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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...to the assembly using HISAT (Kim et al. 2015). StringTie was then used to interpret the mapping result for gene location and structure. In parallel processing, we assembled transcripts from the mapping result using Trinity (Haas et al. 2013) and aligned them to the using Splign (Kapustin et al. 2008).We used...
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LETTER: Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex
- Nicos Tripodis,
- Sophie Palmer,
- Sam Phillips,
- Sarah Milne,
- Stephan Beck,
- and Jiannis Ragoussis
Genome Res. April 1, 2000 10: 454-472; doi:10.1101/gr.10.4.454
...Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex Nicos Tripodis 1 , 3 , Sophie Palmer 2 , Sam Phillips 2 , Sarah Milne 2 , Stephan Beck 2...
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Research: Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
- Christiane M. Robbins,
- Waibov A. Tembe,
- Angela Baker,
- Shripad Sinari,
- Tracy Y. Moses,
- Stephen Beckstrom-Sternberg,
- James Beckstrom-Sternberg,
- Michael Barrett,
- James Long,
- Arul Chinnaiyan,
- James Lowey,
- Edward Suh,
- John V. Pearson,
- David W. Craig,
- David B. Agus,
- Kenneth J. Pienta,
- and John D. Carpten
Genome Res. January 2011 21: 47-55; Published in Advance December 8, 2010, doi:10.1101/gr.107961.110
...were detected at 8p22, 10q23.31, 13q13.1, 13q14.11, and 13q14.12. Key genes mapping within these deleted regions include PTEN , BRCA2 , C13ORF15 , and SIAH3 . Focal high-level amplifications were detected at 5p13.2-p12, 14q21.1, 7q22.1, and Xq12. Key amplified genes mapping within these regions...
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Research: An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer
- Nora F. Wasserman,
- Ivy Aneas,
- and Marcelo A. Nobrega
Genome Res. September 2010 20: 1191-1197; Published in Advance July 13, 2010, doi:10.1101/gr.105361.110
...gene desert for regulatory elements, we surveyed the region using a broad-scale BAC scan approach Figure 1. The 8q24MYCgene desert harbors prostate andmammary gland transcriptional enhancers. (A) Five susceptibility loci within the 440-kb interval shown to be associated with prostate cancer (all shaded...
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LETTER: Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3
- Michael Centola,
- Xiaoguang Chen,
- Raman Sood,
- Zuoming Deng,
- Ivona Aksentijevich,
- Trevor Blake,
- Darrell O. Ricke,
- Xiang Chen,
- Geryl Wood,
- Nurit Zaks,
- Neil Richards,
- David Krizman,
- Elizabeth Mansfield,
- Sinoula Apostolou,
- Jingmei Liu,
- Neta Shafran,
- Anil Vedula,
- Melanie Hamon,
- Andrea Cercek,
- Tanaz Kahan,
- Deborah Gumucio,
- David F. Callen,
- Robert I. Richards,
- Robert K. Moyzis,
- Norman A. Doggett,
- Francis S. Collins,
- P. Paul Liu,
- Nathan Fischel-Ghodsian,
- and Daniel L. Kastner
Genome Res. November 1, 1998 8: 1172-1191; doi:10.1101/gr.8.11.1172
...is drawn in three levels with resolution increasing on descending levels. Transcripts are not drawn to scale. ( A ) Transcripts identified by direct selection in the flanking intervals are indicated as are the physical map positions of large-insert genomic clones used for analysis. The position of cosmids...
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REPORT: Identification of Human Epidermal Differentiation Complex (EDC)-Encoded Genes by Subtractive Hybridization of Entire YACs to a Gridded Keratinocyte cDNA Library
- Ingo Marenholz,
- Maja Zirra,
- David F. Fischer,
- Claude Backendorf,
- Andreas Ziegler,
- and Dietmar Mischke
Genome Res. March 1, 2001 11: 341-355; doi:10.1101/gr.114801
...). After subtracting non-specific cDNA clones as indicated by hybridization with both of the YACs, characterization of the remaining clones yielded transcripts of 19 EDC genes, 10 of which were assigned to this gene complex for the first time. Although sequencing and mapping was restricted to 50 c...
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Research: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Young Seok Ju,
- Jose M.C. Tubio,
- William Mifsud,
- Beiyuan Fu,
- Helen R. Davies,
- Manasa Ramakrishna,
- Yilong Li,
- Lucy Yates,
- Gunes Gundem,
- Patrick S. Tarpey,
- Sam Behjati,
- Elli Papaemmanuil,
- Sancha Martin,
- Anthony Fullam,
- Moritz Gerstung,
- ICGC Prostate Cancer Working Group,
- ICGC Bone Cancer Working Group,
- ICGC Breast Cancer Working Group,
- Jyoti Nangalia,
- Anthony R. Green,
- Carlos Caldas,
- Åke Borg,
- Andrew Tutt,
- Ming Ta Michael Lee,
- Laura J. van't Veer,
- Benita K.T. Tan,
- Samuel Aparicio,
- Paul N. Span,
- John W.M. Martens,
- Stian Knappskog,
- Anne Vincent-Salomon,
- Anne-Lise Børresen-Dale,
- Jórunn Erla Eyfjörd,
- Ola Myklebost,
- Adrienne M. Flanagan,
- Christopher Foster,
- David E. Neal,
- Colin Cooper,
- Rosalind Eeles,
- G. Steven Bova,
- Sunil R. Lakhani,
- Christine Desmedt,
- Gilles Thomas,
- Andrea L. Richardson,
- Colin A. Purdie,
- Alastair M. Thompson,
- Ultan McDermott,
- Fengtang Yang,
- Serena Nik-Zainal,
- Peter J. Campbell,
- and Michael R. Stratton
Genome Res. June 2015 25: 814-824; Published in Advance May 11, 2015, doi:10.1101/gr.190470.115
...****** ****** ***** ****** *** **** ***** *** ***** **** ******* ******** *** ******* ************ *** *** *** **** **** ******** ******* ******** ********* ******* ****************** **** *** *** *** *** ****** *** ****** ******* **** *** *** ************* *** *************** *** ******* *** ******* *** *** **** ***** *********** ********** **** ******* ****** *** ******* ****** *** ****** *** **** ********** **** *** *** *** 0 2 10 mtDNA PD11372a deletion type tandem duplication type inversion type (head-head) inversion type (tail-tail) mtDNA chr10: 80Mb chr10: 78Mb merged mitochondrial DNA (inserted segment) (2) DRs (1) SRs (Nu) nuclear DNA nuclear DNA Mapping to the reference (using BWA) cancer (3) SRs (MT) nuclear...
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Method: Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
- Anand Patel,
- Richard Schwab,
- Yu-Tsueng Liu,
- and Vineet Bafna
Genome Res. February 2014 24: 318-328; Published in Advance December 4, 2013, doi:10.1101/gr.161497.113
...protein contributes to initial leukemia cell growth mostly through transcriptional repression of wild-type RUNX1 targets (Downing 1999). Alternatively, the loss of DNA may also contribute to cancer progression. For example, many human cancers frequently delete the chromosome 9p21-22 locus containing MTAP...
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Research: Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes
- Tae-Min Kim,
- Ruibin Xi,
- Lovelace J. Luquette,
- Richard W. Park,
- Mark D. Johnson,
- and Peter J. Park
Genome Res. February 2013 23: 217-227; Published in Advance November 6, 2012, doi:10.1101/gr.140301.112
..., microphthalmia-associated transcription factor MITF (3p14.1), known as a master regulator of melanocyte development and a melanoma-specific oncogene (Garraway et al. 2005), was only included in the lineage-specific alterations of melanoma. One of the 17 prostate cancer-specific deletions was observed within...
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Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
- Musa A. Hassan,
- Vincent Butty,
- Kirk D.C. Jensen,
- and Jeroen P.J. Saeij
Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
...CpG-stimulated 102.7 POU3F2 2.84 3 10#2;6 B-cell proliferation 0.002548 Utp15 Pathway enrichment was assessed using the TRANSFAC database. (Chr) Chromosome; (TF) transcription factor; (Mb) megabase pairs. We used Poisson distribution to estimate the minimum number of sQTLs needed to map to a single...

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