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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...frequent haplotypes represented, based on 1000 Genomes EUR reference population) (Supplemental Fig. S1C). SNP selection was based on one of two approaches. First, we utilized our recent QTL analyses (Stolze et al. 2020) to prioritize variants (58% SNPs in the library) using combinations of the following...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...overlap, at least partially, those genotyped in the database. Each identified SNP may have a unique probability associated with the alternate allele dosage (reflecting certainty) or an overall error rate may be assigned. The Li-Stephens HMM (Fig. 1A) then maps recombination and mutation processes onto...
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Method: Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance
- Christopher J. Yoon,
- Su Yeon Kim,
- Chang Hyun Nam,
- Junehawk Lee,
- Jung Woo Park,
- Jihyeob Mun,
- Seongyeol Park,
- Soyoung Lee,
- Boram Yi,
- Kyoung Il Min,
- Brian Wiley,
- Kelly L. Bolton,
- Jeong Ho Lee,
- Eunjoon Kim,
- Hee Jeong Yoo,
- Jong Kwan Jun,
- Ji Seon Choi,
- Malachi Griffith,
- Obi L. Griffith,
- and Young Seok Ju
Genome Res. November/December 2022 32: 2134-2144; Published in Advance December 6, 2022, doi:10.1101/gr.276794.122
...a homo-ref genotype), any alternative alleles in the offspring are either a sequencing/mapping error or contamination by nonfamilial DNA. TrioMix reports the de novo–like alteration rate, the total alternative read fraction in GroupC SNPs in the offspring. Contribution from true de novo variants...
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RESOURCE: A SNP Resource for Human Chromosome 22: Extracting Dense Clusters of SNPs From the Genomic Sequence
- Elisabeth Dawson,
- Yuan Chen,
- Sarah Hunt,
- Luc J. Smink,
- Adrienne Hunt,
- Kate Rice,
- Simon Livingston,
- Suzannah Bumpstead,
- Richard Bruskiewich,
- Pak Sham,
- Rocky Ganske,
- Mark Adams,
- Kazuhiko Kawasaki,
- Nobuyoshi Shimizu,
- Shinsei Minoshima,
- Bruce Roe,
- David Bentley,
- and Ian Dunham
Genome Res. January 1, 2001 11: 170-178; doi:10.1101/gr.156901
...library ( Altshuler et al. 2000 ; Mullikin et al. 2000 ), or to use the overlapping clones from large-scale sequencing projects ( Kawasaki et al. 1997 ; Horton et al. 1998 ; Taillon-Miller et al. 1998 ). Although SNPs in coding sequences (cSNPs) are potentially functional and therefore, invaluable...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...is indicated by the label on the left. (C) SNPs along the gene body for each inbred strain. The reference genotype is shown in gray. SNPs are colored by genotype as shown in the legend. (D) Percent DNA methylation for each inbred strain along the Pkd2 gene body. Percentages are binned into 0% (blue) 50...
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Research: Natural variation in the histone demethylase, KDM4C, influences expression levels of specific genes including those that affect cell growth
- Brittany L. Gregory and
- Vivian G. Cheung
Genome Res. January 2014 24: 52-63; Published in Advance November 27, 2013, doi:10.1101/gr.156141.113
...the expression of the two allelic forms of KDM4C in 15 individuals heterozygous for an A/C SNP, rs913590, in the 39 UTR of KDM4C (;12 kb from rs7868863, and the A-allele of rs7868863 and the C-allele of rs913590 are on the same haplotype).We found that the expression levels of the C-bearing KDM4C transcripts...
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Research: A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry
- Raghothama Chaerkady,
- Dhanashree S. Kelkar,
- Babylakshmi Muthusamy,
- Kumaran Kandasamy,
- Sutopa B. Dwivedi,
- Nandini A. Sahasrabuddhe,
- Min-Sik Kim,
- Santosh Renuse,
- Sneha M. Pinto,
- Rakesh Sharma,
- Harsh Pawar,
- Nirujogi Raja Sekhar,
- Ajeet Kumar Mohanty,
- Derese Getnet,
- Yi Yang,
- Jun Zhong,
- Aditya P. Dash,
- Robert M. MacCallum,
- Bernard Delanghe,
- Godfree Mlambo,
- Ashwani Kumar,
- T.S. Keshava Prasad,
- Mobolaji Okulate,
- Nirbhay Kumar,
- and Akhilesh Pandey
Genome Res. November 2011 21: 1872-1881; Published in Advance July 27, 2011, doi:10.1101/gr.127951.111
...of such analyses is the identification of novel genes that have been entirelymissed by other approaches. Proteincoding genes leading to splice variants, truncated proteins, and cSNPs can all also be directly studied by protein sequencing. Several studies have demonstrated the use of mass spectrometry– based...
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LETTER: Identification of Candidate Coding Region Single Nucleotide Polymorphisms in 165 Human Genes Using Assembled Expressed Sequence Tags
- Kavita Garg,
- Philip Green,
- and Deborah A. Nickerson
Genome Res. November 1, 1999 9: 1087-1092; doi:10.1101/gr.9.11.1087
...substitutions. We report the identification and characteristics of 201 candidate single nucleotide polymorphisms found in the coding sequences (cSNPs) of 165 of these genes. Using a conservative calculation, coding region nucleotide diversity (the average number of differences between any pair of chromosomes...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
.... ↵ Buetow, K.H., Edmonson, M.H., and Cassidy, A.B. 1999 . Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet. 21 : 323 –325. ↵ Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S.E., and Scott, H.S. 2001 . A cSNP map and database for human chromosome 21. Genome Res...
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RESOURCE: Integration of the Rat Recombination and EST Maps in the Rat Genomic Sequence and Comparative Mapping Analysis With the Mouse Genome
- Steven P. Wilder,
- Marie-Thérèse Bihoreau,
- Karène Argoud,
- Takeshi K. Watanabe,
- Mark Lathrop,
- and Dominique Gauguier
Genome Res. April 2004 14: 758-765; doi:10.1101/gr.2001604
...inbred and recombinant congenic panels, heterogeneous stocks), whereas comparative maps are still mainly based on the localization of orthologous genes in physical maps. Although comparative analysis will undoubtedly progress with cSNP-based maps and large-scale computational alignments of human, mouse...

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