On February 1, 2024, Contrgulations to Kuan Xie and Yuying Hou, our Deep Cntroid paper has been published on Bioinformatics (Deep centroid: a general deep cascade classifier for biomedical omics data classification).
November 12, 2023 14:30-18:00 PM: Held the 2023 Academic Annual conference of Hubei Key Laboratory of Agricultural Bioinformatics.
Hou Yuying of the research group made a presentation entitled "Systematic Evaluation of Cell-Free DNA Fragmentation Patterns for Cancer
Diagnosis and Enhanced Cancer. Detection through Integration of Multiple Fragmentations "report. The study focused on the use of cell-free
DNA fragments in cancer diagnosis.
The general contents of the study are as follows:
Cell-free DNA (cfDNA) fragmentation patterns hold immense potential for early cancer detection.
However, the definitions of fragmentation vary by genomic scale, ranging from the entire genome to specific genomic regions.
Furthermore, the lack of systematic comparison among these patterns has impeded their broader research and practical implementation.
Here, we collected over 1,382 plasma cfDNA sequencing samples from diverse sources, covering eight cancer types.
Considering that cfDNA within open chromatin regions is more susceptible to fragmentation,
we leveraged ten fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance.
Remarkably, all fragmentation patterns demonstrated discernible classification capabilities,
with EDM (End Motif) showing the highest diagnostic value in cross-validation.
Combining the results of both cross-validation and independent validation,
fragmentation patterns that incorporate both fragment length and coverage information exhibit robust predictive capacities.
Despite their diagnostic potential, these fragmentation patterns exhibited variability in their predictive power.
To address this limitation, we developed an ensemble classifier by integrating all fragmentation patterns,
which achieved significant advancements in cancer detection and tissue-of-origin analysis.
Moreover, thorough biological function investigations of significant feature intervals in our model
have unveiled its impressive ability to discern critical regulatory regions involved in cancer pathogenesis.
Celebrate your graduation journey, enjoy a joyful drifting journey in Yichang, thrilling and thrilling!
The Data Mining and Precision Medical Laboratory, along with a large group of teachers, launched a Home Party! At Carlton Manor in Optics Valley Square, there are three chefs who offer delicious dishes such as mushroom stewed chicken, minced chili fish, winter yin gong soup, and a large number of dumpling experts, Dragon Flying Phoenix Dance. After the enjoyable food segment, we began a carnival of various games such as mahjong, KTV, billiards, barbecue, computers, and more. After the final entertainment, students need to work harder!
On December 8, 2022, our CRAG paper is published on Genome Medicine (CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing). Congratulations!
On November 28, 2022, Peiting Shi et al.’s SRF project (Peiting Shi, Junmin Han, Yinhao Zhang and Guanpu Li. IMI-driver, integrating multi-omics for cancer driver identification) was awarded the "Top Ten Projects" in the 2022 Innovation and Entrepreneurship Training Plan of Huazhong Agricultural University. Congratulations!
On the evening of November 12, 2022, the weather is cold and windy. The four young generals in the laboratory met on the table tennis court to show their skills. To express the pressure of learning in sports, I still don't forget to discuss algorithm ideas.
In the afternoon of October 27, 2022, the 18th "Happy Hour" activity of the School of Information in 2022 was held online. At the invitation of Zhou Xionghui, a teacher from the Institute of Information Technology, Dr. Xiangyu Meng made an academic report.
Bladder cancer is the cancer with the highest incidence rate in China, and its clinical treatment has great differences. There are many factors that can induce cancer, such as men's incidence rate may be higher than women's due to smoking, or age may lead to increased cancer risk and occupational exposure. Dr. Meng Xiangyu introduced the statistical analysis of somatic mutation law of bladder cancer and the systematic exploration and integration of genetic variation information of bladder cancer, and then introduced the impact on bladder cancer mutation from three aspects: APOBEC, smoking and genetic variation.
Dr. Xionghui Zhou introduced the work of the laboratory in precision medicine. The report mainly started with network construction methods such as "ceRNA network" and "gene dependent network", and then started with "early diagnosis and prognosis of cancer", "drug response prediction", "combination drug prediction" and other aspects.
Precision medicine is a kind of medicine that uses genetic information of individual diseases to guide their diagnosis or treatment. Therefore, based on reasonable biological assumptions, a biological network that can reflect some biological phenomena can be built, and key molecular characteristics of diseases can be mined for early diagnosis, prognosis and drug efficacy prediction.