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Research: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
- Ge Gao,
- Maria D. Vibranovski,
- Li Zhang,
- Zheng Li,
- Ming Liu,
- Yong E. Zhang,
- Xinmin Li,
- Wenxia Zhang,
- Qichang Fan,
- Nicholas W. VanKuren,
- Manyuan Long,
- and Liping Wei
Genome Res. April 2014 24: 629-638; Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
...in the main developmental stages in Drosophila melanogaster. Nucleic Acids Res 37: 43084314. Lifschytz E, Lindsley DL Lifschytz E, Lindsley DL. 1972. The role of X-chromosome inactivation during spermatogenesis. Proc Natl Acad Sci 69: 182186. Liu J, Mercer JM, Stam LF, Gibson GC, Zeng ZB, Laurie CC Liu ...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
..., Orlov YL, Zhang W, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 11061117. Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev 25: 10101022. Desjarlais JR, Berg JM. 1992 ...
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Method: A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome
- Fan Gao,
- Xuedong Pan,
- Elissa B. Dodd-Eaton,
- Carlos Vera Recio,
- Matthew D. Montierth,
- Jasmina Bojadzieva,
- Phuong L. Mai,
- Kristin Zelley,
- Valen E. Johnson,
- Danielle Braun,
- Kim E. Nichols,
- Judy E. Garber,
- Sharon A. Savage,
- Louise C. Strong,
- and Wenyi Wang
Genome Res. August 2020 30: 1170-1180; Published in Advance August 18, 2020, doi:10.1101/gr.249599.119
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...A, Lapasset L, Milhavet O, Parrinello H, Dantec C, Marin JM, Lemaitre JM. 2012. Unraveling cell typespecific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol 19: 837844. doi:10.1038/nsmb.2339 Bester AC, Roniger M, Oren YS ...
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Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
- Peng Liu,
- Alexandra A. Soukup,
- Emery H. Bresnick,
- Colin N. Dewey,
- and Sündüz Keleş
Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
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Resource: Modeling molecular development of breast cancer in canine mammary tumors
- Kiley Graim,
- Dmitriy Gorenshteyn,
- David G. Robinson,
- Nicholas J. Carriero,
- James A. Cahill,
- Rumela Chakrabarti,
- Michael H. Goldschmidt,
- Amy C. Durham,
- Julien Funk,
- John D. Storey,
- Vessela N. Kristensen,
- Chandra L. Theesfeld,
- Karin U. Sorenmo,
- and Olga G. Troyanskaya
Genome Res. February 2021 31: 337-347; Published in Advance December 23, 2020, doi:10.1101/gr.256388.119
...B, et al. 2018. Comprehensive characterization of cancer driver genes and mutations. Cell 173: 371385.e18. doi:10.1016/j.cell.2018.02.060 Ben-David U, Ha G, Tseng YY, Greenwald NF, Oh C, Shih J, McFarland JM, Wong B, Boehm JS, Beroukhim R, et al. 2017. Patient-derived xenografts undergo mouse ...
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Resource: Modeling transcriptional regulation of model species with deep learning
- Evan M. Cofer,
- João Raimundo,
- Alicja Tadych,
- Yuji Yamazaki,
- Aaron K. Wong,
- Chandra L. Theesfeld,
- Michael S. Levine,
- and Olga G. Troyanskaya
Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
...368. doi:10.1016/j.cell.2016.05.025 Gaspar JM. 2018. Improved peak-calling with MACS2. bioRxiv doi:10.1101/496521 Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 10171018. doi:10.1093/bioinformatics/btr064 Haeussler M, Zweig AS, Tyner C, Speir ML ...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
...Crcy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM. 2019. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res 47: 21432159. doi:10.1093/nar/gkz011 Dittmar KA, Goodenbour JM, Pan T. 2006. Tissue-specific differences in human ...
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Resource: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
- Jian Ming Khor,
- Jennifer Guerrero-Santoro,
- William Douglas,
- and Charles A. Ettensohn
Genome Res. September 2021 31: 1680-1692; Published in Advance July 30, 2021, doi:10.1101/gr.275684.121

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