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1. P570: Generating a framework for curating mechanism of disease in monogenic conditions: A consensus effort of the Gene Curation Coalition

Author

Marina DiStefano, Fowzan Alkuraya, Joanna Amberger, Christina Austin-Tse, Ola Austine, Marie Balzotti, Jonathan Berg, Elspeth Bruford, Alicia Byrne, Elena Cibrian-Uhalte, Alison Coffey, Helen Firth, Ada Hamosh, Sarah Hunt, Teri Klein, Catherine Kurtz, Sarah Leigh, Ivone Leong, Caterina Lucano, Sateesh Maddirevula, Audrey O'Neill, Arina Puzriakova, Ana Rath, Angharad Roberts, Kelly Radtke, Erin Ramos, Erin Riggs, Charlotte Rodwell, Julie Taylor, Katrin Sangkuhl, Catherine Snow, Zornitza Stark, James Ware, Bess Wayburn, Phillip Weller, and Heidi Rehm

Subjects
Genetics, QH426-470, Medicine
Published
2024
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2. The Role of Early Schooling in Shaping Inequality in Academic, Executive Functioning, and Social-Emotional Skills

Author

Marissa E. Thompson, Christina Weiland, Meghan P. McCormick, Catherine Snow, and Jason Sachs

Subjects
Social Sciences, Sociology (General), HM401-1281
Abstract

Children from historically marginalized racial/ethnic and socioeconomic groups, on average, score lower on widely used assessments of academic, executive functioning, and social-emotional skills at kindergarten entry, but the extent to which these differences are shaped by exposure to early schooling is unclear. Using data from a public prekindergarten and kindergarten program in Boston, we leverage a seasonal comparison design to examine how patterns change during the school year relative to summer periods. Although trends vary somewhat by the skill domain and groups compared, we largely find that exposure to early schooling is compensatory or neutral in shaping inequality. This suggests that prekindergarten and kindergarten together contribute to more equitable outcomes than would otherwise be expected in the absence of schooling. However, we find no evidence of systematic differences in access to high-impact classroom processes, which leaves open the question of which aspects of early schooling are most associated with declining inequality.

Published
2023
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3. P451: The Gene Curation Coalition works to resolve discrepancies in gene-disease validity assertions

Author

Marina DiStefano, Joanna Amberger, Christina Austin-Tse, Marie Balzotti, Mutaz Amin, Jonathan Berg, Carol Bocchini, Elspeth Bruford, Fowzan Alkuraya, Alison Coffey, Heather Collins, Fiona Cunningham, Helen Firth, David Fitzpatrick, Yaron Einhorn, Jennifer Goldstein, Ada Hamosh, Sarah Leigh, Ivone Leong, Christa Martin, Ellen McDonagh, Arina Puzriakova, Ana Rath, Angharad Roberts, Kelly Radtke, Erin Ramos, Erin Riggs, Charlotte Rodwell, Katrin Sangkuhl, Catherine Snow, Zornitza Stark, Jackie Tahiliani, James Ware, Eleanor Williams, Caroline Wright, Michael Yates, Phillip Weller, and Heidi Rehm

Subjects
Genetics, QH426-470, Medicine
Published
2023
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5. Exploring the academic reading challenges of graduate students of applied linguistics

Author

Hassan Nejadghanbar, Mahmood Reza Atai, and Catherine Snow

Subjects
Language and Literature, Philology. Linguistics, P1-1091
Abstract

Academic reading and writing abilities are prerequisites to success in postgraduate programs. These should be domains of competence in particular for students in applied linguistics, whose studies and future performance as teachers require insight into these skills. A questionnaire was administered to 194 students, who assessed their own academic reading skills. In addition, open-ended questions added to the questionnaire and interviews with 14 students were analyzed, yielding eight domains identified as particular challenges. The results revealed that students assessed their information literacy to be the weakest one. The eight areas of challenge included: shortage of time, information literacy, content knowledge, critical literacy, writers’ language style and generic features of texts, teachers’ high expectations and vague instructions, insufficient statistical literacy and insufficient interaction with peers.

Published
2022
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6. Off-Task Behavior as a Measure of In-Classroom Executive Function Skills? Evidence for Construct Validity and Contributions to Gains in Prekindergartners' Academic Achievement

Author

Lillie Moffett, Christina Weiland, Meghan P. McCormick, JoAnn Hsueh, Catherine Snow, and Jason Sachs

Abstract

Research Findings: Prior research has demonstrated the importance of young children's executive functioning (EF) skills for their success in schooling and beyond. However, the field lacks an understanding of how children's EF skills manifest in context. In the present study, we relate children's classroom off-task behavior to their EF skills. Prekindergarten children (N=263) were first assessed on their EF skills via direct assessments and a teacher report, and then they were observed on the amount of time spent off-task across classroom contexts like small-group instruction, whole-class instruction, independent work, transitions, and center time. Children's off-task behavior was weakly correlated with their directly assessed EF skills and moderately correlated with teacher reports of EF. The strength of associations was strongest for children's off-task behavior during whole-class instruction and transitions. Off-task behavior during whole-class instruction and transitions had the most within-classroom variation compared to other classroom settings, and off-task behavior during transitions most strongly predicted gains in math skills. Practice and Policy: Our study suggests that although direct EF assessments are the most predictive of children's academic achievement gains, it is beneficial to identify when children are going off-task and when this behavior is driven more by differences between children or classrooms.

Published
2024
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7. One Score to Rule Them All? Comparing the Predictive and Concurrent Validity of 30 Hearts and Flowers Scoring Approaches

Author

Tiffany Wu, Christina Weiland, Meghan McCormick, JoAnn Hsueh, Catherine Snow, and Jason Sachs

Abstract

The Hearts and Flowers (H&F) task is a computerized executive functioning (EF) assessment that has been used to measure EF from early childhood to adulthood. It provides data on accuracy and reaction time (RT) across three different task blocks (hearts, flowers, and mixed). However, there is a lack of consensus in the field on how to score the task that makes it difficult to interpret findings across studies. The current study, which includes a demographically diverse population of kindergarteners from Boston Public Schools (N = 946), compares the predictive and concurrent validity of 30 ways of scoring H&F, each with a different combination of accuracy, RT, and task block(s). Our exploratory results provide evidence supporting the use of a "two-vector average" score based on Zelazo et al.'s approach of adding accuracy and RT scores together only after individuals pass a certain accuracy threshold. Findings have implications for scoring future tablet-based developmental assessments. [This is the online version of an article published in "Assessment."]

Published
2024
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8. Teen Culture, Technology and Literacy Instruction: Urban Adolescent Students’ Perspectives

Author

Jia Li, Catherine Snow, and Claire White

Subjects
New technologies, social media, teen culture, language and literacy, technology adoption, age differences, middle school students, urban schools, Education
Abstract

Modern teens have pervasively integrated new technologies into their lives, and technology has become an important component of teen popular culture. Educators have pointed out the promise of exploiting technology to enhance students’ language and literacy skills and general academic success. However, there is no consensus on the effect of technology on teens, and scant literature is available that incorporates the perspective of urban and linguistically diverse students on the feasibility of applying new technologies in teaching and learning literacy in intact classrooms. This paper reports urban adolescents’ perspectives on the use of technology within teen culture, for learning in general and for literacy instruction in particular. Focus group interviews were conducted among linguistically diverse urban students in grades 6, 7 and 8 in a lower income neighborhood in the Northeastern region of the United States. The major findings of the study were that 1) urban teens primarily and almost exclusively used social media and technology devices for peer socializing, 2) they were interested in using technology to improve their literacy skills, but did not appear to voluntarily or independently integrate technology into learning, and 3) 8th graders were considerably more sophisticated in their use of technology and their suggestions for application of technology to literacy learning than 6th and 7th graders. These findings lead to suggestions for developing effective literacy instruction using new technologies.

Published
2015
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14. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

Author

Gill Wilson, Anna de Burca, Marta Bleda, Lucy R. Wedderburn, Matthew Welland, Kathleen Stirrups, Valentina Cipriani, Kerrie Woods, Vijeya Ganesan, Susan Hill, Rosaline Quinlivan, Georgia Chan, Mehul T. Dattani, Robert McFarland, Graeme C.M. Black, Rutendo Mapeta, Augusto Rendon, Francesco Muntoni, James O.J. Davies, Mina Ryten, Rebecca E. Foulger, Arianna Tucci, Dina Halai, Tom Fowler, Noemi B.A. Roy, Sarah Leigh, Dragana Josifova, Philip Twiss, Ana L.T. Tavares, Zerin Hyder, Detlef Bockenhauer, Patrick Yu-Wai-Man, Lara Abulhoul, Nikolas Pontikos, Anthony T. Moore, Huw R. Morris, Patrick F. Chinnery, Nicholas W. Wood, Ellen A. Thomas, Shehla Mohammed, Sofia Douzgou, Tanya Lam, Kate Gibson, Robert Sarkany, Teofila Bueser, Wei Wei, Siddharth Banka, Alexander Broomfield, Hiva Fassihi, Nils Koelling, Carolyn Campbell, James Buchanan, Melita Irving, Sandrine Compeyrot-Lacassagne, Karola Rehmström, Austen Worth, Nikhil Thapar, Andrew R. Webster, Paul Brennan, Rita Horvath, Gavin Arno, Richard H Scott, Sam Malka, Andrew O.M. Wilkie, Sofie Ashford, Maria Bitner-Glindzicz, Jana Vandrovcova, William G. Newman, Caroline F. Wright, Andrew M. Schaefer, Roger F.L. James, Robert W. Taylor, Melanie Babcock, Arjune Sen, Emma Baple, Ellen M. McDonagh, Stephanie Grunewald, Loukas Moutsianas, Melissa A. Haendel, Olivera Spasic-Boskovic, Eleanor G. Seaby, Anna Need, Clarissa Pilkington, Sarah Wordsworth, Shamima Rahman, Christine Patch, Colin Wallis, Kristina Ibanez, Bishoy Habib, Eik Haraldsdottir, Huw B. Thomas, Razvan Sultana, Andrea H. Németh, Agata Wolejko, Claire Palles, Phil Beales, Adam C. Shaw, Letizia Vestito, Emily Li, Sarah Rose, Sarah Hunter, Angela Matchan, Genevieve Say, Dalia Kasperaviciute, Henry Houlden, Raymond T. O’Keefe, R. Andres Floto, Jill Clayton-Smith, John B. Taylor, Hywel J. Williams, Volker Straub, Val Davison, Helen Savage, John Chisholm, Eleanor Dewhurst, Charles Crichton, Andrea Haworth, Clare Turnbull, Carolyn Tregidgo, Carme Camps, Christopher Penkett, Emer O’Connor, Georgina Hall, Lyn S. Chitty, Sally Halsall, Andrew D. Mumford, Annette G. Wagner, Eleanor Williams, Mark Bale, Julius O. Jacobsen, Willem H. Ouwehand, Charu Deshpande, Gavin Burns, Smita Y. Patel, James Polke, Thiloka Ratnaike, Gavin Fuller, John Burn, Kenneth E. S. Poole, Emma Footitt, John R. Bradley, Suzanne Wood, Russell J. Grocock, Jenny C. Taylor, Louise Izatt, Kikkeri N. Naresh, Katherine R. Smith, Nigel Burrows, Katrina Newland, Peter N. Robinson, Sarju G. Mehta, Michael A. Simpson, Michael R. Barnes, Pilar Cacheiro, Olivia Niblock, Tracy Lester, Dimitris Polychronopoulos, Helen Brittain, John A. Sayer, Antonio Martin, Eshika Haque, Sean Humphray, Douglass M. Turnbull, Damian Smedley, Andrew Devereau, Stefan Gräf, Sian Ellard, Ivone U.S. Leong, Martin G. Reese, Matthias Wielscher, Louise C. Daugherty, Perry M. Elliott, F. Lucy Raymond, Cecilia Compton, David Bentley, Catherine Snow, James Welch, Frances Flinter, Dom McMullan, Mark J. Caulfield, Paul Aurora, Mark Gurnell, Mary Kasanicki, I. Karen Temple, Michel Michaelides, Deborah Ruddy, Leema Robert, Janice Yip, Grainne S. Gorman, Andrew C. Browning, Richard Quinton, Maureen Cleary, Jamie M. Ellingford, Angela Douglas, Christopher Boustred, and Investigators, The 100,000 Genomes Project Pilot

Subjects
Adult, Male, Proband, medicine.medical_specialty, Adolescent, Pilot Projects, Genomics, Polymerase Chain Reaction, Genome, State Medicine, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Health care, Human Phenotype Ontology, Humans, Medicine, Child, Exome sequencing, 030304 developmental biology, Family Characteristics, 0303 health sciences, Whole Genome Sequencing, Genome, Human, business.industry, Genetic Variation, Rare Diseases/diagnosis, General Medicine, Middle Aged, United Kingdom, 3. Good health, Child, Preschool, Family medicine, Medical genetics, Female, business, Bristol, 030217 neurology & neurosurgery, Rare disease
Abstract

BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection.METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis.RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives.CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.).

Published
2021
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15. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources

Author

Marina T. DiStefano, Scott Goehringer, Lawrence Babb, Fowzan S. Alkuraya, Joanna Amberger, Mutaz Amin, Christina Austin-Tse, Marie Balzotti, Jonathan S. Berg, Ewan Birney, Carol Bocchini, Elspeth A. Bruford, Alison J. Coffey, Heather Collins, Fiona Cunningham, Louise C. Daugherty, Yaron Einhorn, Helen V. Firth, David R. Fitzpatrick, Rebecca E. Foulger, Jennifer Goldstein, Ada Hamosh, Matthew R. Hurles, Sarah E. Leigh, Ivone US. Leong, Sateesh Maddirevula, Christa L. Martin, Ellen M. McDonagh, Annie Olry, Arina Puzriakova, Kelly Radtke, Erin M. Ramos, Ana Rath, Erin Rooney Riggs, Angharad M. Roberts, Charlotte Rodwell, Catherine Snow, Zornitza Stark, Jackie Tahiliani, Susan Tweedie, James S. Ware, Phillip Weller, Eleanor Williams, Caroline F. Wright, T Michael. Yates, Heidi L. Rehm, Wellcome Trust, and British Heart Foundation

Subjects
Genetics & Heredity, GenCC, 0604 Genetics, Genetic Variation, 1103 Clinical Sciences, Genomics, Gene curation, Database, Genetic diagnosis, The Gene Curation Coalition, Databases, Genetic, Humans, Genetic Testing, Genetics (clinical)
Abstract

PURPOSESeveral groups and resources provide information that pertains to the validity of gene-disease relationships used in genomic medicine and research; however, universal standards and terminologies to define the evidence base for the role of a gene in disease, and a single harmonized resource were lacking. To tackle this issue, the Gene Curation Coalition (GenCC) was formed.METHODSThe GenCC drafted harmonized definitions for differing levels of gene-disease validity based on existing resources, and performed a modified Delphi survey with three rounds to narrow the list of terms. The GenCC also developed a unified database to display curated gene-disease validity assertions from its members.RESULTSBased on 241 survey responses from the genetics community, a consensus term set was chosen for grading gene-disease validity and database submissions. As of December 2021, the database contains 15,241 gene-disease assertions on 4,569 unique genes from 12 submitters. When comparing submissions to the database from distinct sources, conflicts in assertions of gene-disease validity ranged from 5.3% to 13.4%.CONCLUSIONTerminology standardization, sharing of gene-disease validity classifications, and resolution of curation conflicts will facilitate collaborations across international curation efforts and in turn, improve consistency in genetic testing and variant interpretation.

Published
2021

18. Publishing Journal Articles

Author

Zheng Yan and Catherine Snow

Abstract

Journal publication and grant writing are two core professional skills for new scholars today. However, systematic training is not typically offered in graduate programs worldwide. This book equips readers with the current scientific knowledge by providing a concise introduction to the science of journal article publication. The overall structure generally matches the curriculum of a graduate course and each chapter features a learning sequence based on Daniel Kahneman's intuitive judgement theory. The volume analyzes the intuitive thoughts of new authors from a variety of countries, uses over fifty real-life cases, and focuses on core concepts from nearly 100 research articles. It provides scientific advice for new authors, junior researchers, and graduate students to publish their scholarly work and advance their academic careers.

Published
2020
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19. ArrayExpress update – from bulk to single-cell expression data

Author

Anja Füllgrabe, Catherine Snow, Nuno A. Fonseca, Ahmed Ali, Irene Papatheodorou, Alvis Brazma, Haider Iqbal, Ugis Sarkans, Robert Petryszak, Nancy George, Laura Huerta, and Awais Athar

Subjects
0303 health sciences, Information retrieval, Application programming interface, business.industry, Sequencing data, Biology, Metadata, 03 medical and health sciences, 0302 clinical medicine, Software, Expression data, Data quality, Bulk samples, Databases, Genetic, Genetics, Database Issue, RNA-Seq, Single-Cell Analysis, business, Functional genomics, 030217 neurology & neurosurgery, Oligonucleotide Array Sequence Analysis, 030304 developmental biology
Abstract

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments in the last 12 months. Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq. To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments. Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the data easily but also serves as a test for data quality. With an increasing number of studies that combine different assay modalities (multi-omics experiments), a new more general archival resource the BioStudies Database has been developed, which will eventually supersede ArrayExpress. Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained.

Published
2018
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20. Common Themes in Teaching Reading for Understanding: Lessons From Three Projects

Author

Susan R. Goldman, Catherine Snow, and Sharon Vaughn

Subjects
Vocabulary, Process (engineering), media_common.quotation_subject, Teaching method, 05 social sciences, 050301 education, Vocabulary development, Education, Variety (cybernetics), Social support, Reading (process), Pedagogy, Learning to read, 0501 psychology and cognitive sciences, Psychology, 0503 education, 050104 developmental & child psychology, media_common
Abstract

This article reflects a metaview of the work of the three research projects funded through the Institute for Education Sciences under the Reading for Understanding competition that addressed middle-grade through high school readers (grades 4–12). All three projects shared the assumption that instruction is necessary for successful reading to learn just as it is for learning to read. Through multiple studies conducted independently, the three projects arrived at common themes and features of productive instruction for reading for understanding with adolescent readers. These common themes are elaborated with instructional examples and include the following: (a) Students purposefully engage with multiple forms of texts and actively process them, (b) instructional routines incorporate social support for reading through a variety of participation structures, and (c) instruction supports new content learning by leveraging prior knowledge and emphasizing key constructs and vocabulary.

Published
2016
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22. Pragmatic Development

Author

Anat Ninio, Catherine Snow, Anat Ninio, and Catherine Snow

Subjects
Language acquisition, Pragmatics, Speech acts (Linguistics)
Abstract

The pragmatic system consists of the rules for appropriate and communicatively-effective language use. This book provides an integrated view of the acquisition of the various pragmatic subsystems, including expression of communicative intents, participation in conversation, and production of extended discourse. The three components of the pragmatic system are presented in a way that makes clear how they relate to each other and why they all fall under the rubric of'pragmatics'. The authors combine their own extensive work in these three domains with an overview of the field of pragmatic development, describing how linguistic pragmatics relates to other aspects of language development, to social development, and to becoming a member of one's culture.

Published
2018

23. Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Author

Anja Füllgrabe, James C. Wright, Robert Petryszak, Satu Koskinen, Alvis Brazma, Pankaj Jaiswal, Laura Huerta, Elisabet Barrera, Mitra Barzine, Tony Burdett, Jyoti S. Choudhary, Catherine Snow, Emma Hastings, Oliver Mannion, Simon Jupp, Y. Amy Tang, Wolfgang Huber, Eleanor Williams, Nuno A. Fonseca, Maria Keays, Karyn Megy, Hendrik Weisser, Helen Parkinson, and Alfonso Muñoz-Pomer Fuentes

Subjects
Proteomics, 0301 basic medicine, InterPro, Gene Expression Profiling, Human Protein Atlas, Proteins, Computational biology, Plants, Biology, ENCODE, Bioinformatics, Hierarchical clustering, Gene expression profiling, Transcriptome, User-Computer Interface, 03 medical and health sciences, 030104 developmental biology, Cell Line, Tumor, Databases, Genetic, Genetics, Database Issue, Animals, Humans, Gene
Abstract

Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.

Published
2015
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25. The BioStudies database—one stop shop for all data supporting a life sciences study

Author

Catherine Snow, Mikhail Gostev, Jasmine Minguet, Olga Melnichuk, Ehsan Behrangi, Awais Athar, Alvis Brazma, Johanna McEntyre, Ahmed Ali, Andrew Tikhonov, Juan Camillo Rada, and Ugis Sarkans

Subjects
0301 basic medicine, Databases, Factual, Process (engineering), Data management, Biology, computer.software_genre, Biological Science Disciplines, 03 medical and health sciences, One stop shop, 0302 clinical medicine, Resource (project management), Genetics, Animals, Humans, Database Issue, Structure (mathematical logic), Internet, SIMPLE (military communications protocol), Database, business.industry, Term (time), 030104 developmental biology, Data access, business, computer, 030217 neurology & neurosurgery, Software
Abstract

BioStudies (www.ebi.ac.uk/biostudies) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process. It also can support data management needs of collaborative projects. The growth in multiomics experiments and other multi-faceted approaches to life sciences research mean that studies result in a diversity of data outputs in multiple locations. BioStudies presents a solution to ensuring that all these data and the associated publication(s) can be found coherently in the longer term.

Published
2017
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26. Implementation Challenges for Tier One and Tier Two School-Based Programs for Early Adolescents

Author

Maria D, LaRusso, Suzanne, Donovan, and Catherine, Snow

Subjects
Outcome and Process Assessment, Health Care, Schools, Adolescent, Reading, Humans, Curriculum, Child
Abstract

This mixed-method study examined the implementation and the challenges to implementation for participants in randomized controlled trials of two school-based programs for early adolescents: the Tier One Word Generation (WG) program, and the Tier Two Strategic Adolescent Reading Intervention (STARI). Levels of implementation for WG and STARI varied substantially across teachers and classrooms, with mean levels of 40% for fourth- and fifth-grade WG, 31% for sixth- and seventh-grade WG, and 47% for STARI. The three most common implementation challenges for WG were lack of time, multiple new programs/curricula happening at the same time, and time lost to testing and test prep. The three most common implementation challenges for STARI were student misbehavior, student absences, and time lost to testing and test prep. In order to succeed, efforts to find programs that work and to improve educational outcomes must address these formidable problems in U.S. public schools.

Published
2016

27. The SERP Approach to Problem-Solving Research, Development, and Implementation

Author

M. Suzanne Donovan, Catherine Snow, and Phil Daro

Subjects
Education
Abstract

Education researchers are increasingly working in practice-based partnerships in order to direct their research efforts toward important problems of practice. We argue for the creation of an infrastructure to support routine and sustained interaction among researchers, practitioners, and designers in order to make partnership efforts more efficient and effective over time. We describe SERP's efforts to initiate such an infrastructure through the creation and operation of “field sites”—long-term research, development, and implementation partnerships with school districts. We describe principles for field site operation and for product design that are emerging through our “learning by doing” approach. And we argue that the field site partnerships have produced work that is fundamentally different in character and content because of the SERP rules of engagement. SERP work is also more coherent because of its interdisciplinary character, and the sophistication of the partnership's work grows over time as related lines of work become integrated and as those engaged in sustained collaboration learn from each other.

Published
2013
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29. Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions

Author

Catherine Snow, Steven Hayward, and Guoying Qi

Subjects
Protein domain, Adenylate kinase, Citrate (si)-Synthase, Plasma protein binding, Ligands, medicine.disease_cause, Biochemistry, Motion, Molecular dynamics, Protein structure, Structural Biology, medicine, Citrate synthase, Computer Simulation, Molecular Biology, Escherichia coli, chemistry.chemical_classification, biology, Escherichia coli Proteins, Adenylate Kinase, Protein Structure, Tertiary, Enzyme, chemistry, biology.protein, Biophysics, Protein Binding
Abstract

Essential dynamics sampling simulations of the domain conformations of unliganded Escherichia coli adenylate kinase have been performed to determine whether the ligand-induced closed-domain conformation is accessible to the open unliganded enzyme. Adenylate kinase is a three- domain protein with a central CORE domain and twoflanking domains, the LID and the NMPbind domains. The sampling simulations were applied to the CORE and NMPbind domain pair and the CORE and LID domain pair separately. One aim is to compare the results to those of a similar study on the enzyme citrate synthase to determine whether a similar domain-locking mechanism operates in adenylate kinase. Although for adenylate kinase the simulations suggest that the closed-domain conformation of the unliganded enzyme is at a slightly higher free energy than the open for both domain pairs, the results are radically different to those found for citrate synthase. In adenylate kinase the targeted domain conformations could always be achieved, whereas this was not the case in citrate synthase due to an apparent free-energy barrier between the open and closed conformations. Adenylate kinase has been classified as a protein that undergoes closure through a hinge mechanism, whereas citrate synthase has been assigned to the shear mechanism. This was quantified here in terms of the change in the number of interdomain contacting atoms upon closure which showed a considerable increase in adenylate kinase. For citrate synthase this number remained largely the same, suggesting that the domain faces slide over each other during closure. This suggests that shear and hinge mechanisms of domain closure may relate to the existence or absence of an appreciable barrier to closure for the unliganded protein, as the latter can hinge comparatively freely, whereas the former must follow a more constrained path. In general though it appears a bias toward keeping the unliganded enzyme in the open-domain conformation may be a common feature of domain enzymes.

Published
2007
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30. Word Generation in Boston Public Schools: Natural History of a Literacy Intervention

Author

Catherine Snow, Catherine Snow, Joshua F. Lawrence, Catherine Snow, Catherine Snow, and Joshua F. Lawrence

Abstract

Describes a program to teach high-frequency academic vocabulary and discourses skills, promote effective teaching strategies for vocabulary, comprehension, and discussion, and facilitate faculty collaboration; its implementation; and evaluation results.

Published
2011

31. Measure for Measure: A Critical Consumers' Guide to Reading Comprehension Assessments for Adolescents

Author

Catherine Snow, Catherine Snow, Leila Morsy, Michael Kieffer, Catherine Snow, Catherine Snow, Leila Morsy, and Michael Kieffer

Abstract

A companion report to Carnegie's Time to Act, analyzes and rates commonly used reading comprehension tests for various elements and purposes. Outlines trends in types of questions, stress on critical thinking, and screening or diagnostic functions.

Published
2009

32. Reading Next: A Vision for Action and Research in Middle and High School Literacy

Author

Catherine Snow, Catherine Snow, Gina Biancarosa, Catherine Snow, Catherine Snow, and Gina Biancarosa

Abstract

Outlines fifteen key elements that educators can use to develop an effective adolescent literacy intervention program. Focuses on elements of interventions that are most promising for students that struggle with reading and writing after third grade.

Published
2004

33. Summary Review of Developmental Research on Language Development and Emergent Literacy in Preschool-Kindergarten- Aged Second Language Learners (SLL)

Author

L. Antonio Gonzales, Michael A. Lopez, and Catherine Snow

Subjects
Language assessment, Comprehension approach, Developmental and Educational Psychology, Developmental linguistics, Developmental research, Second-language attrition, Psychology, Emergent literacy, On Language, Natural language, Linguistics, Education
Published
2000
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34. Adolescent Literacy and the Achievement Gap: What Do We Know and Where Do We Go From Here?

Author

Catherine Snow, Catherine Snow, Gina Biancarosa, Catherine Snow, Catherine Snow, and Gina Biancarosa

Abstract

Reviews research and program initiatives focused on improving adolescent academic achievement by targeting literacy. Provides ideas for collaboration and coordination of funding efforts to improve the literacy achievement of under-performing adolescents.

Published
2003

35. Current status and new features of the Consensus Coding Sequence database

Author

Catherine Snow, Robert Baertsch, Marie-Marthe Suner, Shashikant Pujar, Susan M. Hiatt, Toby Hunt, Tim Hubbard, José M. González, Wendy Wu, Lillian D. Riddick, Kim D. Pruitt, M. Kay, Janet Weber, David Haussler, Garth Brown, Nuala A. O'Leary, Adam Frankish, Jennifer Harrow, James G. R. Gilbert, Bronwen Aken, Ruth Bennett, Jeena Rajan, Andrei Shkeda, Jonathan M. Mudge, Laurens G. Wilming, Stephen J. Trevanion, Kelly M. McGarvey, Pamela Tamez, Jennifer Hart, Mark Diekhans, Stephen M. J. Searle, James Ostell, Bhanu Rajput, Rachel A. Harte, Craig Wallin, Michael R. Murphy, Mark G. Thomas, Charles A. Steward, Jane E. Loveland, Catherine M. Farrell, Sanjida H. Rangwala, Daniel Barrell, and David Webb

Subjects
Genomics, Biology, Bioinformatics, Genome, Databases, Annotation, Mice, Genetic, Information and Computing Sciences, Databases, Genetic, Genetics, Ensembl, Animals, Humans, Internet, Information retrieval, Human Genome, Proteins, Molecular Sequence Annotation, Genome project, Exons, V. Human genome, model organisms, comparative genomics, Biological Sciences, Identifier, Sequence Analysis, Environmental Sciences, Developmental Biology, Reference genome
Abstract

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

Published
2013

36. An integrated encyclopedia of DNA elements in the human genome

Author

Robert Altshuler, Laura Elnitski, Michael Anaya, Alec Victorsen, Deborah Winter, Javier Herrero, Katherine Varley, Andrea Sboner, Oscar Junhong Luo, Marco Mariotti, Cristina Sisu, Mike Kay, Timothy Dreszer, Jane Loveland, Alexandra Bignell, Ewan Birney, Tim @timjph Hubbard, Kuljeet Sandhu, Eric Haugen, Chris Gunter, Alexej Abyzov, Lucas Ward, Georgi Marinov, Michael Pazin, Thomas Gingeras, Alexander Dobin, Kimberly Foss, Xianjun Dong, Benoit Miotto, Piotr Mieczkowski, Cedric Notredame, Andrew Berry, Shawn Gillespie, Axel Visel, Shawn Levy, Richard Sandstrom, Jose M Gonzalez, Melissa Fullwood, Timo Lassmann, Michael Tress, Julien Lagarde, Kevin Yip, Leslie Adams, Sylvain Foissac, Bronwen Aken, Piero Carninci, Suganthi Balasubramanian, Andrea Tanzer, Sarah Djebali, Michael Hoffman, Gloria Despacio-Reyes, Peter Park, Felix Kokocinski, Katherine Fisher-Aylor, Juan M Vaquerizas, Peggy Farnham, Patrick Collins, Amonida Zadissa, Pedro Ferreira, Philippe Batut, Michael Snyder, Electra Tapanari, Adam Frankish, Paul Flicek, AMARTYA SANYAL, Tyler Alioto, Giovanni Bussotti, Laurence Meyer, Jingyi Jessica Li, Matthew Blow, Tristan FRUM, Roger Alexander, Rory Johnson, Charles Steward, Meizhen Zheng, Margus Lukk, Ross Hardison, Claire Davidson, Gary Saunders, Alan Boyle, Luiz Penalva, Rajinder Kaul, Lazaro Centanin, Florencia Pauli Behn, Thomas Derrien, Nathan Sheffield, Toby Hunt, Eric Nguyen, Jeff Vierstra, Konrad Karczewski, Kimberly Bell, Yanbao Yu, Hagen U Tilgner, James Taylor, Balázs Bánfai, Catherine Snow, Benjamin Vernot, Stephan Kirchmaier, Michael Sammeth, Steven Wilder, Angelika Merkel, Joanna Mieczkowska, Guoliang Li, Wei Lin, Jennifer Harrow, Thomas Oliver Auer, Daniel Barrell, Eddie Park, Alvis Brazma, Hazuki Takahashi, Nathan Johnson, Daniel Sobral, Terry Furey, Alexandre Reymond, Jonathan Mudge, Anshul Kundaje, Jose Rodriguez, Akshay Bhinge, James Gilbert, Jakub Karczewski, Venkat Malladi, Troy Whitfield, Orion Buske, Ian Dunham, Jennifer Moran, Joachim Wittbrodt, Charles B. Epstein, Laurens Wilming, Jason Gertz, Joshua Akey, Joel Rozowsky, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), National Human Genome Research Institute (NHGRI), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Antonarakis, Stylianos, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Altshuler, Robert Charles, Ernst, Jason, Kellis, Manolis, Kheradpour, Pouya, Ward, Lucas D., Eaton, Matthew Lucas, Hendrix, David A., Jungreis, Irwin, Lin, Michael F., Washietl, Stefan, Lists of participants and their affiliations appear at the end of the paper and in the 'Collaboration/Projet' field., The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein), U01HG004695 (E. Birney), U54HG004563 (G. E. Crawford), U54HG004557 (T. R. Gingeras), U54HG004555 (T. J. Hubbard), U41HG004568 (W. J. Kent), U54HG004576 (R. M. Myers), U54HG004558 (M. Snyder), U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker), RC2HG005591 and R01HG003700 (M. C. Giddings), R01HG004456-03 (Y. Ruan), U01HG004571 (S. A. Tenenbaum), U01HG004561 (Z. Weng), RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541,U01HG004561,RC2HG005679andR01HG003988(L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323, E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California., Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kellis M, Khatun J, Kheradpour P, Kundaje A, Lassmann T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elnitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent W, Lieb JD, Margulies EH, Myers RM, Snyder M, Stamatoyannopoulos JA, Tenenbaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandhu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent W, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge E, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry J, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanari E, Tress ML, van Baren MJ, Walters N, Washietl S, Wilming L, Zadissa A, Zhang Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Reymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyengar S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Lamarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenenbaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, Auer T, Centanin L, Eichenlaub M, Gruhl F, Heermann S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Frum T, Garg K, Gist E, Hansen R, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TV, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JM, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AD, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E., and Miotto, Benoit

Subjects
Encyclopedias as Topic, [SDV]Life Sciences [q-bio], DNA Footprinting, Genoma humà, Binding Sites/genetics, Histones/chemistry/metabolism, 0302 clinical medicine, Exons/genetics, ddc:576.5, 0303 health sciences, Multidisciplinary, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], DNA-Binding Proteins/metabolism, region, Chemistry, Genetic Predisposition to Disease/genetics, Genomics, Polymorphism, Single Nucleotide/genetics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Neoplasms/genetics, Chromatin, Cell biology, in vivo, Genetic Variation/genetics, 030220 oncology & carcinogenesis, Deoxyribonuclease I/metabolism, Proteins/genetics, transcription factor-binding, chromosome conformation capture, DNA Methylation/genetics, Chromosomes, Human/genetics/metabolism, Chromatin Immunoprecipitation, Mammals/genetics, DNA/genetics, determinant, Article, 03 medical and health sciences, map, Animals, Humans, Transcription Factors/metabolism, Alleles, mouse, 030304 developmental biology, Transcription, Genetic/genetics, Chromatin/genetics/metabolism, Sequence Analysis, RNA, human cell, Molecular Sequence Annotation, Regulatory Sequences, Nucleic Acid/genetics, Promoter Regions, Genetic/genetics, DNA binding site, Genòmica, Genome, Human/genetics, chromatin, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Genètica, Genome-Wide Association Study
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 /n(W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder);/nU54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and/nReinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591,R01HG003541, U01HG004561, RC2HG005679andR01HG003988(L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research/nProgram of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.

Published
2012
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38. The role of home literacy and language environment on bilinguals' English and Spanish vocabulary development.

Author

ELISABETH DUURSMA, SILVIA ROMERO-CONTRERAS, ANNA SZUBER, PATRICK PROCTOR, CATHERINE SNOW, DIANE AUGUST, and MARGARITA CALDERÓN

Subjects
MONOLINGUALISM, VOCABULARY, READING, BILINGUALISM, ENGLISH language
Abstract

For the monolingual population, research has shown that vocabulary knowledge is closely related to reading achievement. However, the role of vocabulary has not been studied as extensively in the bilingual population. It is important to look at vocabulary to better understand reading achievement in the bilingual population in the United States. This study investigated the predictors of Spanish and English vocabulary for 96 fifth-grade Latino English language learners. Our results suggest that becoming or staying proficient in English did not require parental use of English in the home. However, proficiency in Spanish required both instructional support at school and social support at home; it is likely that the low social status of Spanish is related to its greater dependence on home support. [ABSTRACT FROM AUTHOR]

Published
2007
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39. Eckerd Corp. tries to cut debt with public offering

Author

Smith, Catherine Snow

Subjects
Jack Eckerd Corp. -- Securities, Pharmaceutical industry -- Securities, Business, Business, regional
Abstract

As Jack Eckerd Corp. gets ready to offer 5.1 million shares of stock to the public, its preliminary prospectus gives a look at a $3.8-billion drug retailer that's making money [...]

Published
1993

40. Therapy as social interaction

Author

Catherine Snow, Shelley Midkiff-Borunda, Anita Small, and Adele Proctor

Subjects
Speech and Hearing, Linguistics and Language, Comprehension approach, Developmental linguistics, Psychology, Language acquisition, Second-language acquisition, Language and Linguistics, Speech therapy, Natural language, Linguistics, Social relation
Published
1984
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42. Foreword

Author

Catherine Snow

Subjects
Speech and Hearing, Linguistics and Language, Language and Linguistics
Published
1984
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