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Method: Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs
- Sara Silva Pereira,
- Aitor Casas-Sánchez,
- Lee R. Haines,
- Moses Ogugo,
- Kihara Absolomon,
- Mandy Sanders,
- Steve Kemp,
- Álvaro Acosta-Serrano,
- Harry Noyes,
- Matthew Berriman,
- and Andrew P. Jackson
Genome Res. September 2018 28: 1383-1394; Published in Advance July 13, 2018, doi:10.1101/gr.234146.118
...), a metric of VSG diversity based on the relative frequencies of each phylotype in a or transcriptome. Typically, the VSG repertoire is characterized manually using sequence similarity searches. However, this is time-consuming and requires technical expertise to detect sequence identification errors inherent...
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Research: Cell-type–specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes
- Tongwu Zhang,
- Jiyeon Choi,
- Michael A. Kovacs,
- Jianxin Shi,
- Mai Xu,
- NISC Comparative Sequencing Program,
- Melanoma Meta-Analysis Consortium,
- Alisa M. Goldstein,
- Adam J. Trower,
- D. Timothy Bishop,
- Mark M. Iles,
- David L. Duffy,
- Stuart MacGregor,
- Laufey T. Amundadottir,
- Matthew H. Law,
- Stacie K. Loftus,
- William J. Pavan,
- and Kevin M. Brown
Genome Res. November 2018 28: 1621-1635; Published in Advance October 17, 2018, doi:10.1101/gr.233304.117
...for identification of novel trait-associated loci via imputation of genotype-correlated gene expression levels into GWAS data sets (Gamazon et al. 2015; Gusev et al. 2016). Such approaches, usually referred to as transcriptome-wide association studies (TWASs), enable assignments of potentially disease...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...and sequencebased alignments (Managadze et al. 2011) have indicated that RNA secondary structures are depleted in lncRNAs (Ulitsky and Bartel 2013). The low sequence conservation of most lncRNAs, while complicating identification of CRSs, does not preclude their existence, such as in telomerase RNA (structurally...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...,B ). The resulting hybridization pattern provides a “SNP signature” that has been exploited by several algorithms to predict SNPs from resequencing array data ( Patil et al. 2001 ; Hinds et al. 2005 ; Clark et al. 2007 ). However, where multiple SNPs or insertion/deletion (indel) polymorphisms are closely adjacent...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
...mirtron biogenesis. These features contrast in many respects with canonical miRNAs and highlighted that mirtrons are not simply short miRNA hairpins, nor are they specifically defined solely by searching for intronic hairpins. For comparison, we checked the ability of the miRscan III algorithm (Ruby et al...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...+ constructs initial GRNs using coexpression-based algorithms such as GENIE3 or GRNBoost2 (which are also baselines) and then refines the network by integrating motif enrichment to enforce biologically informed constraints. However, instead of inferring regulatory directionality directly from data, it relies...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
..., colored de Bruijn graphs from short-read data for all samples, align long-read–derived haplotypes and multiple reference data sources to restore graph connectivity information, and call variants using graph path-finding algorithms and a model for simultaneous alignment and recombination. We validate...
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Methods: Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
- Ivan Iossifov,
- Tian Zheng,
- Miron Baron,
- T. Conrad Gilliam,
- and Andrey Rzhetsky
Genome Res. July 2008 18: 1150-1162; Published in Advance April 16, 2008, doi:10.1101/gr.075622.107
...propose a novel probabilistic method. This method restricts the search space for candidate gene sets by using knowledge about molecular pathways and explicitly incorporates information about within-data set heterogeneity. Our approach extends the well-established multipoint genetic linkage model...
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ARTICLE: Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome
- Adam Pavlicek,
- Reniqua House,
- Andrew J. Gentles,
- Jerzy Jurka,
- and Bernice E. Morrow
Genome Res. November 2005 15: 1487-1495; doi:10.1101/gr.4281205
...by searching for single nucleotide polymorphic positions in BAC clones from different libraries mapped to LCR22-2 and LCR22-4. This method distinguishes single nucleotide polymorphisms from paralogous sequence variants and complex polymorphic positions. Sites of shared polymorphism are considered potential...
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Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
- Sahar Gelfman,
- David Burstein,
- Osnat Penn,
- Anna Savchenko,
- Maayan Amit,
- Schraga Schwartz,
- Tal Pupko,
- and Gil Ast
Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
..., we were interested in examining how the splice site motifs have changed through vertebrate evolution and how these changes affected the length of the flanking introns. In order to achieve that goal, we reconstructed the ancestral motifs of both 39 and 59ss using a maximum-likelihood based algorithm...

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