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Ting Wang

Bio: Ting Wang is an academic researcher from Pennsylvania State University. The author has contributed to research in topics: Medicine & Wavelength-division multiplexing. The author has an hindex of 82, co-authored 1217 publications receiving 43318 citations. Previous affiliations of Ting Wang include East China Normal University & Florida International University.


Papers
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Journal ArticleDOI
TL;DR: In this article, the authors found that conventionalization of adult germ-free C57BL/6 mice with a normal microbiota harvested from the distal intestine (cecum) of conventionally raised animals produces a 60% increase in body fat content and insulin resistance within 14 days despite reduced food intake.
Abstract: New therapeutic targets for noncognitive reductions in energy intake, absorption, or storage are crucial given the worldwide epidemic of obesity. The gut microbial community (microbiota) is essential for processing dietary polysaccharides. We found that conventionalization of adult germ-free (GF) C57BL/6 mice with a normal microbiota harvested from the distal intestine (cecum) of conventionally raised animals produces a 60% increase in body fat content and insulin resistance within 14 days despite reduced food intake. Studies of GF and conventionalized mice revealed that the microbiota promotes absorption of monosaccharides from the gut lumen, with resulting induction of de novo hepatic lipogenesis. Fasting-induced adipocyte factor (Fiaf), a member of the angiopoietin-like family of proteins, is selectively suppressed in the intestinal epithelium of normal mice by conventionalization. Analysis of GF and conventionalized, normal and Fiaf knockout mice established that Fiaf is a circulating lipoprotein lipase inhibitor and that its suppression is essential for the microbiota-induced deposition of triglycerides in adipocytes. Studies of Rag1-/- animals indicate that these host responses do not require mature lymphocytes. Our findings suggest that the gut microbiota is an important environmental factor that affects energy harvest from the diet and energy storage in the host. Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY 667702--AY 668946).

5,221 citations

Journal ArticleDOI
Anshul Kundaje1, Wouter Meuleman2, Wouter Meuleman1, Jason Ernst3, Misha Bilenky4, Angela Yen2, Angela Yen1, Alireza Heravi-Moussavi4, Pouya Kheradpour1, Pouya Kheradpour2, Zhizhuo Zhang2, Zhizhuo Zhang1, Jianrong Wang2, Jianrong Wang1, Michael J. Ziller2, Viren Amin5, John W. Whitaker, Matthew D. Schultz6, Lucas D. Ward1, Lucas D. Ward2, Abhishek Sarkar1, Abhishek Sarkar2, Gerald Quon2, Gerald Quon1, Richard Sandstrom7, Matthew L. Eaton1, Matthew L. Eaton2, Yi-Chieh Wu2, Yi-Chieh Wu1, Andreas R. Pfenning1, Andreas R. Pfenning2, Xinchen Wang2, Xinchen Wang1, Melina Claussnitzer2, Melina Claussnitzer1, Yaping Liu2, Yaping Liu1, Cristian Coarfa5, R. Alan Harris5, Noam Shoresh2, Charles B. Epstein2, Elizabeta Gjoneska2, Elizabeta Gjoneska1, Danny Leung8, Wei Xie8, R. David Hawkins8, Ryan Lister6, Chibo Hong9, Philippe Gascard9, Andrew J. Mungall4, Richard A. Moore4, Eric Chuah4, Angela Tam4, Theresa K. Canfield7, R. Scott Hansen7, Rajinder Kaul7, Peter J. Sabo7, Mukul S. Bansal1, Mukul S. Bansal10, Mukul S. Bansal2, Annaick Carles4, Jesse R. Dixon8, Kai How Farh2, Soheil Feizi1, Soheil Feizi2, Rosa Karlic11, Ah Ram Kim1, Ah Ram Kim2, Ashwinikumar Kulkarni12, Daofeng Li13, Rebecca F. Lowdon13, Ginell Elliott13, Tim R. Mercer14, Shane Neph7, Vitor Onuchic5, Paz Polak15, Paz Polak2, Nisha Rajagopal8, Pradipta R. Ray12, Richard C Sallari1, Richard C Sallari2, Kyle Siebenthall7, Nicholas A Sinnott-Armstrong1, Nicholas A Sinnott-Armstrong2, Michael Stevens13, Robert E. Thurman7, Jie Wu16, Bo Zhang13, Xin Zhou13, Arthur E. Beaudet5, Laurie A. Boyer1, Philip L. De Jager2, Philip L. De Jager15, Peggy J. Farnham17, Susan J. Fisher9, David Haussler18, Steven J.M. Jones19, Steven J.M. Jones4, Wei Li5, Marco A. Marra4, Michael T. McManus9, Shamil R. Sunyaev2, Shamil R. Sunyaev15, James A. Thomson20, Thea D. Tlsty9, Li-Huei Tsai1, Li-Huei Tsai2, Wei Wang, Robert A. Waterland5, Michael Q. Zhang21, Lisa Helbling Chadwick22, Bradley E. Bernstein2, Bradley E. Bernstein15, Bradley E. Bernstein6, Joseph F. Costello9, Joseph R. Ecker11, Martin Hirst4, Alexander Meissner2, Aleksandar Milosavljevic5, Bing Ren8, John A. Stamatoyannopoulos7, Ting Wang13, Manolis Kellis2, Manolis Kellis1 
19 Feb 2015-Nature
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Abstract: The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

5,037 citations

Journal ArticleDOI
08 Jul 2010-Nature
TL;DR: An in-depth investigation of the human SHANK3 locus and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo.
Abstract: Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5' CpG island (CGI) promoters, whereas a far greater proportion occurs across gene bodies, coinciding with highly conserved sequences. Tissue-specific intragenic methylation might reduce, or, paradoxically, enhance transcription elongation efficiency. Capped analysis of gene expression (CAGE) experiments also indicate that transcription commonly initiates within and between genes. To investigate the role of intragenic methylation, we generated a map of DNA methylation from the human brain encompassing 24.7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were shown to be in intragenic and intergenic regions, whereas less than 3% of CpG islands in 5' promoters were methylated. The CpG islands in all three locations overlapped with RNA markers of transcription initiation, and unmethylated CpG islands also overlapped significantly with trimethylation of H3K4, a histone modification enriched at promoters. The general and CpG-island-specific patterns of methylation are conserved in mouse tissues. An in-depth investigation of the human SHANK3 locus and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo. These methylation-regulated, alternative transcripts are expressed in a tissue- and cell type-specific manner, and are expressed differentially within a single cell type from distinct brain regions. These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies.

1,610 citations

Journal ArticleDOI
TL;DR: An overview of the project and the resources it is generating and the application of ENCODE data to interpret the human genome are provided.
Abstract: The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

1,446 citations

Journal ArticleDOI
Feng Yue1, Feng Yue2, Yong Cheng3, Alessandra Breschi, Jeff Vierstra4, Weisheng Wu5, Weisheng Wu2, Tyrone Ryba6, Tyrone Ryba7, Richard Sandstrom4, Zhihai Ma3, Carrie A. Davis8, Benjamin D. Pope7, Yin Shen1, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman4, Rajinder Kaul4, Eric Rynes4, Anthony Kirilusha9, Georgi K. Marinov9, Brian A. Williams9, Diane Trout9, Henry Amrhein9, Katherine I. Fisher-Aylor9, Igor Antoshechkin9, Gilberto DeSalvo9, Lei Hoon See8, Meagan Fastuca8, Jorg Drenkow8, Chris Zaleski8, Alexander Dobin8, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer10, Olgert Denas11, Kanwei Li11, M. A. Bender4, M. A. Bender12, Miaohua Zhang12, Rachel Byron12, Mark Groudine4, Mark Groudine12, David McCleary1, Long Pham1, Zhen Ye1, Samantha Kuan1, Lee Edsall1, Yi-Chieh Wu13, Matthew D. Rasmussen13, Mukul S. Bansal13, Manolis Kellis13, Manolis Kellis14, Cheryl A. Keller2, Christapher S. Morrissey2, Tejaswini Mishra2, Deepti Jain2, Nergiz Dogan2, Robert S. Harris2, Philip Cayting3, Trupti Kawli3, Alan P. Boyle3, Alan P. Boyle5, Ghia Euskirchen3, Anshul Kundaje3, Shin Lin3, Yiing Lin3, Camden Jansen15, Venkat S. Malladi3, Melissa S. Cline16, Drew T. Erickson3, Vanessa M. Kirkup16, Katrina Learned16, Cricket A. Sloan3, Kate R. Rosenbloom16, Beatriz Lacerda de Sousa17, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian18, Tamer Kahveci19, Dongwon Lee20, W. James Kent16, Miguel Santos17, Javier Herrero21, Cedric Notredame, Audra K. Johnson4, Shinny Vong4, Kristen Lee4, Daniel Bates4, Fidencio Neri4, Morgan Diegel4, Theresa K. Canfield4, Peter J. Sabo4, Matthew S. Wilken4, Thomas A. Reh4, Erika Giste4, Anthony Shafer4, Tanya Kutyavin4, Eric Haugen4, Douglas Dunn4, Alex Reynolds4, Shane Neph4, Richard Humbert4, R. Scott Hansen4, Marella F. T. R. de Bruijn22, Licia Selleri23, Alexander Y. Rudensky24, Steven Z. Josefowicz24, Robert M. Samstein24, Evan E. Eichler4, Stuart H. Orkin25, Dana N. Levasseur26, Thalia Papayannopoulou4, Kai Hsin Chang4, Arthur I. Skoultchi27, Srikanta Gosh27, Christine M. Disteche4, Piper M. Treuting4, Yanli Wang2, Mitchell J. Weiss, Gerd A. Blobel28, Xiaoyi Cao1, Sheng Zhong1, Ting Wang29, Peter J. Good30, Rebecca F. Lowdon29, Rebecca F. Lowdon30, Leslie B. Adams31, Leslie B. Adams30, Xiao Qiao Zhou30, Michael J. Pazin30, Elise A. Feingold30, Barbara J. Wold9, James Taylor11, Ali Mortazavi15, Sherman M. Weissman18, John A. Stamatoyannopoulos4, Michael Snyder3, Roderic Guigó, Thomas R. Gingeras8, David M. Gilbert7, Ross C. Hardison2, Michael A. Beer20, Bing Ren1 
20 Nov 2014-Nature
TL;DR: The mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types as mentioned in this paper.
Abstract: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

1,335 citations


Cited by
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[...]

08 Dec 2001-BMJ
TL;DR: There is, I think, something ethereal about i —the square root of minus one, which seems an odd beast at that time—an intruder hovering on the edge of reality.
Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

33,785 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
23 Jan 2009-Cell
TL;DR: The current understanding of miRNA target recognition in animals is outlined and the widespread impact of miRNAs on both the expression and evolution of protein-coding genes is discussed.

18,036 citations

Journal ArticleDOI
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Abstract: MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. RESULTS: We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. AVAILABILITY AND IMPLEMENTATION: featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

14,103 citations