Search Results - "Weng, Zhiping"

Deletion and replacement of long genomic sequences using prime editing by Jiang, Tingting, Zhang, Xiao-Ou, Weng, Zhiping, Xue, Wen

“…Genomic insertions, duplications and insertion/deletions (indels), which account for ~14% of human pathogenic mutations, cannot be accurately or efficiently…”
Get full text

The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes by Zhang, Donglei, Tu, Shikui, Stubna, Michael, Wu, Wei-Sheng, Huang, Wei-Che, Weng, Zhiping, Lee, Heng-Chi

“…Piwi-interacting RNAs (piRNAs) silence transposons to safeguard genome integrity in animals. However, the functions of the many piRNAs that do not map to…”
Get full text

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers by Pierce, Brian G, Wiehe, Kevin, Hwang, Howook, Kim, Bong-Hyun, Vreven, Thom, Weng, Zhiping

“…Protein-protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure…”
Get full text

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation by He, Lizhi, Pratt, Henry, Gao, Mingshi, Wei, Fengxiang, Weng, Zhiping, Struhl, Kevin

“…The YAP and TAZ paralogs are transcriptional co-activators recruited to target sites by TEAD proteins. Here, we show that YAP and TAZ are also recruited by…”
Get full text

Regulation of histone H3K4 methylation in brain development and disease by Shen, Erica, Shulha, Hennady, Weng, Zhiping, Akbarian, Schahram

“…The growing list of mutations implicated in monogenic disorders of the developing brain includes at least seven genes (ARX, CUL4B, KDM5A, KDM5C, KMT2A, KMT2C,…”
Get full text

Protein-protein docking benchmark version 4.0 by Hwang, Howook, Vreven, Thom, Janin, Joël, Weng, Zhiping

“…We updated our protein–protein docking benchmark to include complexes that became available since our previous release. As before, we only considered…”
Get full text

Accelerating protein docking in ZDOCK using an advanced 3D convolution library by Pierce, Brian G, Hourai, Yuichiro, Weng, Zhiping

“…Computational prediction of the 3D structures of molecular interactions is a challenging area, often requiring significant computational resources to produce…”
Get full text

TEMP: a computational method for analyzing transposable element polymorphism in populations by Zhuang, Jiali, Wang, Jie, Theurkauf, William, Weng, Zhiping

“…Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the…”
Get full text

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production by Han, Bo W., Wang, Wei, Li, Chengjian, Weng, Zhiping, Zamore, Phillip D.

“…PIWI-interacting RNAs (piRNAs) protect the animal germ line by silencing transposons. Primary piRNAs, generated from transcripts of genomic transposon…”
Get full text

The correlation between histone modifications and gene expression by Dong, Xianjun, Weng, Zhiping

Get more information

Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function by Zhang, Xiao-Ou, Gingeras, Thomas R, Weng, Zhiping

“…elements are one of the most successful families of transposons in the human genome. A portion of elements is transcribed by RNA Pol III, whereas the remaining…”
Get full text

Unsupervised pattern discovery in human chromatin structure through genomic segmentation by Hoffman, Michael M, Buske, Orion J, Wang, Jie, Weng, Zhiping, Bilmes, Jeff A, Noble, William Stafford

“…Segway, a method using dynamic Bayesian network techniques, segments a genome and produces functional labels defined by histone modifications,…”
Get full text

DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data by Tsuji, Junko, Weng, Zhiping

“…With the rapid accumulation of publicly available small RNA sequencing datasets, third-party meta-analysis across many datasets is becoming increasingly…”
Get full text

Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope by Jiang, Tingting, Henderson, Jordana M., Coote, Kevin, Cheng, Yi, Valley, Hillary C., Zhang, Xiao-Ou, Wang, Qin, Rhym, Luke H., Cao, Yueying, Newby, Gregory A., Bihler, Hermann, Mense, Martin, Weng, Zhiping, Anderson, Daniel G., McCaffrey, Anton P., Liu, David R., Xue, Wen

“…CRISPR-Cas9-associated base editing is a promising tool to correct pathogenic single nucleotide mutations in research or therapeutic settings. Efficient base…”
Get full text

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers by Fu, Yu, Wu, Pei-Hsuan, Beane, Timothy, Zamore, Phillip D, Weng, Zhiping

“…RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase…”
Get full text

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods by Moore, Jill E, Pratt, Henry E, Purcaro, Michael J, Weng, Zhiping

“…Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge…”
Get full text

Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline by Shen, En-Zhi, Chen, Hao, Ozturk, Ahmet R., Tu, Shikui, Shirayama, Masaki, Tang, Wen, Ding, Yue-He, Dai, Si-Yuan, Weng, Zhiping, Mello, Craig C.

“…piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies…”
Get full text

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility by Wu, Pei-Hsuan, Fu, Yu, Cecchini, Katharine, Özata, Deniz M., Arif, Amena, Yu, Tianxiong, Colpan, Cansu, Gainetdinov, Ildar, Weng, Zhiping, Zamore, Phillip D.

“…Pachytene PIWI-interacting RNAs (piRNAs), which comprise >80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like…”
Get full text

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics by Belaghzal, Houda, Borrman, Tyler, Stephens, Andrew D., Lafontaine, Denis L., Venev, Sergey V., Weng, Zhiping, Marko, John F., Dekker, Job

“…Nuclear compartmentalization of active and inactive chromatin is thought to occur through microphase separation mediated by interactions between loci of…”
Get full text

Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses by Wang, Dan, Mou, Haiwei, Li, Shaoyong, Li, Yingxiang, Hough, Soren, Tran, Karen, Li, Jia, Yin, Hao, Anderson, Daniel G, Sontheimer, Erik J, Weng, Zhiping, Gao, Guangping, Xue, Wen

“…CRISPR/Cas9 derived from the bacterial adaptive immunity pathway is a powerful tool for genome editing, but the safety profiles of in vivo delivered Cas9…”
Get more information