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Colin Collins

Research Profile

Procedures

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Nucleic Acid Hybridization

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Gene Amplification

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Publications

TOP 3
Andrew McPherson; Sohrab Shah; Chunxiao Wu; Alexander W Wyatt; Colin Collins; S Cenk Sahinalp
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Mark Jesus M Magbanua; Colin Collins; Dan Pinkel; Charles J Ryan; Janet H Scott; Jeff Simko; Eduardo V Sosa; John W Park
Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer.
Phuong Dao; Martin Ester; Anna Lapuk; Colin Collins; Kendric Wang; S Cenk Sahinalp
Optimally discriminative subnetwork markers predict response to chemotherapy.

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All Publications

2012: Andrew McPherson; Sohrab Shah; Chunxiao Wu; Alexander W Wyatt; Colin Collins; S Cenk Sahinalp
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome research 2012;22(11):2250-61.
2012: Mark Jesus M Magbanua; Colin Collins; Dan Pinkel; Charles J Ryan; Janet H Scott; Jeff Simko; Eduardo V Sosa; John W Park
Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer.
BMC cancer 2012;12():78.
2011: Phuong Dao; Martin Ester; Anna Lapuk; Colin Collins; Kendric Wang; S Cenk Sahinalp
Optimally discriminative subnetwork markers predict response to chemotherapy.
Bioinformatics (Oxford, England) 2011;27(13):i205-13.
2011: Andrew McPherson; Chunxiao Wu; IMAN HAJIRASOULIHA; Fereydoun Hormozdiari; Faraz Hach; Anna Lapuk; Stanislav Volik; Sohrab Shah; Colin Collins; S Cenk Sahinalp
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinformatics (Oxford, England) 2011;27(11):1481-8.
2010: Pamela L Paris; Vivian Weinberg; Giancarlo Albo; Ritu Roy; Catherine Burke; Jeff Simko; Peter Carroll; Colin Collins
A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2010;16(1):195-202.
2009: Pamela L Paris; S Sridharan; A B Hittelman; Y Kobayashi; S Perner; G Huang; Jeff Simko; Peter Carroll; Mark A Rubin; Colin Collins
An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer.
Prostate cancer and prostatic diseases 2009;12(2):184-91.
2008: Ali Bashir; Stanislav Volik; Colin Collins; Vineet Bafna; Benjamin J Raphael
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.
PLoS computational biology 2008;4(4):e1000051.
2007: Adam Hittelman; Shivaranjani Sridharan; Ritu Roy; Jane Fridlyand; Massimo Loda; Colin Collins; Pamela L Paris
Evaluation of whole genome amplification protocols for array and oligonucleotide CGH.
Diagnostic molecular pathology : the American journal of surgical pathology, part B 2007;16(4):198-206.
2007: Pamela L Paris; Shivaranjani Sridharan; Alicia Scheffer; Anya Tsalenko; Laurakay Bruhn; Colin Collins
High resolution oligonucleotide CGH using DNA from archived prostate tissue.
The Prostate 2007;67(13):1447-55.
2007: Sven Perner; Juan-Miguel Mosquera; Francesca Demichelis; Matthias D Hofer; Pamela L Paris; Jeff Simko; Colin Collins; Tarek A Bismar; Arul M Chinnaiyan; Angelo M DeMarzo; Mark A Rubin
TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion.
The American journal of surgical pathology 2007;31(6):882-8.
2007: Juan-Miguel Mosquera; Sven Perner; Francesca Demichelis; Robert Kim; Matthias D Hofer; Kirsten D Mertz; Pamela L Paris; Jeff Simko; Colin Collins; Tarek A Bismar; Arul M Chinnaiyan; Mark A Rubin
Morphological features of TMPRSS2-ERG gene fusion prostate cancer.
The Journal of pathology 2007;212(1):91-101.
2006: Pamela L Paris; Matthias D Hofer; Giancarlo Albo; Rainer Kuefer; Juergen E Gschwend; Richard E Hautmann; Jane Fridyland; Jeff Simko; Peter R Carroll; Mark A Rubin; Colin Collins
Genomic profiling of hormone-naïve lymph node metastases in patients with prostate cancer.
Neoplasia (New York, N.Y.) 2006;8(12):1083-9.
2006: Stanislav Volik; Benjamin J Raphael; Guiqing Huang; Michael R Stratton; Graham Bignel; John Murnane; John H Brebner; Krystyna Bajsarowicz; Pamela L Paris; Quanzhou Tao; David Kowbel; Anna Lapuk; Dmitry A Shagin; Irina A Shagina; Joe Gray; Jan-Fang Cheng; Pieter J de Jong; Pavel A Pevzner; Colin Collins
Decoding the fine-scale structure of a breast cancer genome and transcriptome.
Genome research 2006;16(3):394-404.
2005: Mark van Duin; Ronald van Marion; Kees J Vissers; J E Vivienne Watson; Wytske M Van Weerden; Fritz H Schröder; Wim C J Hop; Theo Van der Kwast; Colin Collins; Herman van Dekken
High-resolution array comparative genomic hybridization of chromosome arm 8q: evaluation of genetic progression markers for prostate cancer.
Genes, chromosomes & cancer 2005;44(4):438-49.
2005: Guiqing Huang; Sheryl Krig; David Kowbel; Hongmei Xu; Bill Hyun; Stanislav Volik; Burt Feuerstein; Gordon B Mills; David Stokoe; Paul Yaswen; Colin Collins
ZNF217 suppresses cell death associated with chemotherapy and telomere dysfunction.
Human molecular genetics 2005;14(21):3219-25.
2005: R A Baldocchi; Richard J Glynne; Koei Chin; David Kowbel; Colin Collins; D H Mack; Joe Gray
Design considerations for array CGH to oligonucleotide arrays.
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2005;67(2):129-36.
2005: Pamela L Paris; Vivian Weinberg; Jeff Simko; Armann Andaya; G Albo; Mark A Rubin; Peter R Carroll; Colin Collins
Preliminary evaluation of prostate cancer metastatic risk biomarkers.
The International journal of biological markers 2005;20(3):141-5.
2005: Mark van Duin; Ronald van Marion; J E Vivienne Watson; Pamela L Paris; Anna Lapuk; Nils Brown; Vanessa V Oseroff; Donna G Albertson; Daniel Pinkel; Pieter De Jong; Elisabeth P Nacheva; Winand N M Dinjens; Herman van Dekken; Colin Collins
Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization.
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2005;63(1):10-9.
2004: Jill A Macoska; Pamela L Paris; Colin Collins; Armann Andaya; Ben Beheshti; Hassan Chaib; Rajiv Kant; Lesa Begley; James W MacDonald; Jeremy A Squire
Evolution of 8p loss in transformed human prostate epithelial cells.
Cancer genetics and cytogenetics 2004;154(1):36-43.
2004: J E Vivienne Watson; Sherwin Kamkar; Karen James; David Kowbel; Armann Andaya; Pamela L Paris; Jeff Simko; Peter Carroll; Stephanie J McAlhany; David Rowley; Colin Collins
Molecular analysis of WFDC1/ps20 gene in prostate cancer.
The Prostate 2004;61(2):192-9.
2004: Stephanie J McAlhany; Gustavo E Ayala; Anna Frolov; Steven J Ressler; Thomas M Wheeler; J E Vivienne Watson; Colin Collins; David R Rowley
Decreased stromal expression and increased epithelial expression of WFDC1/ps20 in prostate cancer is associated with reduced recurrence-free survival.
The Prostate 2004;61(2):182-91.
2004: Pamela L Paris; Armann Andaya; Jane Fridlyand; Ajay N Jain; Vivian Weinberg; David Kowbel; John H Brebner; Jeff Simko; J E Vivienne Watson; Stanislav Volik; Donna G Albertson; Daniel Pinkel; Janneke C Alers; Theo Van der Kwast; Kees J Vissers; Fritz H Schroder; Mark F Wildhagen; Phillip G Febbo; Arul M Chinnaiyan; Kenneth J Pienta; Peter R Carroll; Mark A Rubin; Colin Collins; Herman van Dekken
Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.
Human molecular genetics 2004;13(13):1303-13.
2004: Mark A Rubin; Sooryanarayana Lnu; Rameen Beroukhim; Scott A Tomlins; Daniel R Rhodes; Pamela L Paris; Matthias D Hofer; Martina Storz-Schweizer; Rainer Kuefer; Jonathan A Fletcher; Bae-Li Hsi; Jennifier A Byrne; Kenneth J Pienta; Colin Collins; William R Sellers; Arul M Chinnaiyan
Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer.
Cancer research 2004;64(11):3814-22.
2004: Anna Lapuk; Stanislav Volik; Robert Vincent; Koei Chin; Wen-Lin Kuo; Pieter De Jong; Colin Collins; Joe Gray
Computational BAC clone contig assembly for comprehensive genome analysis.
Genes, chromosomes & cancer 2004;40(1):66-71.
2004: J E Vivienne Watson; Norman A Doggett; Donna G Albertson; Armann Andaya; Arul M Chinnaiyan; Herman van Dekken; David Ginzinger; Christopher Haqq; Karen James; Sherwin Kamkar; David Kowbel; Daniel Pinkel; Lars Schmitt; Jeff Simko; Stanislav Volik; Vivian Weinberg; Pamela L Paris; Colin Collins
Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer.
Oncogene 2004;23(19):3487-94.
2004: Herman van Dekken; Pamela L Paris; Donna G Albertson; Janneke C Alers; Armann Andaya; David Kowbel; Theo Van der Kwast; Daniel Pinkel; Fritz H Schröder; Kees J Vissers; Mark F Wildhagen; Colin Collins
Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis.
Genes, chromosomes & cancer 2004;39(3):249-56.
2003: Dillon I Beardsley; David Kowbel; Tamara A Lataxes; Jennifer M Mannino; Hong Xin; Wan-Ju Kim; Colin Collins; Kevin D Brown
Characterization of the novel amplified in breast cancer-1 (NABC1) gene product.
Experimental cell research 2003;290(2):402-13.
2003: Benjamin J Raphael; Stanislav Volik; Colin Collins; Pavel A Pevzner
Reconstructing tumor genome architectures.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii162-71.
2003: Stanislav Volik; Shaying Zhao; Koei Chin; John H Brebner; David R Herndon; Quanzhou Tao; David Kowbel; Guiqing Huang; Anna Lapuk; Wen-Lin Kuo; Gregg Magrane; Pieter De Jong; Joe Gray; Colin Collins
End-sequence profiling: sequence-based analysis of aberrant genomes.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(13):7696-701.
2003: Pamela L Paris; Donna G Albertson; Janneke C Alers; Armann Andaya; Peter Carroll; Jane Fridlyand; Ajay N Jain; Sherwin Kamkar; David Kowbel; Pieter-Jaap Krijtenburg; Daniel Pinkel; Fritz H Schröder; Kees J Vissers; Vivienne J E Watson; Mark F Wildhagen; Colin Collins; Herman van Dekken
High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
The American journal of pathology 2003;162(3):763-70.
2001: G Hodgson; J H Hager; Stanislav Volik; Sujatmi Hariono; M Wernick; D Moore; N Nowak; Donna G Albertson; Daniel Pinkel; Colin Collins; Douglas Hanahan; Joe Gray
Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas.
Nature genetics 2001;29(4):459-64.
2001: M Thakur; M Wernick; Colin Collins; Charles L Limoli; Eileen Crowley; James E Cleaver
DNA polymerase eta undergoes alternative splicing, protects against UV sensitivity and apoptosis, and suppresses Mre11-dependent recombination.
Genes, chromosomes & cancer 2001;32(3):222-35.
2001: Colin Collins; Stanislav Volik; David Kowbel; David Ginzinger; Bauke Ylstra; T Cloutier; Trevor L Hawkins; Paul Predki; C Martin; M Wernick; Wen-Lin Kuo; ARTHUR S ALBERTS; Joe Gray
Comprehensive genome sequence analysis of a breast cancer amplicon.
Genome research 2001;11(6):1034-42.
2000: Donna G Albertson; Bauke Ylstra; Richard Segraves; Colin Collins; Shanaz H Dairkee; David Kowbel; Wen-Lin Kuo; Joe Gray; Daniel Pinkel
Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene.
Nature genetics 2000;25(2):144-6.
1999: L Shayesteh; Y Lu; Wen-Lin Kuo; R Baldocchi; T Godfrey; Colin Collins; Daniel Pinkel; B Powell; Gordon B Mills; Joe Gray
PIK3CA is implicated as an oncogene in ovarian cancer.
Nature genetics 1999;21(1):99-102.
1998: Sylvaine Cases; Steven J Smith; Yao-Wu Zheng; Heather M Myers; Steven R Lear; E Sande; S Novak; Colin Collins; C B Welch; AJ Lusis; Sandra K Erickson; Robert V Farese
Identification of a gene encoding an acyl CoA:diacylglycerol acyltransferase, a key enzyme in triacylglycerol synthesis.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(22):13018-23.
1998: Daniel Pinkel; Richard Segraves; Damir Sudar; S Clark; I Poole; David Kowbel; Colin Collins; Wen-Lin Kuo; C Chen; Y Zhai; Shanaz H Dairkee; Britt-Marie Ljung; Joe Gray; Donna G Albertson
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.
Nature genetics 1998;20(2):207-11.
1998: Ling-Chun Chen; S Manjeshwar; Y Lu; Dan Moore; Britt-Marie Ljung; Wen-Lin Kuo; Shanaz H Dairkee; M Wernick; Colin Collins; HS Smith
The human homologue for the Caenorhabditis elegans cul-4 gene is amplified and overexpressed in primary breast cancers.
Cancer research 1998;58(16):3677-83.
1998: V Ratziu; Avraham Lalazar; L Wong; Q Dang; Colin Collins; E Shaulian; S Jensen; S L Friedman
Zf9, a Kruppel-like transcription factor up-regulated in vivo during early hepatic fibrosis.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(16):9500-5.
1998: Colin Collins; J M Rommens; David Kowbel; T Godfrey; M Tanner; S I Hwang; Daniel Polikoff; GH Nonet; JF Cochran; Kenneth Myambo; K E Jay; J Froula; T Cloutier; Wen-Lin Kuo; Paul Yaswen; Shanaz H Dairkee; J Giovanola; G B Hutchinson; J Isola; Olli Kallioniemi; M Palazzolo; C Martin; C Ericsson; Daniel Pinkel; Donna G Albertson; W B Li; Joe Gray
Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(15):8703-8.
1998: S Hiraguri; T Godfrey; H Nakamura; J Graff; Colin Collins; L Shayesteh; N Doggett; K Johnson; M Wheelock; James G Herman; Stephen B Baylin; Daniel Pinkel; Joe Gray
Mechanisms of inactivation of E-cadherin in breast cancer cell lines.
Cancer research 1998;58(9):1972-7.
1997: Colin Collins; Jan Nehlin; J D Stubbs; David Kowbel; Wen-Lin Kuo; G Parry
Mapping of a newly discovered human gene homologous to the apoptosis associated-murine mammary protein, MFG-E8, to chromosome 15q25.
Genomics 1997;39(1):117-8.
1996: Pius Brzoska; H Chen; N A Levin; Wen-Lin Kuo; Colin Collins; K K Fu; Joe Gray; M F Christman
Cloning, mapping, and in vivo localization of a human member of the PKCI-1 protein family (PRKCNH1).
Genomics 1996;36(1):151-6.
1996: MM Tanner; Mika Tirkkonen; Anne Kallioniemi; Jorma Isola; Tuula Kuukasjärvi; Colin Collins; David Kowbel; XY Guan; Jeffrey M. Trent; Joe Gray; Paul Meltzer; Olli Kallioniemi
Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer.
Cancer research 1996;56(15):3441-5.
1995: MM Tanner; Mika Tirkkonen; Anne Kallioniemi; Kaija Holli; Colin Collins; David Kowbel; Joe Gray; Olli Kallioniemi; Jorma Isola
Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications.
Clinical cancer research : an official journal of the American Association for Cancer Research 1995;1(12):1455-61.
1995: Heinz-Ulrich G Weier; A P Rhein; F Shadravan; Colin Collins; Daniel Polikoff
Rapid physical mapping of the human trk protooncogene (NTRK1) to human chromosome 1q21-q22 by P1 clone selection, fluorescence in situ hybridization (FISH), and computer-assisted microscopy.
Genomics 1995;26(2):390-3.
1995: T Stokke; Colin Collins; Wen-Lin Kuo; David Kowbel; F Shadravan; M Tanner; Anne Kallioniemi; Olli Kallioniemi; Daniel Pinkel; L Deaven
A physical map of chromosome 20 established using fluorescence in situ hybridization and digital image analysis.
Genomics 1995;26(1):134-7.
1994: MM Tanner; Mika Tirkkonen; Anne Kallioniemi; Colin Collins; T Stokke; Ritva Karhu; David Kowbel; F Shadravan; M Hintz; Wen-Lin Kuo
Increased copy number at 20q13 in breast cancer: defining the critical region and exclusion of candidate genes.
Cancer research 1994;54(16):4257-60.
1994: Joe Gray; Colin Collins; I C Henderson; Jorma Isola; Anne Kallioniemi; Olli Kallioniemi; H Nakamura; Daniel Pinkel; T Stokke; M Tanner
Molecular cytogenetics of human breast cancer.
Cold Spring Harbor symposia on quantitative biology 1994;59():645-52.
1991: Colin Collins; Wen-Lin Kuo; R Segraves; J Fuscoe; Daniel Pinkel; Joe Gray
Construction and characterization of plasmid libraries enriched in sequences from single human chromosomes.
Genomics 1991;11(4):997-1006.
1988: Daniel Pinkel; J Landegent; Colin Collins; J Fuscoe; R Segraves; J Lucas; Joe Gray
Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4.
Proceedings of the National Academy of Sciences of the United States of America 1988;85(23):9138-42.