Yip Lab news:
1 Jul 2024 Sarina has joined our lab as a LEAP postbacc. LEAP (Lab Experience As Pathway) is a new program established by the SBP Cancer Center to provide one year training to post-baccalaureates who plan to apply for graduate school. The program involves conducting research in a laboratory, eduation modules, and training workshops. Welcome onboard, Sarina!
    
9 May 2024 Kevin received the Educator of The Year award from SBP Graduate School of Biomedical Sciences!
Rather than a personal honor, this is truly a recognition of the joint effort of a great team. Salute to our course co-instructor Rabi Murad, teaching assistants Alex Arzamasov, Chiara Nicoletti, Kelly Li, Ryan Loughran, and Xue Lei, current and former Cancer Center colleagues Donmonique Chambliss, Victoria Carrillo, Tja Owens, Svasti Haricharan, and Ani Deshpande, OETIS, GSBS, DEIB, and many others! 		8 May 2024 Zhenghao has passed his thesis defense. Congratulations, Dr. Zhang !
30 Apr 2024 Commonly used Software Tools Produce Conflicting and Overly-Optimistic AUPRC Values Imagine you joined a competition and got the 11th place among 29 teams. Not too bad, but you aren't too happy as well. Turns out that using the same evaluation metric but just a different tool to compute the scores, you would rank 1st. This is exactly what we found in a collaborative project with Qin, work mostly done by Wenyu and Chen. Read our preprint on bioRxiv. To appear in Genome Biology soon. 5 Mar 2024 A Long-Read Sequencing Strategy with Overlapping Linkers on Adjacent Fragments (OLAF-Seq) for Targeted Resequencing and Enrichment A paper in collaboration with Ming Xiao's lab has been accepted for publiction in Scientific Reports. This paper introduces the OLAF-seq method for creating long-read sequencing libraries that have overlapping linkers between adjacent fragments. The linkers make genome assembly and haplotype phasing much easier. Congratulations to the co-first authors, Lahari@Xiao Lab and Christina!
26 Feb 2024 We welcome Eugene joining us as a postdoc! Eugene studied cell and molecular biology and bioinformatics before. He will work on a project related to extrachromosomal DNA in cancer.
 18 Dec 2023 Accurate Identification of Structural Variations from Cancer Samples Le and Chenyang's paper, in collaboration with Jie Xu from Feng Yue's lab and other collaborators, has been accepted for publiction in Briefings in Bioinformatics. In this paper, we propose the COMSV method that identifies structural variations from cancer samples accurately, taking into account complex properties such as cell type misture and cancer sub-clones.
15 Sep 2023 Kelly was awarded the Dudl Scholarship! It is a scholarship for supporting the research of postdoctoral scholars in memory of Dr. Eric Dudl, a former postdoc at SBP who devoted to research while fighting cancer. We deeply appreciate the great support provided by the Eric Dudl Endowed Scholarship Fund!
 17 Jul 2023 Ricky has defended his thesis!
20 Jun 2022 We welcome Kai joining us as a lab assistant!
 18 May 2022 Daniel received a training grant from California Institute for Regenerative Medicine (CIRM). Congratulations!
3 Apr 2023 DNA Methylation Markers for Kidney Function and Progression of Diabetic Kidney Disease Kelly's paper on diabetic kidney disease has been accepted for publication in Nature Communications. In this work, we studied DNA methylation signals associated with kidney function and its future decline in type 2 diabetes. We used two complementary approaches, namely the single-site epigenome-wide association study approach that identifies individually strong sites and a multi-site modeling approach that identifies sites that are collectively strong. Congratulations, Kelly!
 6 Feb 2023 ICI Efficacy Information Portal: A Knowledgebase for Responder Prediction to Immune Checkpoint Inhibitors Vito's paper on an information portal about biomarkers and prediction models that indicate efficacy of immune checkpoint inhibition (ICI) therapies has been accepted for publication in NAR Cancer!
26 Jan 2023 Kevin received the Faculty Member of the Year Award 2022 for Bioinformatics, Biomedical Informatics & Computational Biology from Faculty Opinions!
 13 Sep 2022 Yong has passed his oral defense. Congratulations, Dr. Zhang !
9 Sep 2022 Kevin received the Crystal Apple Award from SBP Graduate School of Biomedical Sciences!
 9 Aug 2022 Kelly has passed her oral defense. She will work with us as a postdoctoral scientist at SBP. Congratulations, Dr. Li !
7 Aug 2022 Chenyang has passed his oral defense. Congratulations, Dr. Hong !
 25 Jul 2022 Yueqing (Amanda) has joined us as a research assistant. Welcome!
5 Jul 2022 Edward has defended his thesis!
 27 Jun 2022 Savio has defended his master thesis! He will continue his PhD study with us at SBP.
24 May 2022 Hypomorphic and Dominant Negative Impact of Truncated SOX9 Dysregulates Hedgehog-Wnt Signalling, Causing Campomelia Sau Dan's work on ASPIRE, a pipeline for reconstructing viral genomes from host whole-genome sequencing data, has been accepted for publication in BMC Genomics.
 18 Mar 2022 Savio received a training grant from California Institute for Regenerative Medicine (CIRM). Congratulations!
11 Mar 2022 Daniel Rebibo and Savio Chow will both join us as a PhD student in Fall 2022. Welcome, both!
 1 Feb 2022 Reusability Report: Capturing Properties of Biological Objects and Their Relationships using Graph Neural Networks Chenyang and Qin's paper about the use of graph neural networks in finding cancer genes and beyond is accepted for publication in Nature Machine Intelligence. This paper is part of the reusability report collection, which seriously evaluates the reproducibility of published work and reusability of methods in novel applications. We are proud to be part of this effort!
18 Jan 2022 Kevin has started his new position as a professor at Sanford Burnham Prebys Medical Discovery Institute (SBP), in the Tumor Initiation and Maintenance Program of the NCI-designated Cancer Center.
 13 Nov 2021 A postdoctoral associate position in bioinformatics is available. See this page for details. Interested candidates please first email CV and any questions to Kevin before submitting application on that page.
13 Oct 2021 Quantifying Full-Length Circular RNAs in Cancer Ken and Christina's paper about psirc, a computational method for quantifying full-length circular RNA isoforms, has been accepted for publication in Genome Research.

 1 Sep 2021 Kevin has been promoted to full professor, with a retrospective effective date of 1 August 2021.
1 Aug 2021 Qinyao is joining us as a PhD student, while Savio is changing his role to an MPhil stuent. Welcome, both!
 15 Sep 2020 Whole-Genome Analysis of Noncoding Genetic Variations Identifies Multi-Scale Regulatory Element Perturbations Associated with Hirschsprung Disease 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 A General Near-Exact K-mer Counting Method with Low Memory Consumption Enables De Novo Assembly of 106x Human Sequence Data in 2.7 Hours 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 A Unified Framework for Integrative Study of Heterogeneous Gene Regulatory Mechanisms 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 Flexible K-mers with Variable-Length Indels for Identifying Binding Sequences of Protein Dimers 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 Shaping the Nebulous Enhancer in the Era of High-Throughput Assays and Genome Editing Edwin and Qin's paper that discusses issues related to ambiguous definitions of transcriptional enhancers will appear in Briefings in Bioinformatics.
 12 Feb 2019 Genome Maps Across 26 Human Populations Reveal Population-specific Patterns of Structural Variation 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 New Guidelines for DNA Methylome Studies Regarding 5-hydroxymethylcytosine for Understanding Transcriptional Regulation 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 Aberrant Enhancer Hypomethylation Contributes to Hepatic Carcinogenesis through Global Transcriptional Reprogramming 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 A Comprehensive Web Tool for Toehold Switch Design 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 A Network Approach to Exploring the Functional Basis of Gene-Gene Epistatic Interactions in Disease Susceptibility Danny and Landon's paper on the functional basis of epistatic gene-gene interactions has been accepted for publication in Bioinformatics.
23 Nov 2017 Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines 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 OMSV Enables Accurate and Comprehensive Identification of Large Structural Variations from Nanochannel-based Single-Molecule Optical Maps Le, Alden and Bill's paper about 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 Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines Qin's paper on enhancer-target networks and the JEME method has been published online in Nature Genetics.
 16 Aug 2017 START: A System for Flexible Analysis of Hundreds of Genomic Signal Tracks in Few Lines of SQL-like Queries 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 Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms Le's paper on automatic inference of Gene Ontology (GO) based on the Unicorn method 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 Exome and Genome Sequencing of Nasopharynx Cancer Identifies NF-kB Pathway Activating Mutations A paper about 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 OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach 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's, 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 Kevin if you are interested.
20 Apr 2016 A Novel Method for Discovering Local Spatial Clusters of Genomic Regions with Functional Relationships from DNA Contact Maps 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 Yin Yang 1-Mediated Epigenetic Silencing of Tumor-Suppressive MicroRNAs Activates Nuclear Factor-kB in Hepatocellular Carcinoma We are glad that a paper describing 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 Analysis of Sequencing Data for Probing RNA Secondary Structures and Protein-RNA Binding in Studying Post-Transcriptional Regulations 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 Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays A paper that describes 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 Are Special Read Alignment Strategies Necessary and Cost-Effective when Handling Sequencing Reads from Patient-Derived Tumor Xenografts? 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 Systematic Exploration of Autonomous Modules in Noisy MicroRNA-Target Networks for Testing the Generality of the ceRNA Hypothesis 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 VAS: A Convenient Web Portal for Efficient Integration of Genomic Features with Millions of Genetic Variants 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 Comparative Analysis of the Transcriptome across Distant Species 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 Whole-Genome Bisulfite Sequencing of Multiple Individuals Reveals Complementary Roles of Promoter and Gene Body Methylation in Transcriptional Regulation 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 ECplot: An Online Tool for Making Standardized Plots from Large Datasets for Bioinformatics Publications 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 Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity 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 Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data Xihao's paper on RNA domains and the ProbRNA method 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.