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GETORGANELLE

1/1/2021

This pipeline assemblies organelle genome from genomic skimming data with an input reference, which should be the same organelle genome sequences but not necessarily a related species within the focal clade.

Citation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Ting-Shuang Yi, De-Zhu Li (2018). GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. bioRxiv, 256479. http://doi.org/10.1101/256479 （*, Equal contributors）

How to get it: https://github.com/Kinggerm/GetOrganelle

You can also download the latest version here:

getorganelle-1.4.4b.tar.gz
File Size:	602 kb
File Type:	gz

If you want to know how to use Bandage to view and edit the FASTG file, please click HERE to watch the videos in Youtube, or HERE in Tencent.

Open positions -- in chinese

12/1/2019

生物多样性研究组岗位招聘启事

中国科学院西双版纳热带植物园生物多样性研究组是由中组部千人计划、热带植物生态学家Richard Corlett 研究员领导的国际研究团队，主要从事热带、亚热带植物多样性保护生物学研究。因科研需要，现面向社会公开招聘对中国热带及亚热带、东南亚植物多样性及其保护研究感兴趣的科研人员。欢迎各位符合条件者竞聘。
一、招聘岗位和工作地点
1. 副研究员岗位：1人
2. 助理研究员岗位：1人
3. 博士后：1-2人
工作地点：云南省勐腊县勐仑镇。
二、研究方向
植物领域的相关研究方向：生态学、保护生物学、植物分类学、民族植物学、系统发育学、种群遗传学、气候变化生物学、传粉生物学、迁地保护、保护策略研究，以及植物教育等，致力于研究和保护区域的植物多样性。
三、应聘条件
1. 热爱科研工作，治学严谨，学风正派，具有良好的合作意识、团队精神和沟通能力；具有很好的中英文听、说、读、写能力。
2. 应聘副研究员岗位，年龄一般在40周岁以下，具有博士学位；有博士后研究经历，或博士毕业任中级岗位满2年。同时须符合版纳植物园副研究员岗位任职条件。
3. 应聘助理研究员岗位，年龄一般在35岁以下，具有博士学位；有博士后、国外留学经历者优先考虑。
4. 应聘博士后岗位，年龄一般在35岁以下，新获得学位、即将获得博士学位，博士后第一站出站人员。
5. 以第一作者或者通讯作者在SCI收录的国际期刊上已公开发表较高水平的研究论文；能利用植物园所处的地理气候优势以及提供的软硬件平台以及国际合作平台等展望于未来的研究方向。
四、待遇和须知
1. 工资及福利待遇按中国科学院西双版纳热带植物园有关规定执行。
2. 应聘副研究员岗位，填写《中国科学院西双版纳热带植物园引进高层次人才候选人自荐材料》，并按《自荐材料》的要求提供相关的附件材料。
3. 应聘助理研究员岗位，填写《中国科学院西双版纳热带植物园岗位招聘表》，并提交学历/学位证等其它材料。《岗位招聘表》下载及其它具体要求，请登陆中国科学院西双版纳热带植物园网站（http://www.xtbg.ac.cn），查看“公告栏—招聘”中的“应聘须知”。
4. 本招聘启事长期有效，直至招聘到合适人员。
五、联系方式
应聘人员请将应聘材料发送至Richard Corlett研究员邮箱（corlett@xtbg.org.cn）或郁文彬副研究员（yuwenbin@xtbg.ac.cn），并抄送人事教育处陈志云（czy@xtbg.org.cn）。
请通过邮件方式投递简历和咨询！

Welcome to Wen-Bin Yu's website

1/1/2019

Opportunity to join our group

I can be a host for PIFI Postdoctoral Fellowship. If you are a new Ph.D. holder and are looking for potential collaborations in any fields of systematics, evolutionary biology and conservation biology for TWO YEARS. Please send me a research plan before AUGUST (every year), so we can work and submit the application in SEPTEMBER.

For International students, please apply for an International Master Program at the University of Chinese Academy of Sciences. This program will focus on the biodiversity of southeast Asia. To get the information about this program, please click here. If you want to apply for a Ph.D. program, you are also welcome.

For Chinese students, you must take the national entrance examination for graduate students. I am qualified to advise Master student, and to co-advise Ph.D. student in Botany/Ecology. Please visit XTBG page for graduate program.

Research Heatmap

1/1/2019

Undergraduate internship opportunities

6/10/2018

I would like to host undergraduate interns from the second and third year in the summer break. ANYONE can apply if having interesting in any research in botany, ecology, evolutionary biology and bioinformatics. The freshman is also welcome if you have good background in biology or computer sciences. Two kinds of interns you can apply.

1) Training course interns for TWO weeks in the summer. I will give 45 to 60 mins introduction lecture about Bioinformatics, Botanical Nomenclature, DNA Barcoding, Evolution, Genetics, Molecular Biology, Sequencing Technologies, Systematics, Taxonomy, and others in every morning Monday through Friday. You are required to do HOMEWORK after the lecture. All the lectures will be presented in Chinese, but the slides are in English.

2) Research interns for FOUR to SIX weeks in the summer, and can continue in the winter break or returning to the University or College. According to personal interest, we will develop a small research project during the staying at XTBG. I strongly recommend continuing to work on the project after returning to the school.

I try to get funds to support the accommodation when you are staying at XTBG. However, this is not guaranteed. I can accept up to 6 interns for the first type and 1 or 2 interns for the second type. If you are interested in the internship, please feel free to contact by email (yuwenbin@xtbg.ac.cn), including your CV or a brief introduction. If you have CRAZY ideas want to work. Just do it if I can support. The deadline will be on 10 June.

Phylotranscriptomics working pipeine

6/6/2018

Postdoctoral Positions

3/16/2018

Postdoctoral position: Biodiversity Research Group (Yunnan, China)
Author：Richard Corlett

The Biodiversity Research Group at the Xishuangbanna Tropical Botanical Garden (XTBG), Yunnan, invites applications for a full-time postdoctoral position in climate change biology. This group is led by Professor Richard Corlett, who is also head of the Center for Integrative Conservation at XTBG. The Center focuses on applying state-of-the art science to practical conservation questions and is involved in several major national, regional, and global collaborations. XTBG is part of the Chinese Academy of Sciences (CAS), through which these appointments will be made. Please visit the garden's website at http://english.xtbg.cas.cn/for more information about XTBG.

We are looking for someone to participate in the Asian section of an international project that is investigating the potential impacts of climate change on protected areas in the tropics and subtropics: SPARC (Spatial Planning for Protected Areas in Response to Climate Change). The successful applicant will be expected to help with the project as whole, as well as conducting research into using trait-based approaches to assessing climate-change vulnerability of plants and animals in the region, or possibly into another relevant topic. They will be expected to publish in international journals as well as helping to produce practical advice for protected area planners and managers in the region.
The position will require a strong background in basic biology and a PhD in Ecology, Conservation Biology, Environmental Science, Geography, or a related field. If you are not sure if your qualifications are suitable, please contact Professor Corlett at the email address below.
Candidates with a strong record of accomplishment should submit a CV, a statement of research interests, and pdfs of publications. Please include three potential referees who could provide letters of recommendation. Send these materials to Professor Richard Corlett <corlett@xtbg.org.cn> and Ms. Fang Chunyan <fcy@xtbg.org.cn>.

Open faculty positions

3/16/2018

Faculty Positions: Biodiversity Research Group

The Biodiversity Research Group at the Xishuangbanna Tropical Botanical Garden (XTBG), Yunnan, invites applications from experienced scientists with interests related to plant biodiversity and conservation in tropical and subtropical China, and Southeast Asia. The Biodiversity Research Group forms part of the Center for Integrative Conservation at XTBG, which focuses on applying state-of-the art science to practical conservation questions.  We welcome applications from specialists in a wide range of botanical fields, including ecology, conservation biology, taxonomy, ethnobotany, phylogeny, population genetics, climate change biology, pollination biology, ex situ conservation, conservation policy, and botanical education, as long as the proposed research contributes to our ultimate goal of conserving plant diversity in the region.
Applicants need a track record of publications in the leading scientific journals in their field and a vision for future research that makes use of the opportunities that XTBG offers. Xishuangbanna is in tropical southwest China, near the borders with Laos and Myanmar, and showcases both the great diversity of the tropics and the many challenges of conserving it. Uniquely for the region, XTBG offers state-of-the-art research facilities in a rural location, surrounded by a mosaic of forest fragments and plantation agriculture.  XTBG has strong links with other research institutions in Yunnan, on-going research collaborations in Myanmar and Thailand, and ambitious plans for Laos. Put ‘Xishuangbanna’ in any academic search engine to see the diversity of the research being done in this part of China.
This group is led by Professor Richard Corlett, who is also head of the Center for Integrative Conservation. XTBG is part of the Chinese Academy of Sciences (CAS), through which these appointments will be made. Please visit the garden's website at http://english.xtbg.cas.cn/  for more information about XTBG.

Applying for the positions:
Applicants should submit a CV including contact details for three referees, a statement of research interests/plans, and pdfs of representative publications. Please send these materials to Prof. Richard Corlett (corlett@xtbg.org.cn). Applications will be reviewed as they are received and the positions will remain open until filled.

If you have questions, please contact Prof Richard Corlett (corlett@xtbg.org.cn).

"GETORGANELLE" is on the way ....

3/14/2018

This GetOrganelle pipeline assemblies organelle genome from genomic skimming data with an input reference, which should be the same organelle genome sequences but not necessarily a related species within the focal clade.

Citation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Ting-Shuang Yi, De-Zhu Li (2018). GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. bioRxiv, 256479. http://doi.org/10.1101/256479 （*, Equal contributors）

How to get it: https://github.com/Kinggerm/GetOrganelle

Phylogeny of Phtheirospermum published

2/3/2018

https://www.frontiersin.org/articles/10.3389/fpls.2018.00142/abstract