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METHODS: In Silico Cloning of Novel Endothelial-Specific Genes
- Lukasz Huminiecki and
- Roy Bicknell
Genome Res. November 1, 2000 10: 1796-1806; doi:10.1101/gr.150700
...S.F. , Madden T.L. , Schäffer A.A. , Zhang J. , Zhang Z. , Miller W. , Lipman D.J. ( 1997 ) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 : 3389 – 3402 . ↵ Banerji S. , Ni J. , Wang S.X. , Clasper S. , Su J. , Tammi R. , Jones M. , Jackson D...
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LETTER: Gene Expression Profiling in Human Fetal Liver and Identification of Tissue- and Developmental-Stage-Specific Genes through Compiled Expression Profiles and Efficient Cloning of Full-Length cDNAs
- Yongtao Yu,
- Chenggang Zhang,
- Gangqiao Zhou,
- Songfeng Wu,
- Xianghu Qu,
- Handong Wei,
- Guichun Xing,
- Chunna Dong,
- Yun Zhai,
- Jinghong Wan,
- Shuguang Ouyang,
- Li Li,
- Shaowen Zhang,
- Kaixin Zhou,
- Yinan Zhang,
- Chutse Wu,
- and Fuchu He
Genome Res. August 1, 2001 11: 1392-1403; doi:10.1101/gr.175501
...amount of energy supply and protein synthesis is occurring. The genes expressed in HFL22w in the highest proportion were functionally related to the general housekeeping responsibilities of the cells, such as general metabolism, protein synthesis, and synthesis of nucleic acids and amino acids, which...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...obtained for 616 TFs and 56 chromatin or nucleic acid-binding proteins (Table 1; Supplemental File S1). (Of these TF strains, 189 were generated after Kudron et al. [2018]). The tagged TF strains capture all but 43 of the estimated 659 TFs (93.5%) in our curated list. The number of estimated TFs in the fly...
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Research: A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells
- Kei Fukuda,
- Akihiko Okuda,
- Kosuke Yusa,
- and Yoichi Shinkai
Genome Res. June 2018 28: 846-858; Published in Advance May 4, 2018, doi:10.1101/gr.227280.117
...) and a corepressor complex containing tripartite motif containing 28 (TRIM28 [also known as KAP1 or TIF1B]) (Rowe et al. 2010). This SETDB1/TRIM28 complex is recruited to target retroelements by TRIM28-associating, nucleic acid binding zinc-finger proteins (ZFPs), including KRAB-ZFPs and YY1 (Schlesinger et al. 2013...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...as viable cells (%) by flow cytometry based on the uptake of the fluorescent molecules propidium iodide (PI) and YO-PRO-1 iodide (YP). Propidium iodide and YO-PRO-1 are membrane-impermeable nucleic acid binding molecules that enter into necrotic but not into alive cells. Therefore, nonfluorescent cells...
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Research: Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target
- Myungjin Jo,
- Ah Young Chung,
- Nozomu Yachie,
- Minchul Seo,
- Hyejin Jeon,
- Youngpyo Nam,
- Yeojin Seo,
- Eunmi Kim,
- Quan Zhong,
- Marc Vidal,
- Hae Chul Park,
- Frederick P. Roth,
- and Kyoungho Suk
Genome Res. September 2017 27: 1487-1500; Published in Advance June 8, 2017, doi:10.1101/gr.211649.116
...Yes CCHC-type zinc finger nucleic acid binding protein (CNBP) Myotonic dystrophy Yes DFNA5, deafness associated tumor suppressor (DFNA5) Deafness Yes Hydroxysteroid 11 beta dehydrogenase 1 (HSD11B1) Cortisone reductase deficiency Yes Inducible T-cell costimulator (ICOS) Immunodeficiency Yes Leucine...
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Research: RNA structure replaces the need for U2AF2 in splicing
- Chien-Ling Lin,
- Allison J. Taggart,
- Kian Huat Lim,
- Kamil J. Cygan,
- Luciana Ferraris,
- Robbert Creton,
- Yen-Tsung Huang,
- and William G. Fairbrother
Genome Res. January 2016 26: 12-23; Published in Advance November 13, 2015, doi:10.1101/gr.181008.114
.... Further analysis of other available fish and lamprey s suggests AC and GT repeats are potentially performing some sort of lineage-restricted role in splicing (Supplemental Table 1; Supplemental Figs. 2, 3). Upstream repeats of AC co-occur with GT repeats across introns but not exons To better understand...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
..., protein binding activity, kinase activity, phosphatase activity, nucleic acid binding, transporter activity, ligase activity, protease activity, and cation binding activity were associated with significantly higher odds of Salicoid duplicate retention. Conversely, the presence of transmembrane regions...
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Research: High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates
- Jun Matsumoto,
- Ken Dewar,
- Jessica Wasserscheid,
- Graham B. Wiley,
- Simone L. Macmil,
- Bruce A. Roe,
- Robert W. Zeller,
- Yutaka Satou,
- and Kenneth E.M. Hastings
Genome Res. May 2010 20: 636-645; Published in Advance March 8, 2010, doi:10.1101/gr.100271.109
...RAR < 0.1) and undetectably trans-spliced (cRAR = 0) gene subpopulations (Supplemental Table S6). Three of these overrepresented GO terms were related to ribosomes/translation/nucleic acid binding, consistent with our previous findings (Satou et al. 2006) that ribosomal protein genes were strongly...
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LETTER: Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia
- Aaron A. Best,
- Hilary G. Morrison,
- Andrew G. McArthur,
- Mitchell L. Sogin,
- and Gary J. Olsen
Genome Res. August 2004 14: 1537-1547; doi:10.1101/gr.2256604
...; Huang and Maraia 2001 ). For each RNAP subunit, the average of interkingdom distance (plant–animal, plant–fungal, and animal–fungal) provides a measure of the relative divergence rate of the protein. Table 2 presents these distances, sorted in ascending order (most conserved to least). Several patterns...

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