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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...for this article.] The human reference assembly remains a critical resource for the biological and clinical research communities (International Human Genome Sequencing Consortium 2001, 2004). It is distinguished from the growing number of human assemblies in public databases by virtue of its long contig...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...and Birney 2008) (version 1.2.07), and SOAPdenovo2 (Luo et al. 2012) (version 2.04). When the assembly test of human chromosome 14 was performed in the GAGE study (Salzberg et al. 2012), these assemblers recorded the largest scaffold NG50 values and were ranked first through fourth, respectively. ALLPATHS...
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Method: Inferring chromatin-bound protein complexes from genome-wide binding assays
- Eugenia G. Giannopoulou and
- Olivier Elemento
Genome Res. August 2013 23: 1295-1306; Published in Advance April 3, 2013, doi:10.1101/gr.149419.112
...expression in regression models. Computational discovery of protein complexes Genome Research 1297 www..org gaged more frequently in physical interactions than expected by chance (P < 0.01 inH1 ESC, P < 0.02 inGM12878, P < 0.03 in K562) (Table 1; Supplemental Table 3). Third, several of the complexes...
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Method: A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
...A comprehensively molecular haplotype-resolved genome of a European individual Eun-Kyung Suk 1 , 4 , Gayle K. McEwen 1 , 4 , Jorge Duitama 1 , Katja Nowick 1 , Sabrina Schulz 1 , Stefanie Palczewski 1 , Stefan Schreiber 2...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...of their chromosomes (ploidy), fully resolving the haplotypes is a key component to accurate assembly, and chromosome-phasing metrics assess this (Rhie et al. 2020; Cheng et al. 2021). Another critical set of metrics evaluates the base-level accuracy of the assembled sequence (Rhie et al. 2020).All sequencing...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...% for the evaluation data set, whereas all cells were used for 10-fold cross-validation. We utilized four machine learning algorithms without Gaussian distribution assumption, including SVM, RF, AdaBoost, and MLP. Python package scikit-learn 1.2.1 was used to construct the machine learning models. We initially...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
..., Grishina I, Narvaiza I, Selleri L, Gage FH, Swigut T, Wysocka J. 2015. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell 163: 68–83. doi:10.1016/j.cell.2015.08.036 ↵Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire Ali Mortazavi 1 , Evonne Chen Leeper Thompson 2 , Sarah T. Garcia 2 , Richard M. Myers 2 , and Barbara Wold 1 , 3...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...), and the X and Y Chromosomes (Wagner et al. 2025). The latest draft benchmarks currently being evaluated by GIAB are based on a T2T assembly of HG002 and include 3.6 million SNVs, 950,000 indels, and 29,000 SVs in 2.74 and 2.76 Gbp of GRCh38 (2.77 and 2.82 Gbp of CHM13) for small variants and SVs...
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