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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Carlson, Joseph

    TitleSoftware Developer 4
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5766

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Genova AD, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015 Jul 1; 43(W1):W589-98.
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      2. Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015 Mar; 25(3):445-58.
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      3. Gabrielson M, Björklund M, Carlson J, Shoshan M. Expression of mitochondrial regulators PGC1a and TFAM as putative markers of subtype and chemoresistance in epithelial ovarian carcinoma. PLoS One. 2014; 9(9):e107109.
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      4. Colón E, Carlson JW. Evaluation of the fallopian tubes after neoadjuvant chemotherapy: persistence of serous tubal intraepithelial carcinoma. Int J Gynecol Pathol. 2014 Sep; 33(5):463-9.
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      5. Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. Diversity and dynamics of the Drosophila transcriptome. Nature. 2014 Aug 28; 512(7515):393-9.
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      6. Gremel G, Liew M, Hamzei F, Hardell E, Selling J, Ghaderi M, Stemme S, Pontén F, Carlson JW. A prognosis based classification of undifferentiated uterine sarcomas: Identification of mitotic index, hormone receptors and YWHAE-FAM22 translocation status as predictors of survival. Int J Cancer. 2015 Apr; 136(7):1608-18.
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      7. Köbel M, Bak J, Bertelsen BI, Carpen O, Grove A, Hansen ES, Levin Jakobsen AM, Lidang M, Måsbäck A, Tolf A, Gilks CB, Carlson JW. Ovarian carcinoma histotype determination is highly reproducible, and is improved through the use of immunohistochemistry. Histopathology. 2014 Jun; 64(7):1004-13.
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      8. Tobin NP, Lindström LS, Carlson JW, Bjöhle J, Bergh J, Wennmalm K. Multi-level gene expression signatures, but not binary, outperform Ki67 for the long term prognostication of breast cancer patients. Mol Oncol. 2014 May; 8(3):741-52.
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      9. Stemme S, Ghaderi M, Carlson JW. Diagnosis of endometrial stromal tumors: a clinicopathologic study of 25 biopsy specimens with identification of problematic areas. Am J Clin Pathol. 2014 Jan; 141(1):133-9.
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      10. Elsir T, Edqvist PH, Carlson J, Ribom D, Bergqvist M, Ekman S, Popova SN, Alafuzoff I, Ponten F, Nistér M, Smits A. A study of embryonic stem cell-related proteins in human astrocytomas: identification of Nanog as a predictor of survival. Int J Cancer. 2014 Mar 1; 134(5):1123-31.
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      11. Frings O, Augsten M, Tobin NP, Carlson J, Paulsson J, Pena C, Olsson E, Veerla S, Bergh J, Ostman A, Sonnhammer EL. Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am J Pathol. 2013 Jun; 182(6):2037-47.
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      12. Hjerpe E, Egyhazi S, Carlson J, Stolt MF, Schedvins K, Johansson H, Shoshan M, Avall-Lundqvist E. HSP60 predicts survival in advanced serous ovarian cancer. Int J Gynecol Cancer. 2013 Mar; 23(3):448-55.
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      13. Andersson E, Villabona L, Bergfeldt K, Carlson JW, Ferrone S, Kiessling R, Seliger B, Masucci GV. Correlation of HLA-A02* genotype and HLA class I antigen down-regulation with the prognosis of epithelial ovarian cancer. Cancer Immunol Immunother. 2012 Aug; 61(8):1243-53.
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      14. Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S. A protein complex network of Drosophila melanogaster. Cell. 2011 Oct 28; 147(3):690-703.
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      15. Venken KJ, Schulze KL, Haelterman NA, Pan H, He Y, Evans-Holm M, Carlson JW, Levis RW, Spradling AC, Hoskins RA, Bellen HJ. MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat Methods. 2011 Sep; 8(9):737-43.
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      16. Du J, Näsman A, Carlson JW, Ramqvist T, Dalianis T. Prevalence of human papillomavirus (HPV) types in cervical cancer 2003-2008 in Stockholm, Sweden, before public HPV vaccination. Acta Oncol. 2011 Nov; 50(8):1215-9.
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      17. Bellen HJ, Levis RW, He Y, Carlson JW, Evans-Holm M, Bae E, Kim J, Metaxakis A, Savakis C, Schulze KL, Hoskins RA, Spradling AC. The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics. 2011 Jul; 188(3):731-43.
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      18. Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker SE. Development of expression-ready constructs for generation of proteomic libraries. Methods Mol Biol. 2011; 723:257-72.
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      19. Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb; 21(2):182-92.
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      20. Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. 2011 Feb; 21(2):301-14.
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      21. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97.
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      22. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):473-9.
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      23. Venken KJ, Popodi E, Holtzman SL, Schulze KL, Park S, Carlson JW, Hoskins RA, Bellen HJ, Kaufman TC. A molecularly defined duplication set for the X chromosome of Drosophila melanogaster. Genetics. 2010 Dec; 186(4):1111-25.
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      24. Carlson JW, Jarboe EA, Kindelberger D, Nucci MR, Hirsch MS, Crum CP. Serous tubal intraepithelial carcinoma: diagnostic reproducibility and its implications. Int J Gynecol Pathol. 2010 Jul; 29(4):310-4.
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      25. Carlson JW, Lyon E, Walton D, Foo WC, Sievers AC, Shulman LN, Farmer P, Nosé V, Milner DA. Partners in pathology: a collaborative model to bring pathology to resource poor settings. Am J Surg Pathol. 2010 Jan; 34(1):118-23.
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      26. Jarboe EA, Miron A, Carlson JW, Hirsch MS, Kindelberger D, Mutter GL, Crum CP, Nucci MR. Coexisting intraepithelial serous carcinomas of the endometrium and fallopian tube: frequency and potential significance. Int J Gynecol Pathol. 2009 Jul; 28(4):308-15.
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      27. Venken KJ, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, Wan KH, Koriabine M, de Jong PJ, White KP, Bellen HJ, Hoskins RA. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods. 2009 Jun; 6(6):431-4.
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      28. Carlson JW, Miron A, Jarboe EA, Parast MM, Hirsch MS, Lee Y, Muto MG, Kindelberger D, Crum CP. Serous tubal intraepithelial carcinoma: its potential role in primary peritoneal serous carcinoma and serous cancer prevention. J Clin Oncol. 2008 Sep 1; 26(25):4160-5.
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      29. Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9715-20.
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      30. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 8; 450(7167):219-32.
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      31. Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res. 2007 Dec; 17(12):1823-36.
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      32. Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker SE, Goldstein ES, Newfeld SJ. Phylogenetic and genomewide analyses suggest a functional relationship between kayak, the Drosophila fos homolog, and fig, a predicted protein phosphatase 2c nested within a kayak intron. Genetics. 2007 Nov; 177(3):1349-61.
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      33. Guan Y, Kuo WL, Stilwell JL, Takano H, Lapuk AV, Fridlyand J, Mao JH, Yu M, Miller MA, Santos JL, Kalloger SE, Carlson JW, Ginzinger DG, Celniker SE, Mills GB, Huntsman DG, Gray JW. Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clin Cancer Res. 2007 Oct 1; 13(19):5745-55.
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      34. Carlson JW, Birdwell RL, Gombos EC, Golshan M, Smith DN, Lester SC. MRI-directed, wire-localized breast excisions: incidence of malignancy and recommendations for pathologic evaluation. Hum Pathol. 2007 Dec; 38(12):1754-9.
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      35. Javid SH, Carlson JW, Garber JE, Birdwell RL, Lester S, Lipsitz S, Golshan M. Breast MRI wire-guided excisional biopsy: specimen size as compared to mammogram wire-guided excisional biopsy and implications for use. Ann Surg Oncol. 2007 Dec; 14(12):3352-8.
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      36. Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE. Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science. 2007 Jun 15; 316(5831):1625-8.
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      37. Stapleton M, Carlson JW, Celniker SE. RNA editing in Drosophila melanogaster: New targets and functional consequences. RNA. 2006 Nov; 12(11):1922-32.
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      38. Wan KH, Yu C, George RA, Carlson JW, Hoskins RA, Svirskas R, Stapleton M, Celniker SE. High-throughput plasmid cDNA library screening. Nat Protoc. 2006; 1(2):624-32.
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      39. Hoskins RA, Stapleton M, George RA, Yu C, Wan KH, Carlson JW, Celniker SE. Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Res. 2005; 33(21):e185.
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      40. Bergman CM, Carlson JW, Celniker SE. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics. 2005 Apr 15; 21(8):1747-9.
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      41. Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD. Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Biotechniques. 2004 Aug; 37(2):282-4.
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      42. Bellen HJ, Levis RW, Liao G, He Y, Carlson JW, Tsang G, Evans-Holm M, Hiesinger PR, Schulze KL, Rubin GM, Hoskins RA, Spradling AC. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics. 2004 Jun; 167(2):761-81.
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      43. Carvalho AB, Vibranovski MD, Carlson JW, Celniker SE, Hoskins RA, Rubin GM, Sutton GG, Adams MD, Myers EW, Clark AG. Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? Genetica. 2003 Mar; 117(2-3):227-37.
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      44. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen GH. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 2002; 3(12):RESEARCH0085.
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      45. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, Hodgson A, George RA, Hoskins RA, Laverty T, Muzny DM, Nelson CR, Pacleb JM, Park S, Pfeiffer BD, Richards S, Sodergren EJ, Svirskas R, Tabor PE, Wan K, Stapleton M, Sutton GG, Venter C, Weinstock G, Scherer SE, Myers EW, Gibbs RA, Rubin GM. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 2002; 3(12):RESEARCH0079.
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      46. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002; 3(12):RESEARCH0084.
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