News
15 Sep 2020 Alex and Kathy's paper about MARVEL, a computational framework for studying the joint effect of multiple noncoding genetic variants, and its application to Hirschsprung disease, has been accepted for publication in Genome Research.
22 Jul 2020 Christina has passed her PhD thesis defense. Congratulations, Dr. Shi!
29 Jun 2020 Christina's paper about the CQF-deNoise method for efficient k-mer counting and the SH-assembly method for contig assembly from short sequencing reads has been accepted by ECCB 2020. We will present the work in the virtual conference in September. The paper will also be published in a special issue of Bioinformatics.
22 Jun 2020 Qin and Zhenghao's paper about the GEEK framework has been accepted for publication in Nature Machine Intelligence. It allows the integration of heterogeneous types of data related to different gene regulatory mechanisms for studying their joint effect on gene expression levels.
30 Apr 2020 We welcome Savio, who will join us as a student helper in May.
27 Apr 2020 We welcome Jiamin (Vito) and Neel joining our group. Vito will start his PhD study with us in August. Neel will work with us during this summer as a research intern.
19 Jan 2020 We had a nice trip to Yim Tin Tsai, an island with a lot of interesting histories.
1 Nov 2019 Frederik Elberling, a graduate student studying at Karolinska Institutet, is visiting us in these two months through the Global Scholarship Programme for Research Excellence. He will work on single-cell data analysis. Welcome aboard!
27 Sep 2019 Kevin received an Exemplary Service Award from the Department of Computer Science and Engineering.
22 Aug 2019 Kevin has been named an Outstanding Fellow of the Faculty of Engineering of The Chinese University of Hong Kong.
9 Aug 2019 Ken has passed his thesis defense. Congratulations, Dr. Yu!
1 Aug 2019 Yizhen has joined us as a PhD student. Welcome!
23 Jul 2019 Kevin has received the CUHK Young Researcher Award.
22 Jul 2019 Qiong has passed her thesis defense. Congratulations, Dr. Wu!
12 Jul 2019 Chenyang's paper on glk patterns, a type of gapped k-mers allowing variable-length indels, has been accepted for publication in Briefings in Bioinformatics. This type of patterns can be used to discover de novo protein dimer binding sites on DNA.
4 Jun 2019 We welcome Chongzhi joining us as a student helper!
13 Mar 2019 Our new PhD student Yizhen Chen has been awarded the Hong Kong PhD Fellowship. She will join us in August. Congratulations, Yizhen!
26 Feb 2019 Edwin and Qin's paper that discusses issues related to ambiguous definitions of transcriptional enhancers will appear in Briefings in Bioinformatics.
12 Feb 2019 A paper describing our work in comparing genome structures in 26 human populations has been accepted for publication in Nature Communications. It is a collaboration with the labs of Ting-Fung Chan (CUHK), Pui-Yan Kwok (UCSF), Ming Xiao (Drexel), and Bionano Genomics.
12 Feb 2019 Le and Daisy's paper about relationships between two forms of DNA methylation (5-methylcytocine and 5-hydroxymethylcytocine) and gene expression has been accepted for publication in Genome Research.
20 Jan 2019 We had a nice hike to the Victoria Peak with very good weather!
18 Jan 2019 We are recruiting a postdoctoral associate in computational biology and bioinformatics to work on a project related to hepatocellular carcinoma. Please click here for details.
21 Dec 2018 A paper that describes our collaborative project (with Alfred Cheng and K. F. To) on aberrant enhancer methylation in hepatocellular carcinoma has been accepted for publication in Nature Communications.
10 Dec 2018 Alex has successfully defended his master thesis. Congratulations!
12 Nov 2018 A discussion forum for the Hong Kong bioinformatics community has been created. Anyone conducting bioinformatics, using bioinformatics, or simply interested in bioinformatics is welcome to join!
30 Aug 2018 We have just got a new Dr. Li. Congratulations, Le!
29 Jul 2018 Qin received the CUHK Young Scholars Thesis Award 2017. Congratulations, Qin!
1 Apr 2018 Our iGEM paper about a toehold switch design tool has been accepted for publication in Bioinformatics.
1 Mar 2018 We welcome Zhenghao joining us as a research assistant.
21 Jan 2018 We had a wonderful trip to Ngong Ping and Tai O!
31 Dec 2017 Danny and Landon's paper on the functional basis of epistatic gene-gene interactions has been accepted for publication in Bioinformatics.
23 Nov 2017 Qin's paper on enhancer networks has been selected as a top-10 paper in 2016-17 at RECOMB/ISCB Regulatory Systems Genomics 2017.
31 Oct 2017 Le, Alden and Bill's paper on OMSV, a tool for detecting genetic structural variations from optical maps, has been accepted for publication in Genome Biology. This is our third tool for analyzing optical maps, after OMBlast and OMTools.
4 Sep 2017 Qin's paper on enhancer-target networks has been published online in Nature Genetics.
16 Aug 2017 An article describing our Signal Track Query Language (STQL) and Signal Track Analytical Research Tool (START) has been accepted for publication in BMC Genomics.
01 Aug 2017 We welcome Chenyang, Kelly and Yong joining us officially as PhD students.
20 Jul 2017 Qin has successfully defended her thesis. Congratulations, Dr. Cao!
15 Feb 2017 We welcome Chenyang joining us as a research assistant. He will start his PhD study in our group in August.
26 Jan 2017 RECOMB 2017 will be hosted at CUHK and co-organized by HKU CS and CUHK CSE. It is one of the biggest international conferences in bioinformatics and computational biology. Registration will be open soon.
21 Nov 2016 Le's paper on automatic inference of Gene Ontology (GO) has been accepted for publication in Scientific Reports. It describes a method called Unicorn, which combines existing GO and information in biological networks to infer novel GO terms.
04 Nov 2016 Our collaborative project on the exomics of nasopharyngeal carcinoma (NPC), led by Prof. KW Lo, has been accepted for publication in Nature Communications.
26 Sep 2016 Alden's OMBlast paper, our second paper on optical mapping, is accepted for publication in Bioinformatics. It describes a BLAST-like method for efficient alignment of optical maps allowing for split-mapping.
01 Sep 2016 We welcome Dave joining us as a research intern.
01 Aug 2016 Kevin is tenured (substantiated) and promoted to associate professor.
15 Jul 2016 Christina, Kevin and Qin attended ISMB. Qin presented a poster on enhancer network, and Kevin presented a paper of Xihao, with help from Christina, on finding spatial clusters in 3D genome structures. We also had some fun time in Orlando.
16 May 2016 We welcome Angela and Jasmine joining us as student helpers.
27 Apr 2016 Open positions are available for a postdoctoral associate and PhD students, to work on computational biology, bioinformatics and genomics projects. Postdoc candidates should have relevant former research experience. PhD candidates should have strong interest in both biomedical and computer science questions, and a background in bioinformatics, computer science, biology, statistics, or other related areas. Email me if you are interested.
20 Apr 2016 Xihao's paper on identifying spatial clusters in 3D genome structures has been accepted by ISMB. We are looking forward to the July trip to Orlando!
11 Jan 2016 We welcome Christine joining us as a research intern.
06 Jan 2016 We are glad that our collaborative project with Alfred Cheng on the regulatory effects of YY-1 on the NF-kB pathway through epigenetic changes in hepatocellular carcinoma has been accepted for publication in The Journal of Pathology.
09 Nov 2015 Xihao and Yang Wu (from John Lu's group)'s review on high-throughput methods for probing RNA secondary structures and RNA-protein binding has been accepted for publication in Briefings in Bioinformatics.
29 Oct 2015 Our collaborative project on using optical mapping to study structural variations in the CEU trio has been accepted for publication in Genetics. We look forward to other interesting projects related to optical mapping.
11 Aug 2015 Xihao has successfully defended his PhD thesis. Congratulations, Dr. Hu!
01 Aug 2015 We welcome Christina and Edward officially joining our group as PhD students.
31 May 2015 Qin's review on enhancer and enhancer target predictions will appear as a chapter in Computational Biology and Bioinformatics: Gene Regulation.
12 Dec 2014 Ken (Tso)'s paper on the cost-effectiveness of special handling strategies for mouse-contaminated human sequencing reads has been accepted for publication in BMC Genomics.
11 Dec 2014 Danny's paper on the generality of the ceRNA hypothesis has been accepted for publication in BMC Genomics.
13 Oct 2014 Eric has successfully defended his master thesis. Congratulations, Eric!
03 Oct 2014 Eric's paper describing our Variant Annotation System has been accepted for publicaiton in BMC Genomics. We developed this tool to provide efficient integration of whole-genome features with up to several millions of input genetic variants per task.
28 Aug 2014 A series of papers analyzing the latest data produced by the ENCODE and modENCODE consortia has just been published, including a paper comparing the transcriptomes of human, mouse and fly that we are involved.
05 Aug 2014 We welcome Le joining us as a PhD student. Ken Yu has also started his graduate study at CUHK. He will work will Kevin and Prof. KW Ko at the Department of Anatomical and Cellular Pathology on cancer genomics.
03 May 2014 Shaoke's paper on the relationships between promoter and gene body methylation has been accepted for publication in Genome Biology. We are happy to have been involved in this collaborative project, and we look forward to having more publications from it.
09 Feb 2014 Xihao has returned to Hong Kong after half a year of exchange to the Yu Lab at Cornell University. Welcome back, Xihao, and thank you Haiyuan for hosting the exchange.
20 Jan 2014 Ken has successfully defended his master thesis. Congratulations, Ken!
16 Jan 2014 A manuscript describing the final year project of our former undergraduate students Alex Fok and Sunny Mok has been accepted for publication in Bioinformatics. It is about a tool called ECplot that can make many types of plots for bioinformatics and other applications. Try it out!
06 Jan 2014 Our collaborator Ben Turk's paper on serine-threonine kinase phosphoacceptor specificity has been accepted for publication in Molecular Cell. We are happy that our computational predictions contributed to the early work of this beatiful discovery.
14 Dec 2013 Xihao's paper on RNA domains has been accepted for publication in Bioinformatics.
29 Oct 2013 Kevin is going to give a talk on miRNA network at the TriSys conference.
17 Oct 2013 Danny's paper on ceRNA is officially accepted by the RECOMB/ISCB conference. We are looking forward to the Toronto trip.
04 Sep 2013 This news page is created to provide the latest news of the Yip Lab.