Filters








22 Hits in 5.2 sec

PEPATAC: An optimized ATAC-seq pipeline with serial alignments [article]

Jason P. Smith, M. Ryan Corces, Jin Xu, Vincent P. Reuter, Howard Y. Chang, Nathan C. Sheffield
2020 bioRxiv   pre-print
Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis.  ...  Results: PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches.  ...  Acknowledgments We would like to acknowledge helpful discussions and contributions from Yuning Wei, Ying Shen, and Jason Buenrostro on early versions of the pipeline. Works Cited  ... 
doi:10.1101/2020.10.21.347054 fatcat:72ckmnwblnf7li2blhvhwy33ze

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

Jason P Smith, M Ryan Corces, Jin Xu, Vincent P Reuter, Howard Y Chang, Nathan C Sheffield
2021 NAR Genomics and Bioinformatics  
Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis.  ...  PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches.  ...  ACKNOWLEDGEMENTS We would like to acknowledge helpful discussions and contributions from Yuning Wei, Ying Shen and Jason Buenrostro on early versions of the pipeline.  ... 
doi:10.1093/nargab/lqab101 pmid:34859208 pmcid:PMC8632735 fatcat:4ukzx4pslzhqbklfszh52f3qdu

DIGITAL AND VIRTUAL LIBRARIES [chapter]

2014 Engineering Libraries  
As engineering programs are established and grow it is critical for libraries to follow suit, building collections to support the needs o f their clien tele.  ...  Using experience drawn primarily from academic engineering libraries, these papers transcend that venue to pro vide insights applicable across the sciences and to corporate settings.  ...  Subscribers to CORC use an automated Web interface to point the CORC sys tem to a URL they wish to harvest. The CORC software extracts some basic data from the resource to create a base record.  ... 
doi:10.4324/9781315786025-6 fatcat:uomkrzneujalhe4ldmsct6tyoq

Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [article]

Swetansu K Hota, Andrew P Blair, Kavitha S. Rao, Kevin So, Aaron M Blotnick, Ravi V Desai, Leor S Weinberger, Irfan S Kathiriya, Benoit G. Bruneau
2020 bioRxiv   pre-print
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization.  ...  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape.  ...  Regions marked by 685 one of the associated replicates. The number of reads mapping to each of the consensus 686 regions for each of replicates using the subread featureCounts program 61 .  ... 
doi:10.1101/2020.06.03.132654 fatcat:23rhdyirtnh3rchzqlteegb2j4

Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk [article]

Adam W. Turner, Sheng'en Hu, Jose Verdezoto Mosquera, Wei Feng Ma, Chani Hodonsky, Doris Wong, Gaelle Auguste, Katia Sol-Church, Emily A. Farber, Soumya Kundu, Anshul B. Kundaje, Nicolas G. Lopez (+11 others)
2021 bioRxiv   pre-print
We further employed DNA element to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2.  ...  This single cell atlas provides a critical step towards interpreting cis-regulatory mechanisms in the vessel wall across the continuum of CAD risk.  ...  Acknowledgements This work was supported by grants from: the National Institutes of Health (R01HL148239 and R00HL125912 to C.L.M.; R35GM133712 to C.Z.; R01HL141425 to A.V.F; R01HL125863 to J.LM.B.; R01HL130423  ... 
doi:10.1101/2021.06.07.447388 fatcat:4wplarvxfnfyles77fjr25cwxy

EDUCATION FOR SPECIFIC PURPOSES [chapter]

2014 Education for Cataloging and the Organization of Information  
In the first, Beatrice Kovacs and Nancy Dayton surveyed graduates of the University of North Carolina at Greensboro program on their opinions about the usefulness of their cataloging instruction.  ...  Saye examines cataloging instruction in accredited library programs from an entirely different perspective-that of the structure and atmosphere of library school programs, the outlook, background, and  ...  pick the fruit of the OCLC trees and construct incoherent catalogues of increasingly less use to their users.  ... 
doi:10.4324/9781315785837-7 fatcat:vl4obtw4lzexblq3gr4rzbofhq

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

Carmen Bravo González‐Blas, Xiao‐Jiang Quan, Ramon Duran‐Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime Waegeneer, David Mauduit, Suresh Poovathingal (+2 others)
2020 Molecular Systems Biology  
Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers.  ...  of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering).  ...  This approach is included in the ScoMAP R package, with detailed tutorials, at https://github.com/aertslab/ScoMAP.  ... 
doi:10.15252/msb.20209438 pmid:32431014 fatcat:qufyihtbcbco7eep2dc7kpbkgy

Building sustainable collections of free third-party web resources,

2001 The journal of academic librarianship  
(CORC).  ...  The inefficiencies of this approach are numerous, but not necessarily so great as to rule out this approach in all contexts.  ... 
doi:10.1016/s0099-1333(01)00268-3 fatcat:uj4tzdesevekleegpnswnkkww4

From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo [article]

Daria Gavriouchkina, Ruth M Williams, Martyna Lukoseviciute, Tatiana Hochgreb-Hagele, Upeka Senanayake, Vanessa Chong-Morrison, Supat Thongjuea, Emmanouela Repapi, Adam Mead, Tatjana Sauka-Spengler
2017 bioRxiv   pre-print
globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes.  ...  The neural crest (NC) is a transient embryonic stem cell populations characterised by its multipotency and broad developmental potential.  ...  Acknowledgements This work was supported by MRC (G0902418), Lister Institute prize, Leverhulme Trust grant (RPG-2015-026), March of Dimes Basil OConnor Award to TSS, and SNF Fellowship to DG.  ... 
doi:10.1101/213611 fatcat:sdh7t2gfhzcbhgct25hvdooeni

CLASSIFIED Ads

American Library Association
2019 College & research libraries news  
an appropriate approach to metadata and digital archiving.  ...  Preference will be given to relevant work experience in an academic library, especially in the provision of reference and library instruction using both traditional and electronic approaches.  ...  M aster's degree from a program accredited by th e ALA required; two years of professional academic library experience or equivalent; experience arranging and describ ing m anuscript/archival collections  ... 
doi:10.5860/crln.62.3.337 fatcat:bzoezugqnzhwhjmys5xbzegsrm

Workshop on Higher-order Spectral Analysis

1989 Workshop on Higher-Order Spectral Analysis  
Acknowledgement: The author wVould like t(o thank Dr. Ceor-  ...  Your overwhelming response to its announcement allowed us to assemble a truly outstanding technical program consisting of two tutorial sessions. two keynote addresses and ten technical sessions.  ...  After (12) or (13) are used to io(re values for k2 may he allowed for each choice of k 1 compute P~(k, 1) the phase corrected DFT is given by in ( 12) or ( 13) .  ... 
doi:10.1109/hosa.1989.735258 fatcat:fjgqcfwdcbbvbowyygynmzeeme

Learning the Parts of Omics: Inference of Molecular Signatures with Non-negative Matrix Factorization

Andrés Felipe Quintero Moreno
2021
However, running a basic NMF analysis is a challenging task with a steep learning curve and long computing time; furthermore, the usability of these algorithms is lessened by limited resources to interpret  ...  In particular, Nonnegative Matrix Factorization (NMF) has been used to identify signatures in complex genomic datasets.  ...  Appendix C: ShinyButchR tutorial In this appendix, we show the steps to use ShinyButchR, and how to produce interactive visualizations of the NMF results.  ... 
doi:10.11588/heidok.00030629 fatcat:iimfamge35fchbpqenrwbt433i

Tennessee Libraries The Rainbow Effect-Under-Represented Groups and Library Leadership President's Program

Rosa Burnett
unpublished
from the conference program: Ethnically diverse library administrators are still somewhat rare.  ...  Attendees will gain insight needed to navigate the road to leadership. Expect frank talk about mentoring, networking, and avoiding career pitfalls.  ...  In order to get the administration to buy into this new multi-genre approach, I photocopied one article that I found to be particularly useful that chronicled one teacher's success with this approach.  ... 
fatcat:35w2qyohrzfkbowfnp5k52c464

Tennessee Libraries The Rainbow Effect-Under-Represented Groups and Library Leadership President's Program

Rosa Burnett
unpublished
from the conference program: Ethnically diverse library administrators are still somewhat rare.  ...  Attendees will gain insight needed to navigate the road to leadership. Expect frank talk about mentoring, networking, and avoiding career pitfalls.  ...  In order to get the administration to buy into this new multi-genre approach, I photocopied one article that I found to be particularly useful that chronicled one teacher's success with this approach.  ... 
fatcat:f535ptjmr5f4nijd3piufizv3y

Exploring pedagogies for effective teaching and learning in new multimedia environments : a comparative study of schools in Australia and the U.S

Clarke, Olivia Dorothy, 1948-
2017
SVMS US) I takes n ions tirnc to get cvcrything toguthcr, to make 311 the finisl~ing touchcs. and to lcam how to gct through a program stcp by stcp. (Katc. RCS US) It was ncal to do H!  ...  knowledge, and 'the constructs madc csplicit by thc participants of the study'.  ...  But I actually think thcrc is morc possibility in using a nngc of multimedia rather than onc program.  ... 
doi:10.4225/03/59d2fc7b9399a fatcat:x5a2p67zfffobj43pb3kfo4m2i
« Previous Showing results 1 — 15 out of 22 results