Editing Efficiency Prediction

CRISPR与TnpB双系统的设计平台CRISPy-web

TnpB Editing Efficiency Predictor (TEEP): https://go.tnpb.app/

Protein Mutational Effect Predictor (ProMEP): https://github.com/wenjiegroup/ProMEP

EVOLVEpro: https://github.com/mat10d/EvolvePro

AiCE: High-fitness mutation prediction tool: https://github.com/ScorpioLea/AiCE

Bridge RNA Design Tool: https://arcinstitute.org/tools/bridge

CRISPR

CRISPR Integrated DNA Technologies | IDT

Chopchop: http://chopchop.cbu.uib.no/

CCTOP: CCTop – CRISPR/Cas9 target online predictor (uni-heidelberg.de)

CRISPR-CAS++ (paris-saclay.fr)

CRISPRone (indiana.edu)

CRISPRmap (uni-freiburg.de)

CRISPRDetect (otago.ac.nz)

CRISPRloci – CRISPR-Cas annotation (uni-freiburg.de)

crisprSQL – CRISPR off-target database

CRISPR RGEN Tools (rgenome.net)

https://chopchop.cbu.uib.no/

https://benchling.com/pub/c2c2

http://crispr-analyzer.dkfz.de/

http://www.e-crisp.org/E-CRISP/

http://crispresso.pinellolab.org/submission

http://guides.sanjanalab.org/#/

https://www.crisprindelphi.design/

Tools – brounslab

Addgene: CRISPR Plasmids and Resources

TALEN

Tools | TAL Effector Nucleotide Targeter 2.0 (cornell.edu)

http://www.e-talen.org/

Mojo Hand (talendesign.org)

TALENoffer – Jstacs

SAPTA TAL Targeter | Tools | tDnA (rice.edu)

ZNF

DeepZF

ZFNGenome

ZiF PREDICTION

Zibase

Zinc Finger Tools (scripps.edu)

The Zinc Finger Consortium | Software Tools (zincfingers.org)

GitHub – OrensteinLab/DeepZF

Predicting DNA Recognition – Main Menu (princeton.edu)

Mobilome Database

RepBase: https://www.girinst.org/repbase/update/index.html

Dfam: https://dfam.org/browse

ISfinder: https://www-is.biotoul.fr/index.php

AGODB: https://i.uestc.edu.cn/agodb/

GYDB: http://gydb.org/index.php/Collection_alignments

Tncentral: https://tncentral.ncc.unesp.br/TnPedia/index.php/Main_Page

mobileOG-db: https://mobileogdb.flsi.cloud.vt.edu/

TE hub: https://tehub.org/classification/telineages

MsReDB: https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html

FISHTEDB: https://www.fishtedb.com/

PlantRep: http://www.plantrep.cn/

ICEberg: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/index.php

Human RIP: http://dbrip.brocku.ca/

RICE RIP: http://ibi.zju.edu.cn/Rtrip/download.html#

L1 Database: l1base.charite.de

LINE-1 associated neurodegenerative disease gene therapy company: https://www.transposonrx.com/

Tn registry: https://transposon.lstmed.ac.uk/tn-registry

ERV: http://geve.med.u-tokai.ac.jp/

ERV: https://herv.img.cas.cz/

Using Transposons in the Lab:https://blog.addgene.org/plasmids-101-using-transposons-in-the-lab

Gene Engineering Services With TcBuster: https://www.bio-techne.com/services/gene-engineering-services

piggyBac: Wayback Machine (archive.org)

P element: P Elements in Drosophila

RNA

NONCODE

ncRNA databases

RNACentral

Rfam

rRNA

noncoRNA

cncRNAdb

non-coding RNA database resources

Bioinformatics Tools and Databases for Functional RNA Analysis

GtRNAdb

The Genetic Codes：https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Patented sequences search

BLASTP in NCBI: Patented protein sequences (pataa)

BLASTN in NCBI: Patent sequences (pat)

WIPO: 国际专利查询

Google patent

Zebrafish

Chengyi Song Lab

Danio-Code:Ferenc Muller

Society for Zebrafish Research

Protein Prediction

InterPro: InterProScan – InterPro

NCBI Conserved Domain Search: CD-Search: New Query

Biosequence analysis using profile hidden Markov Models: HMMER

Homology detection & structure prediction by HMM-HMM comparison/HHpred: Bioinformatics Toolkit

SMART: SMART: Main page

MOTIF: Searching Protein Sequence Motifs

AlphaFold Protein Structure Database: AlphaFold Protein Structure Database

3D structures from the Protein Data Bank (PDB): RCSB PDB: Homepage

CLANS: a Java application for visualizing protein families based on pairwise similarity

STRING: functional protein association networks

TE annotation

TEtrimmer-2024: https://github.com/qjiangzhao/TEtrimmer

TransposonUltimate-2022: software for transposon classification, annotation and detection

Earl Grey-2024: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

HiTE-2024: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation

RepBox-2023: a toolbox for the identification of repetitive elements

IRF-2025-updated: Inverted Repeats Finder

gt-tirvish – Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.

TSDfinder: The TSDfinder tool identifies TSDs plus non-LTR retrotransposon-driven transductions.

Gene/ORF and domain Prediction

Promoter: https://molbiol-tools.ca/Promoters.htm

GeneMark (Prokaryotic ): GeneMark gene prediction (gatech.edu)

Prodigal (Prokaryotic): Fast, reliable protein-coding gene prediction for prokaryotic genomes

Genscan: New GENSCAN Web Server at MIT

GetORF: EMBOSS: getorf (bioinformatics.nl)

ORFfinder: ORFfinder Home – NCBI (nih.gov)

Database

tRNA database: http://gtrnadb.ucsc.edu/index.html

Rfam: https://rfam.org/

xfam:http://pfam-legacy.xfam.org/

Ensemble: https://www.ensembl.org/index.html

Animal Genome Size: Animal Genome Size Database:: Home

Genome browse: https://www.ncbi.nlm.nih.gov/genome/browse

Galaxy: https://usegalaxy.org/?msclkid=038ffcd4b64211eca081527e1ddb66da

BARCH ENTREZ: https://www.ncbi.nlm.nih.gov/sites/batchentrez

Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/

EMBOSS: http://www.bioinformatics.nl/emboss-explorer/

CD-HIT: http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi

USEARCH： https://drive5.com/

SeqLogo: http://weblogo.berkeley.edu/logo.cgi

Tree

TimeTree: http://www.timetree.org/

TolTree: http://tolweb.org/tree/

Lifemap: http://lifemap-ncbi.univ-lyon1.fr/

RNA

RNA-Protein Interaction Prediction (RPISeq)

hybridRNAbind

RStrucFam

PredRBR

omiXcore: a web server for prediction of protein interactions with large RNA

Protein tools and server

DP-Bind: a web server for sequence-based prediction of DNA binding residues in DNA binding proteins

DNABIND: DNA Binding Protein prediction

TransBind TransBind Web Server

Protein-DNA binding specificity (TIR-DBD): DeepPBS

Expasy: Swiss Institute of Bioinformatics

STRING: a database of known and predicted protein-protein interactions

EVOLVE: Evolutionary Variation Observation Learning and Variant Exploration

Predict Zinc Binding

Zinc finger proteins (ZFP)

ZnF-Prot: Zinc finger motifs in proteome

DNA binding site predictor for Cys₂His₂ Zinc Finger Proteins: Predicting DNA Recognition

ZiF-predict

HADDOCK2.4：https://wenmr.science.uu.nl/haddock2.4/

DNA and RNA fold

RNAfold web server

DNA Folding Form

Internal Link

Storage: kodbox.mobilome.cn

ChatGPT 学术优化 (mobilome.cn)

Website: Mobilome Lab

一、博士及博士后研究方向

研究方向1：靶向DNA转座子挖掘及高效安全载体递送技术研发
主要开展靶向DNA转座子挖掘、活性转座子验证筛选、系统优化和转座酶定向进化，为人类基因治疗和生物转基因研究提一种安全高效的靶向非病毒载体递送系统，为实现较大基因片段在细胞基因组中的高效定点整合，破解制约众多基因治疗和基因组改造应用的关键瓶颈，释放其在生物转基因育种和基因治疗等应用方向巨大潜力提供技术积累。

研究方向2：转座子起源小分子靶向核酸酶挖掘及基因编辑工具开发
通过对原核生物基因组大数据挖掘，揭示IS605，IS607和IS1341转座子起源小分子核酸酶（TnpB和IscB）的系统进化和结构特征，筛选具有开发潜力的小分子核酸酶进行定向进化、分子重构，研发基因编辑效率高、靶向特异性强的新型基因编辑工具，为人类基因治疗和转基因生物育种提供更加安全高效的编辑系统。

研究方向3：基于猪基因组中活性逆转座子插入多态（RIP）为基础的分子标记研发、RIP液相芯片及育种应用评估
主要开展猪等家畜基因组转座子注释，逆转座子介导产生分子标记（也称为转座子插入多态RIP，Retrotransposon insertion polymorphism）规模挖掘及其遗传效应研究，RIP标记配套液相芯片研发及其在育种中的应用评估。

二、博士申请（硕博连读和申请考核）要求

参照学校和学院每年发布的当年申请要求，一般应达到以下要求：

硕博连读基本条件
（一）拥护中国共产党的领导，具有正确的政治方向，热爱祖国，愿意为社会主义现代化建设服务，遵纪守法，品行端正。无任何考试作弊、学术剽窃及其它违法违纪行为。
（二）身体和心理健康状况符合我校体检要求。按照教育部、卫生部、中国残联印发的《普通高等学校招生体检工作指导意见》（教学〔2003〕3号）、《教育部办公厅卫生部办公厅关于普通高等学校招生学生入学身体检查取消乙肝项目检测有关问题的通知》（教学厅〔2010〕2号）规定执行。
（三）英语水平。通过CET-4或具有一年及以上的国外留学经历。
（四）学分课（学术型、专业型分别排名）成绩排名年级前50%，且没有考试不及格的课程。
（五）在满足上述条件的前提下，英语通过CET-6，或近三年雅思（IELTS）成绩≥6.5分或托福（TOEFL）成绩≥85或GRE成绩≥260；或以第一作者发表SCI论文（需Online，截止日期12月31日）；或授权发明专利（排名前2名，截止日期12月31日）者，优先考虑。

申请考核基本要求
专业考核包括申请者科研成果、英语水平审核和面试考核。
（一）科研成果
1.以第一作者身份发表SCI收录论文1篇，或CSCD（核心库）收录论文1篇，或北大中文核心收录论文2篇；
2.在满足条件1的前提下，有授权发明专利（排名前2名）者优先。
（二）英语水平
英语水平达到以下条件之一：
1.提供以下至少一项英语考试的成绩证明，具体包括：国家CET-6成绩≥426分，或近三年雅思（IELTS）成绩≥6.5分或托福（TOEFL）成绩≥85（老TOEFL成绩≥560分）；
2.在英语国家或地区获得硕士学位；
3.具有一年及以上的英语国家国外留学经历；
4.发表SCI三区（中科院分区）以上（含三区）论文1篇，且国家CET-4成绩≥426分。

三、博士后招聘要求

1、具有博士学位，品学兼优，身体健康，年龄不超过35周岁。
2、获得博士学位年限不超过两年。
3、全职全时，不招收在职博士后。
4、专业背景（生物学、遗传学、发育生物学、细胞生物学、生物化学与分子生物学、生物物理学、生物信息学、动物遗传育种），熟悉哺乳动物细胞培养或者生物信息学分析优先考虑。
5、学术要求（以下两项需满足一项即可）：
（1）申请师资博士后需以第一作者在SCI期刊上发表论文至少2篇，且Top期刊研究论文1篇，或一区研究论文1篇。
（2）申请全职博士后需以第一作者在SCI期刊上发表研究论文2篇或二区以上研究论文1篇。
6、符合扬州大学博士后管理的规定

四、博士后应聘材料

1、个人简历，包括个人基本情况、学习工作经历、主要研究工作内容、博士在学期间发表的第一作者论著清单（SCI收录文章需注明影响因子）、获得的奖励情况。
2、博士学位证书、毕业证书（应届毕业生可于毕业后补发）。
3、博士论文全文PDF版（应届毕业生可于毕业后补发）。
4、博士在学期间发表的第一作者SCI收录论著全文。
5、两封专家推荐信（包括博士导师的推荐信）。
6、博士后工作期间研究设想。

五、待遇

1、博士的奖助学金参照学校和学院说明。

2、博士后按照扬州大学相关福利待遇规定执行，税前基本年薪25-30万元/年，详见学校博士后工作 (yzu.edu.cn)。
2、在享受学校相关待遇基础上，课题组将另提供与其业绩相称的年终绩效奖励。

六、应聘方式

1、招聘长期有效，有意向者，请将详细的个人简历（包括完整的学习工作经历及代表成果清单）以邮件形式发送，邮件主题注明“申请扬州大学转座子实验室博士后/博士”；
2、联系人：宋老师 Email：cysong@yzu.edu.cn

国外学术岗位招聘

Job in Bioloxy

https://professorpositions.com/n1388548

PEI, Germany:Prof./Dr Zoltan Ivics Research Division of Medical Biotechnology – Paul-Ehrlich-Institut (pei.de)

University of Birmingham, UK: Professor Ferenc Mueller – Institute of Cancer and Genomic Sciences – University of Birmingham

FNB, Germany: Prof./Dr Klaus Wimmers fbn-dummerstorf.de

Università di Messina, Italy: Prof. Enrico D’Alessandro unime.it

上海细胞治疗集团 shcell.com

先正达集团 Syngenta | China

其它国际知名基因和细胞治疗企业（目前无合作项目）

Tessera Therapeutics

药明康德 (wuxiapptec.com)

药明巨诺 (jwtherapeutics.com)

传奇生物 (legendbiotech.cn)

赛业生物 (cyagen.com)

Distribution of ITM

Distribution of pogo

Distribution of the well-defined familes of hAT

1）国家标准：沙乌头猪（GB/T 40157-2021），起草人：王宵燕、宋成义、朱慈根、潘雨来、唐慧娟、王勇、侯庆永、李平华、陈才、安亚龙、沈富林、陆雪林、徐忠惠、李何君、吴昊旻、张新生、沈东

2）团体标准：猪SINE逆转座子插入多态（RIP）分子标记遗传多样性检测技术规程（T/JASSSS 81-2023），2023-5-23发布，起草人：陈才、王宵燕、宋成义、高波、潘雨来、王勇、朱慈根
3）江苏省地方标准：沙乌头猪（DB32/T 3852-2020） ，起草人：宋成义、王宵燕、陈才、高波、朱慈根、潘雨来、王勇、唐慧娟、侯庆永、刘宗华、李平华
4）江苏省地方标准：姜曲海猪（DB32/T 1009—2006），起草人：宋成义、经荣斌、王宵燕、张金存、杨元清、王勇、侯庆永。
5）江苏省实验用小型猪：遗传质量控制，起草人： 高波、宋成义、王宵燕、陈才等。
6）江苏省地方标准：米猪，起草人： 王宵燕、宋成义、高波、陈才等。

1. RNA引导靶向核酸酶挖掘及其与转座酶融合的基因靶向整合技术研发，横向合作项目，2023.1-2025.1
2. 靶向基因递送系统TnpB关联转座子挖掘、优化及安全性评估（32271508），国家自然科学基金面上项目，2023.1-2026.12
3. 猪脂肪酸智能化快速精准表型测定技术研发（NK202211060209），国家种业振兴专项子项目，2022.6-2026.12
4. 猪全基因组选择RIP标记挖掘、液相芯片研发及其在苏姜猪育种中应用评估（JBGS〔2021〕028），江苏省种业振兴“揭榜挂帅”项目，2022.1-2026.12
5. 农业部国家级地方猪品种（沙乌头猪、米猪、淮猪）遗传材料采集制作专项（19190634），农业部,2019/01-2020/12
6. 转座子介导安全高效基因编辑技术研究（2018ZX08010-08B），国家转基因生物新品种培育重大专项重点项目，2018/01-2019/12；
7. 猪蛋白编码基因内SINE转座子插入多态位点鉴定及其对基因活性和表型的影响（31872977），国家自然科学基金面上项目，2019/01-2022/12
8. 猪基因组中活性转座子的插入多态鉴定及重要经济性状分子标记筛选（31572364），国家自然科学基金面上项目，2016/01-2019/12
9. 猪蛋白编码基因3”UTR区SINE转座子插入多态位点的遗传效应研究（32002146），国家自然科学基金青年基金，2021.1-2023.12
10. 3”UTR区SINE多态对基因活性的影响（2020M671630），中国博士后科学基金面上项目，2020.7-2021.7
11. 转座子介导斑马鱼精子插入突变体库构建及超级增强子分离鉴定（31671313），国家自然科学基金面上项目，2017/01-2020/12
12. 转座子介导克隆及分析鸡胚早期心脏发育相关基因（31200920），国家自然科学基金青年基金项目，2013/01-2015/12
13. 猪精子RNA的起源机制、消亡规律及其早期胚胎发育调控功能研究（31272406），国家自然科学基金面上项目，2013/01-2016/12
14. 优质抗病苏姜猪新品种产业化及持续育种能力建设，国家发展改革委员会生物育种能力建设和产业化专项（[2014]2573），2014/01-2017/12
15. 猪基因定点敲除与RNA靶向干扰研究（2009ZX08010-019B），国家转基因生物新品种培育重点项目子项目，2009/01-2010/12
16. 以转座子多态为基础的猪分子育种关键技术创新及应用，项目编号CX(19)2016），江苏省农业科技自主创新资金项目， 2019.07-2022.06
17. 利用转基因技术创制梅山医用小型猪（BY2013063-03），江苏省产学研联合创新资金–前瞻性联合研究项目，2013/06-2016/12
18. SB转座子甲基化修饰在猪基因组上促转座作用研究（201104168），中国博士后科学基金特别资助项目，2011/10-2013/12
19. 睡美人（SB）转座子在制备转基因猪中的应用（20100480371），中国博士后科学基金项目，2010/10-2013/12。
20. 转座子载体法建立转基因鸡输卵生物反应器技术体系（BK2007555），江苏省自然科学基金项目，2007/06-2009/12。

授权专利

1. 一种基于比较基因组学的转座子插入多态TIP分子标记的挖掘方法，ZL201910384029.7，授权时间：2023.7.28，发明人：陈才、宋成义、王宵燕、高波、沈丹、王赛赛、王亚丽、李奎，专利权人：扬州大学
2. 一种与猪背膘厚关联的GHR基因内SINE转座子多态分子标记检测方法及应用，专利号：ZL201910409360.X，授权时间：2022.6.14，发明人：陈才、宋成义、王宵燕、高波、沈丹、王赛赛、王亚丽、李奎，专利权人：扬州大学
3. 一个与猪背膘厚关联的ZNF2 基因内SINE 转座子多态分子标记及其检测方法，授权专利号：ZL202010690558.2，授权公告日：2022.7.17，发明人：宋成义、顾浩、陈才、高波、王宵燕、李奎，专利权人：扬州大学
4. 一种与猪生长速度关联的SINE转座子多态分子标记及其检测方法和应用，专利号： ZL202011057170.5,授权公告日：2022.7.12，发明人：王宵燕、迟诚林、陈才、宋成义、高波、李奎，专利权人：扬州大学
5. 一种提高猪生长速度的连锁分子标记、其检测方法及应用，专利号：ZL202010629476.7,授权公告日：2022.7.15，发明人：王宵燕、安亚龙、陈才、宋成义、高波、李奎、陈子璇、迟诚林，专利权人：扬州大学
6. 一种PS转座子系统及其介导的基因转移方法，授权专利号：ZL201910366530.0，授权公告日：2022.7.15，发明人：宋成义、王赛赛、高波、宗文成、沈丹、王亚丽、产舒恒、桑亚通，专利权人：扬州大学
7. 一种基于猪SINE转座子插入多态性研发新型分子标记的方法，授权专利号：ZL201710928980.5，授权公告日：2020.7.3，发明人：宋成义、陈才、王伟、杨昆仑、张丽、沈丹、王赛赛、王宵燕、高波，专利权人：扬州大学
8. 一种基于猪LINE1转座子插入多态性研发新型分子标记的方法，授权专利号：ZL201710928978.8，授权公告日：2020年2月14日，发明人：宋成义、陈才、王伟、杨昆仑、张丽、沈丹、王赛赛、王宵燕、高波、赵旭庭、周春宝、陶勇、倪黎纲，专利权人：扬州大学
9. 一种基于LINE1转座子与微卫星引物相结合的猪基因组分子标记挖掘方法，授权专利号：ZL201810068583.X，授权公告日：2020年2月7日，发明人：宋成义、王伟、陈才、张丽、沈丹、王赛赛、王宵燕、高波，专利权人：扬州大学
10. 一种基于猪ERV转座子插入多态性研发新型分子标记的方法，授权专利号：ZL201710928987.7，授权公告日：2020年6月2日，发明人：宋成义、王伟、陈才、杨昆仑、张丽、沈丹、王赛赛、王宵燕、高波，专利权人：扬州大学
11. 一种ZB转座子系统及其介导的基因转移方法，授权专利号：ZL201510429987.3，授权公告日：2019年5月7日，发明人：高波、沈丹、宋成义、钱跃、薛松磊、王赛赛，专利权人：扬州大学
12. 一种转基因动物的制备方法，授权专利号：ZL200810123956.5，授权公告日：2010年12月22日，发明人：宋成义、高波、谢飞、王宵燕、陈国宏、孙丽亚、赵芹、吴晗，专利权人：扬州大学
13. 一种基因免疫方法，授权专利号：ZL200810123602.0，授权公告日：2010年8月18日，发明人：宋成义、高波、谢飞、王宵燕、陈国宏、孙丽亚、赵芹、吴晗，专利权人：扬州大学
14. 一种苏姜猪品种的培育方法，授权专利号：ZL201010178093.9，授权公告日：2012.07.25，发明人：经荣斌、宋成义、王霄燕、张金存、胡在朝，专利权人：扬州大学

申请专利

1. 一种Buster转座子系统及其应用，申请日：2024.6.12，申请号：2024107525095，发明人：宋成义、关中夏、高波、王冰清、石莎莎
2. 一种Spy转座子系统及其介导的基因转移方法，申请日：2024.1.30，申请号：20241012462067，发明人：宋成义、Mohamed Diaby（中文名：莫哈迪；国籍：科特迪瓦）、高波、石莎莎、王冰清、吴晗

Selected

1. Wang S, Zhang P, Sun Y, Fang Y, Wang P, Shao M, Zhang N, Shi S, Chen X, Gao H, Cheng J, Gao B, Liu T, Qian Q, Song C. Engineering of BZ transposase and transposon donor vector for enhanced efficiency and safety in gene delivery applications. Nucleic Acids Res. 2025 Sep 23;53(18):gkaf935. https://academic.oup.com/nar/article/53/18/gkaf935/8262245.
2. Diaby, M., Wu, H., Gao, B., Shi, S., Wang, B., Wang, S., Wang, Y., Wu, Z., Chen, C., Wang, X., & Song, C*. (2024). A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool. Advanced science, e2400969. https://doi.org/10.1002/advs.202400969
3. SONG, C. and IVICS, Z. (2024). Transposable Elements as Tools. In Transposable Elements and Genome Evolution (eds A. Hua-Van and P. Capy). https://doi.org/10.1002/9781394312467.ch10
4. Saisai Wang, Bo Gao, Csaba Miskey, Zhongxia Guan, Yatong Sang, Cai Chen, Xiaoyan Wang, Zoltán Ivics, Chengyi Song*, Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool, Nucleic Acids Research, 2023;, gkad005, https://doi.org/10.1093/nar/gkad005
5. Dan Shen, Chengyi Song, Csaba Miskey, Shuheng Chan, Zhongxia Guan, Yatong Sang, Yali Wang, Cai Chen, Xiaoyan Wang, Ferenc Müller, Zoltán Ivics, Bo Gao* , A native, highly active Tc1/mariner transposon from zebrafish (ZB) offers an efficient genetic manipulation tool for vertebrates, Nucleic Acids Research, 2021 Feb 26;49(4):2126-2140. https://doi.org/10.1093/nar/gkab045.

2026

1. Genome-Wide Identification of SINE‑RIPs in Rabbits and Their Utility for Population Genetic Analysis, submission
2. Development and evaluation of a pig 51K SINE retrotransposon insertion polymorphism chip, in review
3. TypeSINE: a scalable method for genome-wide SINE insertion polymorphism analysis across species, applied to porcine evolution and trait mapping, in revising
4. Leucine-Zipper Fusion with JL Transposase Enables Hyperactive Gene Integration and Rapid CAR-T Cell Production, in revision
5. A comprehensive map of the bovine mobilome and their epigenetic regulation of mastitis, in press
6. Mining and Engineering of Active PB Transposons in Hymenoptera, in press
7. Chen, H.; Shi, S.; Xiang, K.; Wang, Q.; Yang, N.; Gao, B.; Song, C. Divergent Evolutionary Profile of MULE Transposons in Arthropods. Animals 2026, 16, 2011. https://doi.org/10.3390/ani16132011
8. Guan Z, Wang B, Gao B, Shi S, Wang S, Wu H, Diaby M, Chen C, Wang X, Song C. Multiple Buster transposons from hAT superfamily displaying transposition activities in mammal cells. Synth Syst Biotechnol. 2025 Nov 4;11:397-406. doi: 10.1016/j.synbio.2025.10.006. PMID: 41280276; PMCID: PMC12637253.
9. Addy GA, Wang Q, Chen H, Abdu W, Diaby M, Chen X, Asare E, Gao B, Song C. Evolution of Mutator transposons in the genomes of worms. Gene. 2026 Jan 10;975:149855. doi: 10.1016/j.gene.2025.149855. Epub 2025 Oct 30. PMID: 41173222.
10. Zheng Y, Shi S, Yang N, Zhou C, Zhou R, Gan H, Gu Z, Zuo S, Chen C, Wang X, Song C. Classification of SINE Tails in the Porcine Genome and Its Potential Impact on VWA8 Gene. Genes (Basel). 2026 Feb 7;17(2):200. doi: 10.3390/genes17020200. PMID: 41751584; PMCID: PMC12941198.

2025

1. Wang S, Zhang P, Sun Y, Fang Y, Wang P, Shao M, Zhang N, Shi S, Chen X, Gao H, Cheng J, Gao B, Liu T, Qian Q, Song C. Engineering of BZ transposase and transposon donor vector for enhanced efficiency and safety in gene delivery applications. Nucleic Acids Res. 2025 Sep 23;53(18):gkaf935. doi: 10.1093/nar/gkaf935.
2. Zishuai Wang, Zixin Li, Tao Huang, Jianhai Chen, Pan Xu, Ruimin Qiao, Hongwei Yin, Chengyi Song, Dongjie Zhang, Di Liu, Shuhong Zhao, Martien A.M. Groenen, Ole Madsen, Yanlin Zhang, Lijing Bai, Kui Li, Genomic insights into the demographic history and local adaptation of wild boars across Eurasia, Cell Genomics, 2025, https://doi.org/10.1016/j.xgen.2025.100954.
3. Ahmed A. Saleh, Naisu Yang, Amr M.A. Rashad, Nada N.A.M. Hassanine, Ali Shoaib Moawad, Bo Gao, Chengyi Song, Evolution of endogenous retroviruses (ERVs) in the Bovinae subfamily, Gene, Volume 965, 2025, 149663, https://doi.org/10.1016/j.gene.2025.149663.
4. Zong, W., Chen, L., Zhang, D., Zhang, Y., Wang, J., Hou, X., Chai, J., An, Y., Tian, M., He, X., Song, C., He, J., Liu, X., Wang, L., D’Alessandro, E., Wang, L., Yin, Y., Li, M., Liu, D., Wang, J., … Zhang, L. (2025). Two telomere-to-telomere pig genome assemblies and pan-genome analyses provide insights into genomic structural landscape and genetic adaptations. iMeta, 4(2), e70013. https://doi.org/10.1002/imt2.70013
5. Cai Chen, Mengli Wang, Yao Zheng, Ziyan Liu, Phiri Azele, Ahmed A. Saleh, Xiaoyan Wang & Chengyi Song. A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript. J Appl Genetics (2025). https://doi.org/10.1007/s13353-024-00933-5
6. Saleh, A. A., Moawad, A. S., Yang, N., Zheng, Y., Chen, C., Wang, X., Gao, B., & Song, C. (2025). Association of a 7.9 kb Endogenous Retrovirus Insertion in Intron 1 of CD36 with Obesity and Fat Measurements in Sheep. Mobile DNA, 16(1), 12. https://doi.org/10.1186/s13100-025-00349-w
7. Wang Xiaoyan , Zhou Chenyu , Zheng Yao , Yu Miao , He Jia , Chen Cai , Qiao Suwei , Moawad Ali Shoaib , Tian Guoxing , Li Bixia , Song Chengyi. Population structure and genetic diversity of Mi pigs based on SINE-RIPs, Frontiers in Veterinary Science, Volume 12 – 2025, https://doi.org/10.3389/fvets.2025.1500115
8. Wang Q, Shi S, Wang B, Chen X, Yang N, Gao B, Song C. Evolution Landscape of PiggyBac (PB) Transposon in Beetles (Coleoptera). Genes (Basel). 2025 Dec 18;16(12):1521. doi: 10.3390/genes16121521. PMID: 41465194; PMCID: PMC12732532.
9. Zhou C, Qiao S, Zheng Y, Yu M, Chen H, Chen C, Moawad AS, Gao B, Song C, Wang X. Impact of the 294 bp SINE Insertion in 5’UTR of the GLYATL3 Gene on Gene Expression and Phenotypic Variation. Animals (Basel). 2025 May 9;15(10):1375. doi: 10.3390/ani15101375. PMID: 40427253; PMCID: PMC12108459.
10. Saleh A, Yang N, Wang F, Rashad A, Moawad A, Chen C, Wang X, Gao B, Song C. Mining and identification of solitary long terminal repeat (Solo-LTR) presence polymorphisms in the sheep genomes. Genome. 2025 Jan 1;68:1-16. doi: 10.1139/gen-2025-0012. PMID: 41213126.

2024

1. SONG, C. and IVICS, Z. (2024). Transposable Elements as Tools. In Transposable Elements and Genome Evolution (eds A. Hua-Van and P. Capy). https://doi.org/10.1002/9781394312467.ch10
2. Diaby, M., Wu, H., Gao, B., Shi, S., Wang, B., Wang, S., Wang, Y., Wu, Z., Chen, C., Wang, X., & Song, C*. (2024). A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool. Advanced science, e2400969. https://doi.org/10.1002/advs.202400969
3. Wencheng Zong, Runze Zhao, Xiaoyan Wang, Chenyu Zhou, Jinbu Wang, Cai Chen, Naiqi Niu, Yao Zheng, Li Chen, Xin Liu, Xinhua Hou, Fuping Zhao, Ligang Wang, Lixian Wang*, Chengyi Song*, Longchao Zhang*, Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig, DNA Research, 2024;, dsae008, https://doi.org/10.1093/dnares/dsae008
4. Moawad, Ali Shoaib, Fengxu Wang, Yao Zheng, Cai Chen, Ahmed A. Saleh, Jian Hou, and Chengyi Song*. 2024. Evolution of Endogenous Retroviruses in the Subfamily of Caprinae. Viruses 16, no. 3: 398. https://doi.org/10.3390/v16030398
5. Guo, Mengke, George A. Addy, Naisu Yang, Emmanuel Asare, Han Wu, Ahmed A. Saleh, Shasha Shi, Bo Gao, and Chengyi Song*. 2024. PiggyBac Transposon Mining in the Small Genomes of Animals. Biology 13, no. 1: 24. https://doi.org/10.3390/biology13010024
6. Saisai Wang, Zhongxia Guan, Mohamed Diaby, Emmanuel Asare, Numan Ullah, Wenzhu Jia, Bo Gao, Duonan Yu, Chengyi Song*, Evolution of Skipper (SK), a family of DD34E/Tc1 transposons, in animals, Biological Journal of the Linnean Society, 2023;, blad141, https://doi.org/10.1093/biolinnean/blad141.
7. Du, Zhanyu, Cai Chen, Yao Zheng, Xiaoyan Wang, and Chengyi Song. 2024. Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes. Animals 14, no. 4: 621. https://doi.org/10.3390/ani14040621
8. 5) Wang, Bingqing, Ahmed A. Saleh, Naisu Yang, Emmanuel Asare, Hong Chen, Quan Wang, Cai Chen, Chengyi Song, and Bo Gao*. 2024. High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes. Animals 14, no. 10: 1425. https://doi.org/10.3390/ani14101425
9. Book: Livestock Genome Editing Tools, 3. Associated technologies for genome editing, 2024, ISBN: 978-0-12-819099-9 https://doi.org/10.1016/C2018-0-04416-3
10. Moawad, Ali Shoaib, Fengxu Wang, Yao Zheng, Cai Chen, Ahmed A. Saleh, Jian Hou, and Chengyi Song*. 2024. Evolution of Endogenous Retroviruses in the Subfamily of Caprinae. Viruses 16, no. 3: 398. https://doi.org/10.3390/v16030398
11. Chen, Cai, Zhanyu Du, Yao Zheng, Hong Chen, Ahmed A. Saleh, Naisu Yang, Mengli Wang, Phiri Azele, Xiaoyan Wang, and Chengyi Song*. 2024. Investigation of Polymorphisms Induced by the Solo Long Terminal Repeats (Solo-LTRs) in Porcine Endogenous Retroviruses (ERVs). Viruses 16, no. 11: 1801. https://doi.org/10.3390/v16111801

2023

1. Saisai Wang, Bo Gao, Csaba Miskey, Zhongxia Guan, Yatong Sang, Cai Chen, Xiaoyan Wang, Zoltán Ivics, Chengyi Song*, Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool, Nucleic Acids Research, 2023;, gkad005, https://doi.org/10.1093/nar/gkad005
2. Hao Gu, Zhan-yu Du, Eduard Murani, Enrico D’Alessandro, Cai Chen, Xiao-yan Wang, Jiu-de Mao, Klaus Wimmers, Chengyi Song*, A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs, Journal of Integrative Agriculture, Volume 22, Issue 2, 2023, Pages 526-536, ISSN 2095-3119, https://doi.org/10.1016/j.jia.2022.08.128.
3. Li, Xueyuan, Zhongxia Guan, Feng Wang, Yali Wang, Emmanuel Asare, Shasha Shi, Zheguang Lin, Ting Ji, Bo Gao, and Chengyi Song*. 2023. Evolution of piggyBac Transposons in Apoidea. Insects 14, no. 4: 402. https://doi.org/10.3390/insects14040402
4. Wang, Yali, Mengke Guo, Naisu Yang, Zhongxia Guan, Han Wu, Numan Ullah, Emmanuel Asare, Shasha Shi, Bo Gao, and Chengyi Song*. 2023. Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes 14, no. 2: 523. https://doi.org/10.3390/genes14020523
5. Zheng, Yao, Cai Chen, Mengli Wang, Ali Shoaib Moawad, Xiaoyan Wang, and Chengyi Song*. 2023. SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation. Animals 13, no. 12: 1942. https://doi.org/10.3390/ani13121942
6. Xiang, Kuilin, Mikhail Puzakov, Shasha Shi, Mohamed Diaby, Numan Ullah, Bo Gao, and Chengyi Song*. 2023. Mosquito (MS), a DD37E Family of Tc1/Mariner, Displaying a Distinct Evolution Profile from DD37E/TRT and DD37E/L18. Genes 14, no. 7: 1379. https://doi.org/10.3390/genes14071379
7. Shasha Shi, Mikhail V. Puzakov, Ludmila V. Puzakova, Yulia N. Ulupova, Kuilin Xiang, Binqing Wang, Bo Gao, Chengyi Song*,  Hiker, a new family of DNA transposons encoding transposases with DD35E motifs, displays a distinct phylogenetic relationship with most known DNA transposon families of IS630-Tc1-mariner (ITm),  Molecular Phylogenetics and Evolution, 2023 Aug 14:107906. https://doi.org/10.1016/j.ympev.2023.107906.
8. Ullah, Numan, Naisu Yang, Zhongxia Guan, Kuilin Xiang, Yali Wang, Mohamed Diaby, Cai Chen, Bo Gao, and Chengyi Song*. Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea. Genes. 2023; 14(10):1911. https://doi.org/10.3390/genes14101911.
9. He, Jia, Miao Yu, Chenglin Chi, Zhanyu Du, Yao Zheng, Cai Chen, Ali Shoaib Moawad, Chengyi Song, and Xiaoyan Wang*. 2023. Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs. Animals 13, no. http://14: 2355. https://doi.org/10.3390/ani13142355

2022

1. Jia, Wenzhu, Emmanuel Asare, Tao Liu, Pingjing Zhang, Yali Wang, Saisai Wang, Dan Shen, Csaba Miskey, Bo Gao, Zoltán Ivics, Qijun Qian, and Chengyi Song*. 2022. Horizontal Transfer and Evolutionary Profiles of Two Tc1/DD34E Transposons (ZB and SB) in Vertebrates. Genes 13, no. 12: 2239. https://doi.org/10.3390/genes13122239
2. Chi, Chenglin, Jia He, Zhanyu Du, Yao Zheng, Enrico D’Alessandro, Cai Chen, Ali Shoaib Moawad, Emmanuel Asare, Chengyi Song, and Xiaoyan Wang*. 2022. Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation. Life 12, no. 10: 1650. https://doi.org/10.3390/life12101650
3. Wang, Xiaoyan, Chengling Chi, Jia He, Zhanyu Du, Yao Zheng, Enrico D’Alessandro, Cai Chen, Ali Shoaib Moawad, Emmanuel Asare, and Chengyi Song*. 2022. SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits. Genes 13, no. 8: 1422. https://doi.org/10.3390/genes13081422.
4. Du, Zhanyu, Enrico D’Alessandro, Emmanuel Asare, Yao Zheng, Mengli Wang, Cai Chen, Xiaoyan Wang, and Chengyi Song*. 2022. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes. Genes 13, no. 8: 1359. https://doi.org/10.3390/genes13081359
5. Mohamed Diaby, Zhongxia Guan, Shasha Shi, Yatong Sang, Saisai Wang, Yali Wang, Wencheng Zong, Numan Ullah, Bo Gao, and Chengyi Song*. 2022. Revisiting the Tigger Transposon Evolution Revealing Extensive Involvement in the Shaping of Mammal Genomes. Biology 11, no. 6: 921. https://doi.org/10.3390/biology11060921.
6. Jia, Wenzhu, Zhongxia Guan, ShaSha Shi, Kuilin Xiang, Peihong Chen, Fen Tan, Numan Ullah, Mohamed Diaby, Mengke Guo, Chengyi Song, and Bo Gao*. 2022. The Annotation of Zebrafish Enhancer Trap Lines Generated with PB Transposon. Current Issues in Molecular Biology 44, no. 6: 2614-2621. https://doi.org/10.3390/cimb44060178.
7. Zhongxia Guan, Shasha Shi, Mohamed Diaby, Patrick Danley, Numan Ullah, Mikhail Puzakov, Bo Gao, Chengyi Song*, Horizontal transfer of Buster transposons across multiple phyla and classes of animals, Molecular Phylogenetics and Evolution, 2022, 173:107506, https://doi.org/10.1016/j.ympev.2022.107506.
8. Wang, Xiaoyan, Enrico D’Alessandro, Chenglin Chi, Ali S. Moawad, Wencheng Zong, Cai Chen, and Chengyi Song*. Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms. Animals, 2022, 12, no. 11: 1345. https://doi.org/10.3390/ani12111345.
9. Zhanyu Du, Enrico D’Alessandro, Yao Zheng, Mengli Wang, Cai Chen, Xiaoyan Wang, Chengyi Song*. Retrotransposon insertion polymorphisms (RIPs) in pig coat color candidate genes. Animals, 2022, 12, no. 8: 969. https://doi.org/10.3390/ani12080969.

2021

1. Shasha Shi, Mikhail Puzakov, Zhongxia Guan, Kuilin Xiang, Mohamed Diaby, Yali Wang, Saisai Wang, Chengyi Song, and Bo Gao*. 2021. Prokaryotic and Eukaryotic Horizontal Transfer of Sailor (DD82E), a New Superfamily of IS630-Tc1-Mariner DNA Transposons. Biology 10, no. 10: 1005. https://doi.org/10.3390/biology10101005
2. Liu, Yibing, Wencheng Zong, Mohamed Diaby, Zheguang Lin, Saisai Wang, Bo Gao, Ting Ji, and Chengyi Song*. 2021. Diversity and Evolution of pogo and Tc1/mariner Transposons in the Apoidea Genomes. Biology 10, no. 9: 940. https://doi.org/10.3390/biology10090940
3. Yali Wang, Dan Shen, Numan Ullah, Mohamed Diaby, Bo Gao, Chengyi Song*. Characterization and expression pattern of ZB and PS transposons in zebrafish. Gene Expr Patterns. 2021 Sep 1;42:119203. https://doi.org/10.1016/j.gep.2021.119203.
4. Wang X, Chen Z, Murani E, D’Alessandro E, An Y, Chen C, Li K, Galeano G, Wimmers K, Song C*. A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1. Mobile DNA. 2021 Aug 18;12(1):20. https://doi.org/10.1186/s13100-021-00248-w.
5. Naisu Yang, Bohao Zhao, Yang Chen, Enrico D’Alessandro, Cai Chen, Ting Ji, Xinsheng Wu, Chengyi Song*, Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus), Genome Biology and Evolution, Volume 13, Issue 8, August 2021, evab168, https://doi.org/10.1093/gbe/evab168
6. Cai Chen, Enrico D’Alessandro, Eduard Murani, Yao Zheng, Domenico Giosa, Naisu Yang, Xiaoyan Wang, Bo Gao, Kui Li, Klaus Wimmers & Chengyi Song*. SINE jumping contributes to large-scale polymorphisms in the pig genomes. Mobile DNA, 2021 Jun 28;12(1):17. https://doi.org/10.1186/s13100-021-00246-y.
7. Chen, Cai, Yao Zheng, Mengli Wang, Eduard Murani, Enrico D’Alessandro, Ali S. Moawad, Xiaoyan Wang, Klaus Wimmers, and Chengyi Song* . SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor. Animals. 2021 Jun 23;11(7):1871. https://doi.org/10.3390/ani11071871.
8. Chen, Cai, Xiaoyan Wang, Wencheng Zong, Enrico D’Alessandro, Domenico Giosa, Yafen Guo, Jiude Mao, and Chengyi Song* . Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. Animals. 2021 Apr 15;11(4):1136. https://doi.org/10.3390/ani11041136.
9. Saisai Wang, Mohamed Diaby, Mikhail Puzakov, Numan Ullah, Yali Wang, Patrick Danley, Cai Chen, Xiaoyan Wang, Bo Gao, Chengyi Song*, Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes, Molecular Phylogenetics and Evolution, 2021 Mar 10:107143. https://doi.org/10.1016/j.ympev.2021.107143.
10. Dan Shen, Chengyi Song, Csaba Miskey, Shuheng Chan, Zhongxia Guan, Yatong Sang, Yali Wang, Cai Chen, Xiaoyan Wang, Ferenc Müller, Zoltán Ivics, Bo Gao* , A native, highly active Tc1/mariner transposon from zebrafish (ZB) offers an efficient genetic manipulation tool for vertebrates, Nucleic Acids Research, 2021 Feb 26;49(4):2126-2140. https://doi.org/10.1093/nar/gkab045.

2020

1. Bo Gao; Wencheng Zong; Csaba Miskey; Numan Ullah; Mohamed Diaby; Cai Chen; Xiaoyan Wang; Zoltán Ivics; Chengyi Song*. Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. Mobile DNA, 2020 Dec 10;11(1):32. https://doi.org/10.1186/s13100-020-00227-7
2. Bo Gao, Yali Wang, Mohamed Diaby, Wenchen Zong, Dan Shen, Saisai Wang, Cai Chen, Xiaoyan Wang, Chengyi Song*. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. Mobile DNA, 2020 Jul 22;11:25. https://doi.org/10.1186/s13100-020-00220-0
3. Bo Gao, Yatong Sang, Wencheng Zong, Mohamed Diaby, Dan Shen, Saisai Wang, Yali Wang, Cai Chen, Chengyi Song*. Evolution and Domestication of Tc1/mariner transposons in the African coelacanth (Latimeria chalumnae) genome. Genome, 2020 Aug;63(8):375-386. https://doi.org/10.1139/gen-2019-0216.
4. Dan Shen, Bo Gao, Csaba Miskey, Cai Chen, Yatong Sang, Wencheng Zong, Saisai Wang, Yali Wang, Xiaoyan Wang, Zoltán Ivics, Chengyi Song*, Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates, Genome Biology and Evolution, 2020 Jul 1;12(7):1060-1073. https://doi.org/10.1093/gbe/evaa135
5. Wencheng Zong, Bo Gao, Mohamed Diaby, Dan Shen, Saisai Wang, Yali Wang, Yatong Sang, Cai Chen, Xiaoyan Wang, Chengyi Song*. Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently. Genome Biology and Evolution, 2020 Mar 1;12(3):66-76. https://doi.org/10.1093/gbe/evaa034. 

2019 and before

1. Yatong Sang, Bo Gao, Mohamed Diaby, Wencheng Zong, Cai Chen, Dan Shen, Saisai Wang, Yali Wang, Zoltán Ivics & Chengyi Song*. Incomer, a DD36E family of Tc1/mariner transposons newly discovered in animals. Mobile DNA, 2019 Nov 23;10:45. https://doi.org/10.1186/s13100-019-0188-x.
2. S. Wang, Y. Wang, D. Shen, L. Zhang, W. Chen, S. Chan, Z. Guan, C. Song & B. Gao*. ZB transposon and chicken vasa homologue (Cvh) promoter interact to increase transfection efficiency of primordial germ cells in vivo, British Poultry Science, 2019 Dec;60(6):724-728.  https://doi.org/10.1080/00071668.2019.1639138.
3. Cai Chen, Wei Wang, Xiaoyan Wang, Dan Shen, Saisai Wang, Yali Wang, Bo Gao, Klaus Wimmers, Jiude Mao, Kui Li & Chengyi Song*. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mobile DNA. 2019 May 6;10:19. https://doi.org/10.1186/s13100-019-0161-8.     
4. Dan Shen, Songlei Xue, Shuheng Chan, Yatong Sang, Saisai Wang, Yali Wang, Cai Chen, Bo Gao, Ferenc Mueller, Chengyi Song*. Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes. 2018 Dec 13;9(12):630. https://doi.org/10.3390/genes9120630.
5. Bo Gao, Saisai Wang, Yali Wang, Dan Shen, Songlei Xue, Cai Chen, Hengmi Cui & Chengyi Song*. Low diversity, activity, and density of transposable elements in five avian genomes. Functional & Integrative Genomics. 2017 Jul;17(4):427-439. https://doi.org/10.1007/s10142-017-0545-0. 
6. Bo Gao; Dan Shen; Songlei Xue; Cai Chen; Hengmi Cui; Chengyi Song*. The contribution of transposable elements to size variations between four teleost genomes, Mobile DNA. 2016 Feb 9;7:4. https://doi.org/10.1186/s13100-016-0059-7.
7. 桑亚通，沈丹，陈伟，产舒恒，顾浩，高波，宋成义*，Tol2转座子介导斑马鱼rps26基因附近增强子捕获及注解分析，生物工程学报，2018，34(3)：449-458
8. 沈丹，陈才，王赛赛，陈伟，高波，宋成义*，Tc1_Mariner转座子超家族的研究进展，遗传，2017, 39(1)：1-13
9. 谢飞，高波，宋成义*，陈国宏，“睡美人”转座子的研究进展，遗传，2007，29（7）：785-792