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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
...) and ReMap2022 (Hammal et al. 2022) databases. For each peak data set representing one ChIP-seq experiment, we divided CREs into overlapping and nonoverlapping. We then compared the contact frequencies of CRE pairs overlapping the factor on both sides, or not at all, by calculating the Mann–Whitney U...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different...
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Research: BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies
- Guntram Borck,
- Friederike Hög,
- Maria Lisa Dentici,
- Perciliz L. Tan,
- Nadine Sowada,
- Ana Medeira,
- Lucie Gueneau,
- Holger Thiele,
- Maria Kousi,
- Francesca Lepri,
- Larissa Wenzeck,
- Ian Blumenthal,
- Antonio Radicioni,
- Tito Livio Schwarzenberg,
- Barbara Mandriani,
- Rita Fischetto,
- Deborah J. Morris-Rosendahl,
- Janine Altmüller,
- Alexandre Reymond,
- Peter Nürnberg,
- Giuseppe Merla,
- Bruno Dallapiccola,
- Nicholas Katsanis,
- Patrick Cramer,
- and Christian Kubisch
Genome Res. February 2015 25: 155-166; Published in Advance January 5, 2015, doi:10.1101/gr.176925.114
...from the first two families had been independently submitted to the web-based Dysmorphology Diagnostic System (DDS) of the DYSCERNE network (a European network of centers of expertise for dysmorphology) (Douzgou et al. 2014) by the respective attending geneticists (M.L.D. and B.D.; A.M.). After review...
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Resource: Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- Ali Mortazavi,
- Shirley Pepke,
- Camden Jansen,
- Georgi K. Marinov,
- Jason Ernst,
- Manolis Kellis,
- Ross C. Hardison,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. December 2013 23: 2136-2148; Published in Advance October 29, 2013, doi:10.1101/gr.158261.113
...and mining We created an interactive JavaScript web-based SOM viewer with an associated map segment database to facilitate these explorations (http://woldlab.caltech.edu/ENCODESOM). It allows users to visualize and compare units on the map with respect to any input data set or to additional data types (see...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...of ‘‘coding’’ versus ‘‘regulatory’’ may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype. [Supplemental material is available for this article.] Almost four decades ago, it was argued that coding sequence changeswere insufficient...
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Methods: A systems biology approach for pathway level analysis
- Sorin Draghici,
- Purvesh Khatri,
- Adi Laurentiu Tarca,
- Kashyap Amin,
- Arina Done,
- Calin Voichita,
- Constantin Georgescu,
- and Roberto Romero
Genome Res. October 2007 17: 1537-1545; Published in Advance September 4, 2007, doi:10.1101/gr.6202607
...techniques. On several illustrative data sets, the classical analysis produces both false positives and false negatives, while the impact analysis provides biologically meaningful results. This analysis method has been implemented as a Web-based tool, Pathway-Express, freely available as part of the Onto...
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RESOURCE: A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors
- Stuart Huntley,
- Daniel M. Baggott,
- Aaron T. Hamilton,
- Mary Tran-Gyamfi,
- Shan Yang,
- Joomyeong Kim,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. May 2006 16: 669-677; Published in Advance April 10, 2006, doi:10.1101/gr.4842106
.... To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets. Footnotes 4 ↵ 4 Corresponding author. ↵ 4 E-mail stubbs5@llnl...
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Research: Rare allelic forms of PRDM9 associated with childhood leukemogenesis
- Julie Hussin,
- Daniel Sinnett,
- Ferran Casals,
- Youssef Idaghdour,
- Vanessa Bruat,
- Virginie Saillour,
- Jasmine Healy,
- Jean-Christophe Grenier,
- Thibault de Malliard,
- Stephan Busche,
- Jean-François Spinella,
- Mathieu Larivière,
- Greg Gibson,
- Anna Andersson,
- Linda Holmfeldt,
- Jing Ma,
- Lei Wei,
- Jinghui Zhang,
- Gregor Andelfinger,
- James R. Downing,
- Charles G. Mullighan,
- and Philip Awadalla
Genome Res. March 2013 23: 419-430; Published in Advance December 5, 2012, doi:10.1101/gr.144188.112
...disease etiology. To characterize the importance of parental germline events in susceptibility to childhood ALL, we first set out to determine whether meiotic recombination patterns can lead to factors associated with the development of childhood ALL. From exome sequencing and genotyping data, we...
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ARTICLE: Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
- Julius Halaschek-Wiener,
- Jaswinder S. Khattra,
- Sheldon McKay,
- Anatoli Pouzyrev,
- Jeff M. Stott,
- George S. Yang,
- Robert A. Holt,
- Steven J.M. Jones,
- Marco A. Marra,
- Angela R. Brooks-Wilson,
- and Donald L. Riddle
Genome Res. May 2005 15: 603-615; Published in Advance April 18, 2005, doi:10.1101/gr.3274805
...with advanced age. Comparison of our results to recent microarray studies highlights sets of overlapping genes that are highly conserved throughout evolution and thus represent strong candidate genes that control aging and longevity. Footnotes [Supplemental material is available online at www...
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Methods: Survey of allelic expression using EST mining
- Bing Ge,
- Scott Gurd,
- Tiffany Gaudin,
- Carole Dore,
- Pierre Lepage,
- Eef Harmsen,
- Thomas J. Hudson,
- and Tomi Pastinen
Genome Res. November 2005 15: 1584-1591; doi:10.1101/gr.4023805
...versus Caucasian allele frequencies. From the set of 976 genes having in silico allelic imbalance ( P &lt; 0.05) ( http://quebec.mcgill.ca/EST-HapMap ), we chose 40 genes that are expressed in lymphoblastoid cell lines (LCLs), based on earlier DNA-microarray studies ( Pastinen and Hudson 2004...

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