Searching journal content for articles similar to Imai et al. 6 (5): 439.

Displaying results 1-10 of 78

For checked items

view abstracts
download to citation manager

Select this article
Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...suboptimally in our ESCC and LUAD_Xing training data sets (AUCPRC 0.028 vs. 0.592 of our gene signature in ESCC and 0.244 vs. 0.513 in LUAD_Xing).Calculation of cancer cell–specific EMT phenotypes using bulk RNA-seq data offers a promising alternative to assess their link with clinical characteristics in cases...
OPEN ACCESS ARTICLE
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...framework to describe gene-gene relationships and are comprised of nodes that represent genes and edges linking coexpressed genes (Stuart et al. 2003). A comprehensive catalog of gene coexpression relationships has the potential to characterize genes with unknown functions (Schlitt et al. 2003), identify...
OPEN ACCESS ARTICLE
Select this article
Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
.... 2009; Beagan and Phillips-Cremins 2020). Furthermore, they are characterized by accumulation of CTCF and cohesin, which can be identified by ChIP-seq. These idiosyncratic features of TAD borders allow for their precise identification using Hi-C, ChIA-PET, and ChIP-seq data (Sadowski et al. 2019).To...
Select this article
Research: Identification of FMR1-regulated molecular networks in human neurodevelopment
- Meng Li,
- Junha Shin,
- Ryan D. Risgaard,
- Molly J. Parries,
- Jianyi Wang,
- Deborah Chasman,
- Shuang Liu,
- Sushmita Roy,
- Anita Bhattacharyya,
- and Xinyu Zhao
Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119
...the importance of considering both types of measurements for understanding FMR1 function. The hubs fell in the common clusters (Cluster #16: RB1, Cluster #19: AP2A1, and Cluster #25: PTPN11, FYN) as well as in cell type–specific clusters (e.g., NPC-specific hubs, Cluster #4: ATM, Cluster #15: HSPA4, and neuron...
Select this article
Method: Identification of complex genomic rearrangements in cancers using CouGaR
- Misko Dzamba,
- Arun K. Ramani,
- Pawel Buczkowicz,
- Yue Jiang,
- Man Yu,
- Cynthia Hawkins,
- and Michael Brudno
Genome Res. January 2017 27: 107-117; Published in Advance November 14, 2016, doi:10.1101/gr.211201.116
..., the copy counts estimated by qPCR are shown in purple (error bars show standard deviation), and copy counts estimated by CouGaR are shown as orange bars. In all cases, the qPCR results match the predicted copy counts. Dzamba et al. 110 Genome Research www..org Identification and characterization of CGRs...
Select this article
Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
- Zdenek Andrysik,
- Matthew D. Galbraith,
- Anna L. Guarnieri,
- Sara Zaccara,
- Kelly D. Sullivan,
- Ahwan Pandey,
- Morgan MacBeth,
- Alberto Inga,
- and Joaquín M. Espinosa
Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
...53 activity is abrogated by other oncogenic events, such as hyperactivation of its endogenous repressors MDM2 or MDM4. Despite identification of hundreds of genes regulated by this transcription factor, it remains unclear which direct target genes and downstream pathways are essential for the tumor...
OPEN ACCESS ARTICLE
Select this article
Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...enriched in msHSBs and in EBRs (Methods).Mammalian msHSBs were enriched in genes related to developmental process, biological adhesion, and meiosis I (including SPO11, RAD51, and ATM genes), among other GO terms (Supplemental Fig. S4) consistent with our previous findings (Larkin et al. 2009). On the other...
Select this article
Method: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets
- Qing Xiong,
- Nicola Ancona,
- Elizabeth R. Hauser,
- Sayan Mukherjee,
- and Terrence S. Furey
Genome Res. February 2012 22: 386-397; Published in Advance September 22, 2011, doi:10.1101/gr.124370.111
...et al. 2008). The key contributors to the association of these pathways contain the core genes involved in checkpoint response to DNA damage such as TP53, CHEK2 (also called CHK2), and ATM (Supplemental Table S2). In addition, the DNA damage model indicates the involvement of apoptosis and DNA...
OPEN ACCESS ARTICLE
Select this article
Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- Pedro G. Ferreira,
- Pedro Jares,
- Daniel Rico,
- Gonzalo Gómez-López,
- Alejandra Martínez-Trillos,
- Neus Villamor,
- Simone Ecker,
- Abel González-Pérez,
- David G. Knowles,
- Jean Monlong,
- Rory Johnson,
- Victor Quesada,
- Sarah Djebali,
- Panagiotis Papasaikas,
- Mónica López-Guerra,
- Dolors Colomer,
- Cristina Royo,
- Maite Cazorla,
- Magda Pinyol,
- Guillem Clot,
- Marta Aymerich,
- Maria Rozman,
- Marta Kulis,
- David Tamborero,
- Anaïs Gouin,
- Julie Blanc,
- Marta Gut,
- Ivo Gut,
- Xose S. Puente,
- David G. Pisano,
- José Ignacio Martin-Subero,
- Nuria López-Bigas,
- Armando López-Guillermo,
- Alfonso Valencia,
- Carlos López-Otín,
- Elías Campo,
- and Roderic Guigó
Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
...and ATM dysfunction (Wang et al. 2011; Raa et al. 2012). Other genes with altered splicing in SF3B1-mutated cells include the following: FCER2, a B-cell specific antigen that has an essential Transcriptome characterization of CLL Genome Research 215 www..org role in B-cell growth and differentiation; TEAD...
OPEN ACCESS ARTICLE
Select this article
RESEARCH: Ataxia-Telangiectasia Locus: Sequence Analysis of 184 kb of Human Genomic DNA Containing the Entire ATM Gene
- Matthias Platzer,
- Galit Rotman,
- David Bauer,
- Tamar Uziel,
- Kinneret Savitsky,
- Anat Bar-Shira,
- Shlomit Gilad,
- Yosef Shiloh,
- and André Rosenthal
Genome Res. June 1, 1997 7: 592-605; doi:10.1101/gr.7.6.592
.... , Ito H. , Nagase T. , Nomura N. , Hori T. ( 1996 ) Identification and characterization of a new gene physically linked to the ATM gene. Genome Res. 6 : 439 – 447 . ↵ Jackson I.J. ( 1991 ) A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 19 : 3795 – 3798 . ↵ Jurka J. , Klonowski P...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Imai et al. 6 (5): 439.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: