{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T13:39:54Z","timestamp":1775741994593,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Aptamers are \u2018synthetic antibodies\u2019 that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro , rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a M eta-motif-based statistical framework and pipeline to P redict the Bind ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis.<\/jats:p>\n               <jats:p>Availability and implementation : MPBind software and documents are available at http:\/\/www.morgridge.net\/MPBind.html . The human embryonic stem cells whole-cell SELEX-Seq data are available at http:\/\/www.morgridge.net\/Aptamer\/ .<\/jats:p>\n               <jats:p>Contact : RStewart@morgridge.org<\/jats:p>\n               <jats:p>Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu348","type":"journal-article","created":{"date-parts":[[2014,5,29]],"date-time":"2014-05-29T03:33:46Z","timestamp":1401334426000},"page":"2665-2667","source":"Crossref","is-referenced-by-count":58,"title":["MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers"],"prefix":"10.1093","volume":"30","author":[{"given":"Peng","family":"Jiang","sequence":"first","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"Susanne","family":"Meyer","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"Zhonggang","family":"Hou","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"Nicholas E.","family":"Propson","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"H. Tom","family":"Soh","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"James A.","family":"Thomson","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"},{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]},{"given":"Ron","family":"Stewart","sequence":"additional","affiliation":[{"name":"1 Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, 2 Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, 3 Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and 4 Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,5,28]]},"reference":[{"key":"2023012711554254600_btu348-B1","doi-asserted-by":"crossref","first-page":"15373","DOI":"10.1073\/pnas.1009331107","article-title":"Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing","volume":"107","author":"Cho","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711554254600_btu348-B2","doi-asserted-by":"crossref","first-page":"15416","DOI":"10.1073\/pnas.2136683100","article-title":"A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment","volume":"100","author":"Daniels","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711554254600_btu348-B3","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1128\/MCB.06536-11","article-title":"Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing","volume":"32","author":"Dittmar","year":"2012","journal-title":"Mol. Cell. Biol."},{"key":"2023012711554254600_btu348-B4","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrd1955","article-title":"Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease","volume":"5","author":"Ng","year":"2006","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023012711554254600_btu348-B5","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/364550a0","article-title":"An RNA motif that binds ATP","volume":"364","author":"Sassanfar","year":"1993","journal-title":"Nature"},{"key":"2023012711554254600_btu348-B6","article-title":"The American Soldier: Adjustment During Army Life","author":"Stouffer","year":"1949"},{"key":"2023012711554254600_btu348-B7","doi-asserted-by":"crossref","first-page":"e43836","DOI":"10.1371\/journal.pone.0043836","article-title":"Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection","volume":"7","author":"Thiel","year":"2012","journal-title":"PloS One"},{"key":"2023012711554254600_btu348-B8","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1089\/nat.2011.0288","article-title":"Nucleotide bias observed with a short SELEX RNA aptamer library","volume":"21","author":"Thiel","year":"2011","journal-title":"Nucleic Acid Ther."},{"key":"2023012711554254600_btu348-B9","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1126\/science.282.5391.1145","article-title":"Embryonic stem cell lines derived from human blastocysts","volume":"282","author":"Thomson","year":"1998","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2665\/48929430\/bioinformatics_30_18_2665.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2665\/48929430\/bioinformatics_30_18_2665.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:38:43Z","timestamp":1674823123000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/18\/2665\/2475612"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,28]]},"references-count":9,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,9,15]]},"published":{"date-parts":[[2014,5,28]]}}}