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LETTER: Genetic variation in the zebrafish
- Victor Guryev,
- Marco J. Koudijs,
- Eugene Berezikov,
- Stephen L. Johnson,
- Ronald H.A. Plasterk,
- Fredericus J.M. van Eeden,
- and Edwin Cuppen
Genome Res. April 2006 16: 491-497; Published in Advance March 13, 2006, doi:10.1101/gr.4791006
.... , Jacob H. , Fishman M.C. ( 1999 ) Zebrafish genetic map with 2000 microsatellite markers. Genomics 58 : 219 – 232 . ↵ Stickney H.L. , Schmutz J. , Woods I.G. , Holtzer C.C. , Dickson M.C. , Kelly P.D. , Myers R.M. , Talbot W.S. ( 2002 ) Rapid mapping of zebrafish mutations with SNPs and oligonucleotide...
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Methods: Digital Detection of Genetic Mutations Using SPC-Sequencing
- Hameer Ruparel,
- Michael E. Ulz,
- Sobin Kim,
- and Jingyue Ju
Genome Res. February 2004 14: 296-300; doi:10.1101/gr.1344104
...mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 12 : 1929 -1934. ↵ Taranenko, N.I., Allman, S.L., Golovlev, V.V., Taranenko, N.V., Isola, N.R., and Chen, C.H. 1998 . Sequencing DNA using mass spectrometry for ladder detection. Nucleic Acids Res. 26 : 2488 -2490...
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Research: Reprogramming of miRNA networks in cancer and leukemia
- Stefano Volinia,
- Marco Galasso,
- Stefan Costinean,
- Luca Tagliavini,
- Giacomo Gamberoni,
- Alessandra Drusco,
- Jlenia Marchesini,
- Nicoletta Mascellani,
- Maria Elena Sana,
- Ramzey Abu Jarour,
- Caroline Desponts,
- Michael Teitell,
- Raffaele Baffa,
- Rami Aqeilan,
- Marilena V. Iorio,
- Cristian Taccioli,
- Ramiro Garzon,
- Gianpiero Di Leva,
- Muller Fabbri,
- Marco Catozzi,
- Maurizio Previati,
- Stefan Ambs,
- Tiziana Palumbo,
- Michela Garofalo,
- Angelo Veronese,
- Arianna Bottoni,
- Pierluigi Gasparini,
- Curtis C. Harris,
- Rosa Visone,
- Yuri Pekarsky,
- Albert de la Chapelle,
- Mark Bloomston,
- Mary Dillhoff,
- Laura Z. Rassenti,
- Thomas J. Kipps,
- Kay Huebner,
- Flavia Pichiorri,
- Dido Lenze,
- Stefano Cairo,
- Marie-Annick Buendia,
- Pascal Pineau,
- Anne Dejean,
- Nicola Zanesi,
- Simona Rossi,
- George A. Calin,
- Chang-Gong Liu,
- Jeff Palatini,
- Massimo Negrini,
- Andrea Vecchione,
- Anne Rosenberg,
- and Carlo M. Croce
Genome Res. May 2010 20: 589-599; doi:10.1101/gr.098046.109
...be caused by the proliferation of lymphoid progenitors that atypically differentiated into T cells. The disease started early, at 2 and 4 mo of age, respectively, and had a rapid course with the mice dying 2 wk later. Their autopsy revealed a widespread leukemic infiltration, with organomegaly...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
...al. 2017). A “merge” (combine) function can be extraordinary conserved through hundreds of millions of years of evolution: The oncogenic THORLNC ncRNA contains an ultraconserved region responsible for the interaction with the IGF2BP1, and this interaction is conserved from zebrafish to humans (Hosono...
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Method: Mutation mapping and identification by whole-genome sequencing
- Ignaty Leshchiner,
- Kristen Alexa,
- Peter Kelsey,
- Ivan Adzhubei,
- Christina A. Austin-Tse,
- Jeffrey D. Cooney,
- Heidi Anderson,
- Matthew J. King,
- Rolf W. Stottmann,
- Maija K. Garnaas,
- Seungshin Ha,
- Iain A. Drummond,
- Barry H. Paw,
- Trista E. North,
- David R. Beier,
- Wolfram Goessling,
- and Shamil R. Sunyaev
Genome Res. August 2012 22: 1541-1548; Published in Advance May 3, 2012, doi:10.1101/gr.135541.111
...-Krezel L, Schier AF, et al. 1996. Mutations affecting the formation and function of the cardiovascular system in the zebrafish embryo. Development 123: 285–292. Stickney HL, Schmutz J, Woods IG, Holtzer CC, Dickson MC, Kelly PD, Myers RM, Talbot WS. 2002. Rapid mapping of zebrafish mutations with SNPs...
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Methods: Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene
- Edwin Cuppen,
- Eelke Gort,
- Esther Hazendonk,
- Josine Mudde,
- José van de Belt,
- Isaäc J. Nijman,
- Victor Guryev,
- and Ronald H.A. Plasterk
Genome Res. May 2007 17: 649-658; Published in Advance April 6, 2007, doi:10.1101/gr.6080607
...that are expected to be mutated once, which is calculated by N 1 = NAp 1 (1 − p ) (A−1) . NIM calculation Ensembl release 41 sequences and annotations of C. elegans , human, rat, mouse, and zebrafish s and Arabidopsis thaliana chromosome annotations (NCBI entries NC_003070.5, NC_003071.3, NC_003074.4, NC_003075...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
...a common evolutionary response of populations undergoing a shift in environment and, consequently, a change in the pattern of selective pressures.” He went on to suggest that “adaptive loss of function may occur regularly and may spread rapidly through small populations.” With their small size, rapid life...
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PERSPECTIVE: Fish genomics and biology
- Hugues Roest Crollius and
- Jean Weissenbach
Genome Res. December 2005 15: 1675-1682; doi:10.1101/gr.3735805
...are highly informative due to the accumulation of neutral mutations in nonfunctional regions. Yet humans and fishes share many developmental pathways, organ systems, and physiological mechanisms, making conclusions relevant to human biology. The respective advantages of zebrafish, medaka, Tetraodon...
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ARTICLE: Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish
- Angel Amores,
- Tohru Suzuki,
- Yi-Lin Yan,
- Jordan Pomeroy,
- Amy Singer,
- Chris Amemiya,
- and John H. Postlethwait
Genome Res. January 2004 14: 1-10; doi:10.1101/gr.1717804
..., a single Hoxc cluster, and at least two Hoxa clusters, with a portion of a third Hoxa cluster in fugu. Results support genome duplication before divergence of zebrafish and pufferfish lineages, followed by loss of a Hoxc cluster in the pufferfish lineage and loss of a Hoxd cluster...

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