Comparative transcriptomics in human and mouse
TLDR
Cross-species comparisons of genomes, transcriptomes and gene regulation are now feasible at unprecedented resolution and throughput, enabling the comparison of human and mouse biology at the molecular level.Abstract:
Cross-species comparisons of genomes, transcriptomes and gene regulation are now feasible at unprecedented resolution and throughput, enabling the comparison of human and mouse biology at the molecular level. Insights have been gained into the degree of conservation between human and mouse at the level of not only gene expression but also epigenetics and inter-individual variation. However, a number of limitations exist, including incomplete transcriptome characterization and difficulties in identifying orthologous phenotypes and cell types, which are beginning to be addressed by emerging technologies. Ultimately, these comparisons will help to identify the conditions under which the mouse is a suitable model of human physiology and disease, and optimize the use of animal models.read more
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Jill Moore,Michael J. Purcaro,Henry Pratt,Charles B. Epstein,Noam Shoresh,Jessika Adrian,Trupti Kawli,Carrie A. Davis,Alexander Dobin,Rajinder Kaul,Jessica Halow,Eric L. Van Nostrand,Peter Freese,David U. Gorkin,David U. Gorkin,Yin Shen,Yin Shen,Yupeng He,Mark Mackiewicz,Florencia Pauli-Behn,Brian A. Williams,Ali Mortazavi,Cheryl A. Keller,Xiao-Ou Zhang,Shaimae I. Elhajjajy,Jack Huey,Diane E. Dickel,Valentina Snetkova,Xintao Wei,Xiaofeng Wang,Xiaofeng Wang,Juan Carlos Rivera-Mulia,Juan Carlos Rivera-Mulia,Joel Rozowsky,Jing Zhang,Surya B. Chhetri,Jialing Zhang,Alec Victorsen,Kevin P. White,Axel Visel,Axel Visel,Gene W. Yeo,Christopher B. Burge,Eric Lécuyer,Eric Lécuyer,David M. Gilbert,Job Dekker,John L. Rinn,Eric M. Mendenhall,Joseph R. Ecker,Manolis Kellis,Manolis Kellis,Robert J. Klein,William Stafford Noble,Anshul Kundaje,Roderic Guigó,Peggy J. Farnham,J. Michael Cherry,Richard M. Myers,Bing Ren,Bing Ren,Brenton R. Graveley,Mark Gerstein,Len A. Pennacchio,Len A. Pennacchio,Michael Snyder,Bradley E. Bernstein,Barbara J. Wold,Ross C. Hardison,Thomas R. Gingeras,John A. Stamatoyannopoulos,Zhiping Weng,Zhiping Weng,Zhiping Weng +73 more
TL;DR: The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development.
Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
TL;DR: For example, this paper found that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.
ChromHMM: automating chromatin-state discovery and characterization
TL;DR: ChromHMM is developed, an automated computational system for learning chromatin states, characterizing their biological functions and correlations with large-scale functional datasets, and visualizing the resulting genome-wide maps of chromatin state annotations.
Journal ArticleDOI
Animal models of neurodegenerative diseases.
TL;DR: The authors review the current state of rodent models for AD, PD, FTD, and ALS and discusses the limitations and utility of current models, issues regarding translatability, and future directions for developing animal models of these human disorders.
References
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
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Principal Component Analysis
TL;DR: In this article, the authors present a graphical representation of data using Principal Component Analysis (PCA) for time series and other non-independent data, as well as a generalization and adaptation of principal component analysis.
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Principal Component Analysis
TL;DR: Principal component analysis (PCA) as discussed by the authors replaces the p original variables by a smaller number, q, of derived variables, the principal components, which are linear combinations of the original variables.
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An integrated encyclopedia of DNA elements in the human genome
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