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Method: Defining TP53 pioneering capabilities with competitive nucleosome binding assays
- Xinyang Yu and
- Michael J. Buck
Genome Res. January 2019 29: 107-115; Published in Advance November 8, 2018, doi:10.1101/gr.234104.117
...Xinyang Yu1 and Michael J. Buck1,2 1New York State Center of Excellence in Bioinformatics and Life Sciences and Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York 14203, USA; 2Department of Biomedical Informatics, State University of New York at Buffalo, Buffalo...
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GENOME METHODS: PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation
- Jinghui Zhang and
- Thomas L. Madden
Genome Res. June 1, 1997 7: 649-656; doi:10.1101/gr.7.6.649
...PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation Jinghui Zhang 1 and Thomas L. Madden National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...classified genes according to intact start and stop codons, low-quality annotation, and partial annotation. Also, for each gene, a representative transcript was chosen based on reciprocal best hit BLAST results with protein sequences of human representative transcripts. For genes with no reciprocal best hit...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...in the assembly of each isolate using BLAST. The results were manually curated, and multiple protein alignments were generated. The presence and distribution pattern of amino acid substitutions were investigated manually.Data accessThe raw sequence data generated in this study have been submitted to the NCBI Bio...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...) (Vacic et al. 2007). The canonical structure of FZNF genes resembles that of KZNFs, with the FiNZ domain being encoded by a single exon upstream of a second exon consisting of an array of ZNF domains (Imbeault et al. 2017).We reannotated putative FZNF genes using a combination of BLAST (Altschul et al...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...× 10−6. Protein structure similarity was explored using I-TASSER (Roy et al. 2010) as in Ansell et al. (2019) and Supplemental Methods. Blast2GO (Conesa et al. 2005) version 4.1.9 was used to assign Enzyme Code (EC) and Gene Ontology (GO) terms. We compared the existing protein product names to the new...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
...-based methods capture transcripts in an unbiased manner and are capable of whole transcriptome coverage. For example, laser capture microdissection physically separates cells and structures of interest within a tissue, which can then be profiled by a variety of methods including RNA-seq (Emmert-Buck et al. 1996...
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Method: Plasmid detection and assembly in genomic and metagenomic data sets
- Dmitry Antipov,
- Mikhail Raiko,
- Alla Lapidus,
- and Pavel A. Pevzner
Genome Res. June 2019 29: 961-968; Published in Advance May 2, 2019, doi:10.1101/gr.241299.118
...unique cyclocontigs in the ISOLATES data set reconstructed by plasmidSPAdes+ (A) and the Venn diagram for cyclocontigs identified as plasmids by plasmidVerify, cyclocontigs identified as plasmids by BLAST (span >10%), and cyclocontigs containing ARGs (B). (A) Each dot represents a cyclocontig reported...
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Method: A long-read RNA-seq approach to identify novel transcripts of very large genes
- Prech Uapinyoying,
- Jeremy Goecks,
- Susan M. Knoblach,
- Karuna Panchapakesan,
- Carsten G. Bonnemann,
- Terence A. Partridge,
- Jyoti K. Jaiswal,
- and Eric P. Hoffman
Genome Res. June 2020 30: 885-897; Published in Advance July 6, 2020, doi:10.1101/gr.259903.119
...al. 2006; Buck et al. 2010).A paralog of nebulin is the nebulin-related anchoring protein (Nrap) (Luo et al. 1997). Nrap is the second largest (∼196 kDa) member of the nebulin family of proteins (Luo et al. 1997; Pappas et al. 2011). It is a scaffolding protein, with roles in myofibrillar assembly...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...ready cell generation, nontargeting, and HIV-1 targeting guides 5 For CRISPRi cell lines, Jurkat clones were transduced with pseudotyped lentiviruses encoding Lenti-6 dCas9-KRAB-blast (Addgene #89567) by spinoculation. Two days post-transduction, 8 μg/mL blasticidin was 7 added to the culture medium...
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