Searching journal content for articles similar to Agarwala et al. 8 (3): 211.

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  1. Resource: Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees
    • Ehsan Ullah,
    • Raghvendra Mall,
    • Mostafa M. Abbas,
    • Khalid Kunji,
    • Alejandro Q. Nato, Jr,
    • Halima Bensmail,
    • Ellen M. Wijsman,
    • and Mohamad Saad
    Genome Res. January 2019 29: 125-134; Published in Advance December 4, 2018, doi:10.1101/gr.236315.118
    ...with population- and pedigree-based imputation in admixed family data. BMC Proc 10: 295–301. doi:10.1186/s12919-016-0046-5 ↵Scheet P, Stephens M. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet...
    OPEN ACCESS ARTICLE
  2. Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
    • Alicia Petrany,
    • Ruoyu Chen,
    • Shaoqiang Zhang,
    • and Yong Chen
    Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
    ...properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant...
    OPEN ACCESS ARTICLE
  3. Method: SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk
    • Wouter Coppieters,
    • Latifa Karim,
    • and Michel Georges
    Genome Res. August 2020 30: 1201-1207; Published in Advance June 26, 2020, doi:10.1101/gr.256172.119
    ...to verify whether a specific cow did contribute milk to the tank or not (e.g., by testing the significance of the corresponding cow effect in the linear model) (Blard et al. 2012). The described method may have applications in tracing the origins of bulk animal food products other than milk, as well...
  4. Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
    • Joshua M. Akey
    Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
    ...Constructing genomic maps of positive selection in humans: Where do we go from here? Joshua M. Akey , 1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA Abstract Identifying targets of positive selection in humans has...
  5. Method: The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
    • Marcin Cieslik,
    • Rashmi Chugh,
    • Yi-Mi Wu,
    • Ming Wu,
    • Christine Brennan,
    • Robert Lonigro,
    • Fengyun Su,
    • Rui Wang,
    • Javed Siddiqui,
    • Rohit Mehra,
    • Xuhong Cao,
    • David Lucas,
    • Arul M. Chinnaiyan,
    • and Dan Robinson
    Genome Res. September 2015 25: 1372-1381; Published in Advance August 7, 2015, doi:10.1101/gr.189621.115
    ..., capture libraries retain these qualities regardless of RNA quality and provide excellent data from clinical specimens including formalin-fixed paraffin-embedded (FFPE) blocks. Systematic improvements across key applications of RNA-seq are shown on a cohort of prostate cancer patients and a set of clinical...
  6. Method: Application of histone modification-specific interaction domains as an alternative to antibodies
    • Goran Kungulovski,
    • Ina Kycia,
    • Raluca Tamas,
    • Renata Z. Jurkowska,
    • Srikanth Kudithipudi,
    • Chisato Henry,
    • Richard Reinhardt,
    • Paul Labhart,
    • and Albert Jeltsch
    Genome Res. November 2014 24: 1842-1853; Published in Advance October 9, 2014, doi:10.1101/gr.170985.113
    ...Application of histone modification-specific interaction domains as an alternative to antibodies Goran Kungulovski 1 , Ina Kycia 1 , 4 , Raluca Tamas 1 , Renata Z. Jurkowska 1 , Srikanth Kudithipudi 1 , Chisato Henry 2...
  7. Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
    • Marta Tomaszkiewicz,
    • Samarth Rangavittal,
    • Monika Cechova,
    • Rebeca Campos Sanchez,
    • Howard W. Fescemyer,
    • Robert Harris,
    • Danling Ye,
    • Patricia C.M. O'Brien,
    • Rayan Chikhi,
    • Oliver A. Ryder,
    • Malcolm A. Ferguson-Smith,
    • Paul Medvedev,
    • and Kateryna D. Makova
    Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
    ...A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y Marta Tomaszkiewicz 1 , 9 , Samarth Rangavittal 1 , 9 , Monika Cechova 1 , 9 , Rebeca Campos Sanchez 2 , Howard W...
    OPEN ACCESS ARTICLE
  8. Method: Application of microdroplet PCR for large-scale targeted bisulfite sequencing
    • H. Kiyomi Komori,
    • Sarah A. LaMere,
    • Ali Torkamani,
    • G. Traver Hart,
    • Steve Kotsopoulos,
    • Jason Warner,
    • Michael L. Samuels,
    • Jeff Olson,
    • Steven R. Head,
    • Phillip Ordoukhanian,
    • Pauline L. Lee,
    • Darren R. Link,
    • and Daniel R. Salomon
    Genome Res. October 2011 21: 1738-1745; Published in Advance July 14, 2011, doi:10.1101/gr.116863.110
    ...Application of microdroplet PCR for large-scale targeted bisulfite sequencing H. Kiyomi Komori 1 , Sarah A. LaMere 1 , Ali Torkamani 1 , G. Traver Hart 1 , Steve Kotsopoulos 2 , Jason Warner 2 , Michael L. Samuels 2...
  9. Methods: Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
    • Jade P. Vinson,
    • David B. Jaffe,
    • Keith O'Neill,
    • Elinor K. Karlsson,
    • Nicole Stange-Thomann,
    • Scott Anderson,
    • Jill P. Mesirov,
    • Nori Satoh,
    • Yutaka Satou,
    • Chad Nusbaum,
    • Bruce Birren,
    • James E. Galagan,
    • and Eric S. Lander
    Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605
    ...Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi Jade P. Vinson 1 , 3 , David B. Jaffe 1 , Keith O'Neill 1 , Elinor K. Karlsson 1 , Nicole Stange-Thomann 1 , Scott Anderson 1 , Jill P. Mesirov...
  10. RESOURCE: Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs
    • Julie E. Horvath,
    • David W. Weisrock,
    • Stephanie L. Embry,
    • Isabella Fiorentino,
    • James P. Balhoff,
    • Peter Kappeler,
    • Gregory A. Wray,
    • Huntington F. Willard,
    • and Anne D. Yoder
    Genome Res. March 2008 18: 489-499; Published in Advance February 1, 2008, doi:10.1101/gr.7265208
    ...Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs Julie E. Horvath 1 , 7 , David W. Weisrock 2 , Stephanie L. Embry 1 , Isabella Fiorentino 2 , James P. Balhoff 3 , Peter...
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