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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
..., et al. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22: 10015. Li Q, Gloudemans MJ, Geisinger JM, Fan B, Aguet F, Sun T, Ramaswami G, Li YI, Ma JB, Pritchard JK, et al. 2022. RNA editing underlies genetic risk of common inflammatory ...
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REVIEW: An approach to high-throughput genotyping.
- J M Hall,
- C A LeDuc,
- A R Watson,
- and A H Roter
Genome Res. September 1996 6: 781-790; doi:10.1101/gr.6.9.781
...Watson, A Roter Hall, J M LeDuc C A LeDuc, CA AR Watson A.H. Roter Hall, J.M Hall J M LeDuc, C A Watson J M J M Hall J Hall A R J.M. Hall CA LeDuc Roter, A.H Watson, AR C LeDuc Watson, A R A H Hall, JM AH Roter A R, Watson LeDuc, C.A Watson C A LeDuc C.A. LeDuc Roter, A H A Roter A H, Roter Roter ...
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Research: The interaction of PRC2 with RNA or chromatin is mutually antagonistic
- Manuel Beltran,
- Christopher M. Yates,
- Lenka Skalska,
- Marcus Dawson,
- Filipa P. Reis,
- Keijo Viiri,
- Cynthia L. Fisher,
- Christopher R. Sibley,
- Benjamin M. Foster,
- Till Bartke,
- Jernej Ule,
- and Richard G. Jenner
Genome Res. July 2016 26: 896-907; Published in Advance May 9, 2016, doi:10.1101/gr.197632.115
...12/ cells, with and without 4-sU. (B) CLIP for SUZ12 in Eed4 cKO cells before or after the addition of doxycycline to repress expression ofMYC-EED4. An arrowmarks the SUZ12 RNP. Immunoblots for SUZ12, EZH2, and MYC-EED are shown below. (C) CLIP for JARID2 with anti-Flag antibody inWT (JM8 ...
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Method: TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
- Liguo Zhang,
- Yang Zhang,
- Yu Chen,
- Omid Gholamalamdari,
- Yuchuan Wang,
- Jian Ma,
- and Andrew S. Belmont
Genome Res. February 2021 31: 251-264; Published in Advance December 18, 2020, doi:10.1101/gr.266239.120
....M.).Author contributions: L.Z. designed and performed all experiments, collected data, and conducted microscopy image analysis with A.S.B.s guidance. L.Z. and Y.Z. analyzed genomic data with guidance from A.S.B. and J.M. Y.Z. developed the TSA-seq normalization software and updated this software to its new version ...
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LETTER: Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
- W. Scott Watkins,
- Alan R. Rogers,
- Christopher T. Ostler,
- Steve Wooding,
- Michael J. Bamshad,
- Anna-Marie E. Brassington,
- Marion L. Carroll,
- Son V. Nguyen,
- Jerilyn A. Walker,
- B.V. Ravi Prasad,
- P. Govinda Reddy,
- Pradipta K. Das,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2003 13: 1607-1618; Published in Advance June 12, 2003, doi:10.1101/gr.894603
..., or unpublished information as indicated in the paper: J.M. Naiad, B.B. Rao, T. Jenkins, J. Kidd, K. Kidd, and H. Soodyall.] Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.894603. 9 Corresponding author. E-MAIL lbj@genetics.utah.edu ; FAX (801) 585 ...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
...and functional properties of the variant H2A.Bbd nucleosome. EMBO J 25: 42344244. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C. 1982. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10: 27092721. Eirin-Lopez JM ...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
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Method: Single-cell genomics for dissection of complex malaria infections
- Shalini Nair,
- Standwell C. Nkhoma,
- David Serre,
- Peter A. Zimmerman,
- Karla Gorena,
- Benjamin J. Daniel,
- François Nosten,
- Timothy J.C. Anderson,
- and Ian H. Cheeseman
Genome Res. June 2014 24: 1028-1038; Published in Advance May 8, 2014, doi:10.1101/gr.168286.113

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