单细胞转录组分析技术在生命科学研究中的应用
2009年，孙毅教授回国后，开始进行大量转化医学研究主要在干细胞治疗脊髓损伤方面开始了一系列原创性的研究。另外在用干细胞建立孤独症模型方面已取得突破性成果。
她带领的团队在同济大学原创性地研发了体细胞单细胞全基因组转录本的RNA深度测序方法并用于研究成体神经干细胞的分子生物学性状，探讨成体干细胞及肿瘤干细胞静息活化过程中的机制，该技术对未来寻找各类疾病包括衰老的分子标记会有划时代的推动。
转录因子和miRNA在复杂疾病中的共调控网络研究
Transcription factors (TFs) are key regulators controlling the transcription of target genes by binding to specific DNA sequences on the promoter of target genes. Both the TFs and miRNAs are regulators of gene expression and they may mutual regulate each other to form feedback loops (FBL), or they regulate the same target gene to form a feed-forward loop (FFL). It has been reported that hundreds of potential miRNA-mediated feedback and feed-forward loops are available at the genome level. To predict the TF-miRNA co-regulatory FFL and FBL loops, we integrated multiple data of TF targets and miRNA targets including both experimentally validated and predicted. Thus, we developed a strategy to predict the TF-miRNA co-regulatory FFL and FBL loops. We used these methods to study the TF-miRNA co-regulation in specific diseases including schizophrenia and T-cell acute lymphoblastic leukemia (T-ALL). We identified and verified some key miRNA and genes in these diseases. In the T-ALL, we obtained 120 FFLs among T-ALL related genes, miRNAs and TFs. Afterwards, a T-ALL miRNA and TF co-regulatory network was constructed and its significance was tested by statistical methods. Four miRNAs in the miR-17~92 cluster and 4 important genes (CYLD, HOXA9, BCL2L11, and RUNX1) were found as hubs in the network. Particularly, we found that miR-19 was highly expressed in T-ALL patients and cell lines. Ectopic expression of miR-19 repress CYLD expression, while miR-19 inhibitor treatment induce CYLD protein expression and decreases NF-κB expression in the downstream signaling pathway. Thus, miR-19, CYLD and NF-κB form a regulatory feed-forward loop, which provides new clues for sustained activation of NF-κB in T-ALL. Some single nucleotide polymorphisms (SNPs) in miRNA genes or target sites (miRNA-related SNPs) have been proved to be associated with human diseases by affecting the miRNA mediated regulatory function. To systematically analyze miRNA-related SNPs and their effects, we performed a genome-wide scan for SNPs in human pre-miRNAs, miRNA flanking regions, target sites and designed a pipeline to predict the effects of them on miRNA-target interaction. As a result, we identified 48 SNPs in human miRNA seed regions and thousands of SNPs in 3'- untranslated regions with the potential to either disturb or create miRNA-target interactions. Furthermore, we experimentally confirmed 7 loss-of-function SNPs and 1 gain-of-function SNP by luciferase assay. All useful data were complied into miRNASNP, a user-friendly free online database (http://www.bioguo.org/miRNASNP/). These data will be a useful resource for studying miRNA function, identifying disease-associated miRNAs, and further personalized medicine.
转录因子和miRNA在复杂疾病中的共调控网络研究
Transcription factors (TFs) are key regulators controlling the transcription of target genes by binding to specific DNA sequences on the promoter of target genes. Both the TFs and miRNAs are regulators of gene expression and they may mutual regulate each other to form feedback loops (FBL), or they regulate the same target gene to form a feed-forward loop (FFL). It has been reported that hundreds of potential miRNA-mediated feedback and feed-forward loops are available at the genome level.
单分子测序开启转录组学研究新时代
以基因测序技术发展为背景，阐述以第三代测序技术为核心的全长转录组测序与二代测序技术的转录组测序的差异，以及在研究基因结构等问题上所带来的巨大优势。并以经典案例为参考，阐述全长转录组测序在样品制备、实验设计及数据分析等环节的切入点和注意事项。
毛新良：转录因子c-Maf泛素化酶的发现和功能性分析
介绍了染色体易位与多发性骨髓瘤，Maf、c-Maf在多发性肿瘤中的基因表达。提到了蛋白质泛素化酶系统，提到了HERC4基因表达相关问题。
APT多组学联合分析强势来袭—转录蛋白联合搞事情
中心法则告诉我们遗传信息从DNA传递给RNA，再从RNA传递给蛋白质。但是基因表达仅仅是从转录组到蛋白质组的单向流动吗？两者表达量是一一对应的吗？为什么两者联合分析的文章竟然火箭式的增长？为什么辣么多的研究方向都用到这个联合分析？ 想知道这些答案，欢迎大家准时收听本次中科新生命的在线讲座。
蜜蜂及其真菌病原的纳米孔全长转录组研究
高通量的RNA测序方法在生成全长转录本时常常由于逆转录的过早终止而存在困难，由于大多数传统测序方法需要进行片段化，准确组装完整的转录本仍然存在困难。纳米孔长读长..
基于Oxford Nanopore平台的单细胞全长转录组 ——应用和实践
