Links
- Researchers
- Project, Database & Consortium
- Courses and Books
- Journal
- Conference
- Softwares
- Blogs, Forum, and WeChat
- Funding
This is a collection of URLs/links I’m following.
Researchers
My network
- PCTG, Peter Visscher, Naomi Wray, Joseph Powell, Matthew Robinson, Hong Lee, Enda Byrne, Jacob Gratten, Beben Benyamin, Gibran Hemani, Albert Tenesa, Robert Maier, Jian Zeng
- Jian Yang; Alumni from Jian Yang lab; Yang Wu
- Kankan Wang, Hai Fang, Jiantao Shi, Maoxiang Qian, Hui Zhang, Yun Tan, Yizhen Li, Xujie Zhao, Congling Xu
- Feng Han (南京医科大学网站, ResearchGate, His Lab), Gensheng Zhang (Google scholar, His Lab);Jiyun Huang; Yingxian Chen, Rongrong Tao; Yuelong Ji (linkedin, Peking university); Tan Chao
- Jiayu Liao; Linghui Qian; 李歆; Jiajia Wang; Xuejing Shao
- Pengzhan Sun; Shuofeng Hu
- Li Xiang, Xianyang Li (Linkedin); Juming Yan; Zhaohui Gu; Luyi Tian; Yanjun Zan, Linkedin; Jiandong Feng
Genetics
- Ben Hayes, David Evans, Evans lab, Matthew Brown, Manuel A. R. Ferreira, Nicholas Martin, Sarah Medland, Stuart Macgregor
- David Balding, Doug Speed, Michael Goddard
- Benjamin Neale, Alkes Price, Po-Ru Loh, Hilary Finucane, Alexander (Sasha) Gusev, Soumya Raychaudhuri, Xihong Lin, Patrick Turley, Tian Ge (Google Scholar), David Reich, Hailiang Huang, Pier Francesco Palamara, Andrea Ganna
- Peter Donnelly, Molly Przeworski, Graham Coop, Jeremy J Berg, Jonathan Marchini
- Nilanjan Chatterjee, Goncalo Abecasis, Bruce Walsh, Jonathan Pritchard, Shaun Purcell, Bogdan Pasaniuc (Google scholar), Stephen Montgomery, Matthew Keller, Luke Evans, Hongyu Zhao (lab page, google scholar), Michael Snyder (lab, Standrod), Bruce Weir, Patrick Sullivan
- Matthew Stephens, Yang I Li
- Lude Franke, Danielle Posthuma, Nick Barton, Andrea Ganna
- Mark McCarthy, Carl Anderson, George Davey Smith: google scholar, Jie Zheng, Jack Bowden, Stephen Burgess, Chris Haley, Jonathan Mill, Ian Deary, Riccardo E. Marioni (google scholar), Frank Dudbridge (Homepage), John RB Perry (Google Scholar), William Hill, Gil McVean
- Chaolong Wang, Chuanchao Wang, Houfeng Zheng (google scholar, lab page), XU Shuhua, Yongyong Shi, Shen Xia, Qingyuan Zhao, Dongxin Lin, Hongbing Shen, Qiongshi Lu, Xifeng Wu, Xin Sheng, Xushen Xiong, Can Yang, Xuejun Zhang, Sun, Liangdan, Sijia Wang, Zhixiu Li, Wenjian Bi
- Ryo Yamada, Seunggeun (Shawn) Lee
- 第五届全球华人遗传学大会
Genome Research, Computational Biologist & Hematology
- Eric S. Lander, Alexander Stark, Yi Zhang, Howard Chang, John Stamatoyannopoulos, Bin Ren, Zhiping Weng, Stunnenberg, Xiaole(Shirley) Liu, Young Lab, Wang Ting
- Yang Li, Istvan Albert , Xuegong Zhang, Ao Ping, Rafalab, Lior Pachter, Cole Trapnell, Steven Salzberg, Yarden Katz, Wolfgang Huber, Wong Yong Wang
- Peter Campbell, Steven Lane, John E. Dick, Daniel G Tenen, Robert G Roeder, Ellen Rothenberg, James C. Mulloy, Constanze Bonifer, DongEr Zhang, Jinghui Zhang, Margaret A. Goodell, Stephen D. Nimer, Bertie G?ttgens
Single Cell
Project, Database & Consortium
- HapMap, 1000 Genomes, ExAC
- UK Biobank (official web, Nature Collection), The Wellcome Trust UK10K project, All of us program, PGC, BBMRI-NL, GIANT, SSGAC, WTCCC, IIBDGC, HRC(Haplotype Reference Consortium)
- CAGE, eQTLGene, GTEx (official web, Nature Collection), CMC, BLUEPRINT, IHEC
- ENCODE, Fantom5, RoadMap Epigenomics Project, CCLE, HFGP(Human Functional Genomics Project)
- HMP
- TCGA, TARGET, PCAWG
- NCBI, GEO, SRA, GenBank, Array-express, PDB, GO (Gene Ontology) , SO (Sequence Ontology), KEGG, UCSC Genome Browser, Ensembl, dbSNP, COSMIC, ClinVar, OMIM, primer design database, ExAC, Omictools, HGMD
Courses and Books
Bioinformatics
- 龙星计划2013-翁志萍
- Statistical methods and data mining in microarray analysis-George C. Tseng
- Analyzing High Throughput Sequencing Data-Istvan Albert
- Applied Bioinformatics-Istvan Albert
- NGS Data Analysis Course
- SSC Intro to NGS Bioinformatics Course-University of Texas
- Yunlong Liu
- Computational Biology-Shirley Xiaole Liu
- Hot topics-MIT
- Biological Statistic
- ROSALIND
- 简明python教程
- Machine Learning-Andrew Ng
- Machine Learning-Bo(Eric) Xing
- Workshop of Bioinformatic.ca
- edx
- coursera
- Data Structures and Algorithms Specializations by UCSD
- Algorithmic Toolbox
- Data Structures
- Algorithms on Graphs
- Algorithms on Strings
- Advanced Algorithms and Complexity
- Genome Assembly Programming Chanllenge
- Bioinformatics Specializations by UCSD
- Finding Hidden Messages in DNA
- Genome Sequencing
- Comparing Genes, Proteins, and Genomes
- Deciphering Molecular Evolution
- Genomic Data Science and Clustering
- Finding Mutations in DNA and Proteins
- Bioinformatics Capstone: Big Data in Biology
- Bioinformatics Methods I and II
- Data Structures and Algorithms Specializations by UCSD
- Genetic Epidemiology
- An Online Bioinformatics Curriculum by Plos Computational Biology
- A New Online Computational Biology Curriculum
IT
- 《Introduction to Computer Science and Programming Using Python》 by MIT on edx
- 《Introduction to Computational Thinking and Data Science》 by MIT on edx
- 《Algorithms》part I and part II by Princeton on coursera
- 《Algorithms Specialization》 by Stanford on coursera
- 《Build Complete Web Solutions》 by HST on coursera
- 《Learn to Program and Analyze Data with Python》 by University of Michigan on coursera
- 《Become a Rails Developer》 by JHU on couresra
- 《Introduction to Computer Systems》 by CMU
- 《CMU CS Bachelors Curriculum》
- 《Parallel Computer Architecture and Programming》 by CMU
- 《Computer Networks》 by CMU
- 《CS155 Computer and Network Security》 by Stanford
Genetics
- MIA by Broad Institute
- “PRIMER ON MEDICAL AND POPULATION GENETICS” by Broad Institute
- “Summer Institute in Social-Science Genomics”
- “POPULATION GENETICS AND EVOLUTION” @ICTS, India
- “COMPUTATIONAL GENOMICS SUMMER INSTITUTE” @UCLA
- “Genomic Medicine XII: Genomics and Risk Prediction” by NIH/NHGRI
Books
- Pro Git
- HTTP: The Definitive Guide
- HTML and CSS: Design and Build Websites
- JavaScript and JQuery: Interactive Front-end Web Development
- Beginning Linux Programming
- Python Requests Essentials
- Thinking in Java
- 图解HTTP
- Learning Python
- C Primer Plus
- The C Programming Language
- Mastering Sublime Text
- Practical Vim
- Effective Python
- Introduction to Quantitative Genetics
- Genetics and Analysis of Quantitative Traits
- Applied Linear Statistical Models
- Introduction to Linear Algebra
- Population genetics: a concise guide
- Statistical Inference
- The Elements of Statistical Learning
Journal
- Cell, Science, Nature, PNAS, NEJM, Lancet, Annual Review, Nature Communications, Science Advances
- Nature Genetics, Nature Review Genetics, American Journal of Human Genetics, Trend in Genetics, Human Molecular Genetics
- Blood, Leukemia
- Genome Research, Genome Biology, Nature Review Cancer, Nature biotechnology, PLOS Computational Biology
Conference
- American Society of Human Genetics Annual meeting (ASHG)
- International Conference of Quantitative Genetics (ICQG)
- Gene Mappers
- European Society of Human Genetics (ESHG)
- 全球华人遗传学大会
Softwares
- PLINK (v1.07), PLINK2 (v1.9 beta), GCTA, SMR, GSMR, OSCA
- BOLT-LMM, MACH, IMPUTE2, METAL, DEPICT, Beagle, haploview, HaploReg, MERLIN
- bwa, bowtie, MACS, MACS2, SPP, HPeak, meme-chip, GimmeMotif, homer, CEAS, STAMP
- tophat, STAR, HISAT, StringTie, RSeQC, RNA-SeQC, Cufflinks, Scripture, HTSeq, featurecount, GFold, DESeq, DESeq2, DEGseq, DEXSeq, eXpress, RSEM, MISO, MATS, MMSEQ, CIRCexplorer, CIRCfinder
- GATK, MuTect, Pindel, CREST, SomaticSniper, VarScan2, Strelka, JointSNVMix, MutSig, InVEx, Oncotator, bradkDancer, SciClone
- OncoSNP
- RMA, MAS5.0, GCRMA
- samtools- samstat- bedtools- bedops- Fastqc- Fastx_toolkit- trimmomatic- Picard- ucsc tools- CIRCOS- SRAtoolkit- Entrez Direct- GenePattern- pgltools
- Jupyter
Blogs, Forum, and WeChat
General Science Community
Bioinformatics
- Xiaole Shirley Liu’s Blog Site, 雁起平沙- 萧之逸- 云之南- 陈连福- YGC
- yixf- azalea
- David Langenberger- Jiang Li- Heng Li: 1)sourceforge 2)github- onetipperday- Bergman Lab- Ewan’s blog: 1)blogspot 2)wordpress- Yokofakun- Puriney- RNA-seq Bolg- What You’re Doing Is Rahter Desperate- Win-Vector Blog- Genomes Unzipped- MassGenomics- CoreGenomics- Simply Statistics- CureFFI- enseqlopedia.com- The Genome Factory- genetics for fun- Diving into Genetics and Genomics
IT
- 阮一峰- Chengwei’s Words- Mozillazg’s Blog- James Hamilton - VP at Amazon Web Services- Denny Britz, a engineer in Google- Linux工具快速教程
forum
Biostars, Seqanswers, links directory, stackexchange, stackoverflow
Bioinformatic cloud company
Seven Bridge, DNAnexus, Google Genomics, NCI’s Genomic Data Commons, Global Alliance for Genomics and Health, nextflow
Your favorite blog on Biostar
- Your Favorite Bioinformatics Blogs (March 2010)
- Your Favorite Bioinformatics Blogs (October 2011)
- What Are Your Favorite Bioit News Resources / Blogs (2012 Edition)
- Your Favorite Bioinformatics Blog(S) (2013 Edition)
微信公众账号
赛先生, 知识分子, 测序中国, 丁香园, 生物谷, 知因knowgene, 博士圈Illumina