polymorphic MicroRNA-Based Microsatellite Markers in Nelumbo Nucifera (Nelumbonaceae)

article Nelumbo nucifera microsatellite microRNA
Wang Xiaolei, GUI SONGTAO, Pan Lei, Hu Jihong, Ding Yi*
Publication year: 2016
Applications in Plant Sciences, 1500091, 4

The Mitochondrial Genome Map of Nelumbo Nucifera Reveals Ancient Evolutionary Features

article Nelumbo nucifera mitochondrial genome evolution
GUI SONGTAO#, Wu Zhihua#, Zhang Hongyuan, Zheng Yinzhen, Zhu Zhixuan, Liang Dequan, Ding Yi*
Publication year: 2016
Scientific Reports, 30158, 6

Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo Nucifera)

article Nelumbo nucifera WGS SSR SNP
Hu Jihong#, GUI SONGTAO#, Zhu Zhixuan, Wang Xiaolei, Ke Weidong, Ding Yi*
Publication year: 2015
PLOS ONE, e0143765, 10

A Precise Chloroplast Genome of Nelumbo Nucifera (Nelumbonaceae) Evaluated with Sanger, Illumina MiSeq, and PacBio RS II Sequencing Platforms: Insight into the Plastid Evolution of Basal Eudicots

article Nelumbo nucifera Evolutionary Chloroplast Genome Sanger Illumina MiSeq PacBio RS II
Wu Zhihua, GUI SONGTAO, Quan Zhiwu, Pan Lei, Wang Shuzhen, Ke Weidong, Liang Dequan, Ding Yi*
Publication year: 2014
BMC Plant Biology, 289, 14

Molecular Evolution and Functional Characterisation of an Ancient Phenylalanine Ammonia-Lyase Gene (NnPAL1) from Nelumbo Nucifera: Novel Insight into the Evolution of the PAL Family in Angiosperms

article Nelumbo nuciferaEvolutionaryNnPAL1
Wu Zhihua, GUI SONGTAO, Wang Shuzhen, Ding Yi*
Publication year: 2014
BMC Evolutionary Biology, 100, 14

Refer to Achievements for more.

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