Browsing by Author "Wu, Jie"
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Item Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies(Genetics Society America, 2014-11-01) Rajagopal, Nisha; Ernst, Jason; Ray, Pradipta; Wu, Jie; Zhang, Michael Q.; Kellis, Manolis; Ren, Bing; 0000 0001 1707 1372 (Zhang, MQ); 99086074 (Zhang, MQ); Zhang, Michael Q.In eukaryotic cells, histone lysines are frequently acetylated. However, unlike modifications such as methylations, histone acetylation modifications are often considered redundant. As such, the functional roles of distinct histone acetylations are largely unexplored. We previously developed an algorithm RFECS to discover the most informative modifications associated with the classification or prediction of mammalian enhancers. Here, we used this tool to identify the modifications most predictive of promoters, enhancers, and gene bodies. Unexpectedly, we found that histone acetylation alone performs well in distinguishing these unique genomic regions. Further, we found the association of characteristic acetylation patterns with genic regions and association of chromatin state with splicing. Taken together, our work underscores the diverse functional roles of histone acetylation in gene regulation and provides several testable hypotheses to dissect these roles.Item Investigation of High Oxygen Reduction Reaction Catalytic Performance on Mn-Based Mullite SmMn₂O₅(Royal Soc Chemistry, 2017-10) Liu, Jieyu; Yu, Meng; Wang, Xuewei; Wu, Jie; Wang, Changhong; Zheng, Lijun; Yang, Dachi; Liu, Hui; Yao, Yan; Lu, Feng; Wang, Weichao; 0000-0001-5931-212X (Wang, W); Wang, WeichaoAn alternative material SmMn₂O₅ mullite with regard to Pt/C is proposed to catalyze the oxygen reduction reaction (ORR) by combining density functional theory (DFT) calculations and experimental validations. Theoretical calculations are performed to investigate the bulk phase diagram, as well as the stability and electrocatalytic activity of the ORR under alkaline conditions for SmMn₂O₅ (001) surfaces, which are passivated by nitrogen atoms to avoid any spurious interference. The adsorptions of relevant ORR species (O*, OH*, OOH* and OO*) tend to compensate the coordination of manganese atoms to form Mn-centered octahedral or pyramidal crystal fields, and the corresponding binding energies fulfill a linear relationship. An oxygen molecule prefers to be reduced to OH⁻ via a four-electron pathway and this prediction is verified by electrochemical measurements on the as-prepared SmMn₂O₅ catalyst with a nanorod structure. Volcano curves are obtained to describe the trends in theoretical ORR activity as a function of a single parameter, i.e. the oxygen binding energy. An overpotential of 0.43 V is obtained at the O* binding energy around 3.4 eV, which is close to the experimental observation (0.413 V) in this work. SmMn₂O₅ mullite exhibits favorable ORR activity and superior stability with only ~5% decay in activity over 20 000 s of chronoamperometric operation in contrast to ~15% decrease of Pt/C, making it a promising candidate for a cathode catalyst.Item OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds(Oxford University Press, 2013-04) Wu, Jie; Anczuk©w, Olga; Krainer, Adrian R.; Zhang, Michael Q.; Zhang, Chaolin; 0000 0001 1707 1372 (Zhang, MQ); 99086074 (Zhang, MQ); Zhang, Michael Q.A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (∼14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.;