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35 results on '"Pirun, Mono"'

1. Automated real-world data integration improves cancer outcome prediction

Author

Jee, Justin, Fong, Christopher, Pichotta, Karl, Tran, Thinh Ngoc, Luthra, Anisha, Waters, Michele, Fu, Chenlian, Altoe, Mirella, Liu, Si-Yang, Maron, Steven B., Ahmed, Mehnaj, Kim, Susie, Pirun, Mono, Chatila, Walid K., de Bruijn, Ino, Pasha, Arfath, Kundra, Ritika, Gross, Benjamin, Mastrogiacomo, Brooke, Aprati, Tyler J., Liu, David, Gao, JianJiong, Capelletti, Marzia, Pekala, Kelly, Loudon, Lisa, Perry, Maria, Bandlamudi, Chaitanya, Donoghue, Mark, Satravada, Baby Anusha, Martin, Axel, Shen, Ronglai, Chen, Yuan, Brannon, A. Rose, Chang, Jason, Braunstein, Lior, Li, Anyi, Safonov, Anton, Stonestrom, Aaron, Sanchez-Vela, Pablo, Wilhelm, Clare, Robson, Mark, Scher, Howard, Ladanyi, Marc, Reis-Filho, Jorge S., Solit, David B., Jones, David R., Gomez, Daniel, Yu, Helena, Chakravarty, Debyani, Yaeger, Rona, Abida, Wassim, Park, Wungki, O’Reilly, Eileen M., Garcia-Aguilar, Julio, Socci, Nicholas, Sanchez-Vega, Francisco, Carrot-Zhang, Jian, Stetson, Peter D., Levine, Ross, Rudin, Charles M., Berger, Michael F., Shah, Sohrab P., Schrag, Deborah, Razavi, Pedram, Kehl, Kenneth L., Li, Bob T., Riely, Gregory J., and Schultz, Nikolaus

Published
2024
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2. The genomic basis of adaptive evolution in threespine sticklebacks.

Author

Jones, Felicity C, Grabherr, Manfred G, Chan, Yingguang Frank, Russell, Pamela, Mauceli, Evan, Johnson, Jeremy, Swofford, Ross, Pirun, Mono, Zody, Michael C, White, Simon, Birney, Ewan, Searle, Stephen, Schmutz, Jeremy, Grimwood, Jane, Dickson, Mark C, Myers, Richard M, Miller, Craig T, Summers, Brian R, Knecht, Anne K, Brady, Shannon D, Zhang, Haili, Pollen, Alex A, Howes, Timothy, Amemiya, Chris, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Jaffe, David B, Nicol, Robert, Wilkinson, Jane, Lander, Eric S, Di Palma, Federica, Lindblad-Toh, Kerstin, and Kingsley, David M

Subjects
Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Chromosomes, Animals, Smegmamorpha, Sequence Analysis, DNA, Genomics, Fresh Water, Seawater, Adaptation, Physiological, Conserved Sequence, Genome, Molecular Sequence Data, Alaska, Female, Genetic Variation, Chromosome Inversion, Biological Evolution, Aquatic Organisms, Ecotype, General Science & Technology
Abstract

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

Published
2012

4. Supplementary Data from Tumor MHC Class I Expression Associates with Intralesional IL2 Response in Melanoma

Author

Pourmaleki, Maryam, primary, Jones, Caitlin J., primary, Ariyan, Charlotte E., primary, Zeng, Zheng, primary, Pirun, Mono, primary, Navarrete, Daniel A., primary, Li, Yanyun, primary, Zhang, Mianlei, primary, Nandakumar, Subhiksha, primary, Campos, Carl, primary, Nadeem, Saad, primary, Klimstra, David S., primary, Temple-Oberle, Claire F., primary, Brenn, Thomas, primary, Lipson, Evan J., primary, Schenk, Kara M., primary, Stein, Julie E., primary, Taube, Janis M., primary, White, Michael G., primary, Traweek, Raymond, primary, Wargo, Jennifer A., primary, Kirkwood, John M., primary, Gasmi, Billel, primary, Goff, Stephanie L., primary, Corwin, Alex D., primary, McDonough, Elizabeth, primary, Ginty, Fiona, primary, Callahan, Margaret K., primary, Schietinger, Andrea, primary, Socci, Nicholas D., primary, Mellinghoff, Ingo K., primary, and Hollmann, Travis J., primary

Published
2023
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5. Data from Tumor MHC Class I Expression Associates with Intralesional IL2 Response in Melanoma

Author

Pourmaleki, Maryam, primary, Jones, Caitlin J., primary, Ariyan, Charlotte E., primary, Zeng, Zheng, primary, Pirun, Mono, primary, Navarrete, Daniel A., primary, Li, Yanyun, primary, Zhang, Mianlei, primary, Nandakumar, Subhiksha, primary, Campos, Carl, primary, Nadeem, Saad, primary, Klimstra, David S., primary, Temple-Oberle, Claire F., primary, Brenn, Thomas, primary, Lipson, Evan J., primary, Schenk, Kara M., primary, Stein, Julie E., primary, Taube, Janis M., primary, White, Michael G., primary, Traweek, Raymond, primary, Wargo, Jennifer A., primary, Kirkwood, John M., primary, Gasmi, Billel, primary, Goff, Stephanie L., primary, Corwin, Alex D., primary, McDonough, Elizabeth, primary, Ginty, Fiona, primary, Callahan, Margaret K., primary, Schietinger, Andrea, primary, Socci, Nicholas D., primary, Mellinghoff, Ingo K., primary, and Hollmann, Travis J., primary

Published
2023
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6. Data from Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

Author

Al-Ahmadie, Hikmat, primary, Iyer, Gopa, primary, Hohl, Marcel, primary, Asthana, Saurabh, primary, Inagaki, Akiko, primary, Schultz, Nikolaus, primary, Hanrahan, Aphrothiti J., primary, Scott, Sasinya N., primary, Brannon, A. Rose, primary, McDermott, Gregory C., primary, Pirun, Mono, primary, Ostrovnaya, Irina, primary, Kim, Philip, primary, Socci, Nicholas D., primary, Viale, Agnes, primary, Schwartz, Gary K., primary, Reuter, Victor, primary, Bochner, Bernard H., primary, Rosenberg, Jonathan E., primary, Bajorin, Dean F., primary, Berger, Michael F., primary, Petrini, John H.J., primary, Solit, David B., primary, and Taylor, Barry S., primary

Published
2023
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7. Supplementary Figures 1 - 10 from Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

Author

Al-Ahmadie, Hikmat, primary, Iyer, Gopa, primary, Hohl, Marcel, primary, Asthana, Saurabh, primary, Inagaki, Akiko, primary, Schultz, Nikolaus, primary, Hanrahan, Aphrothiti J., primary, Scott, Sasinya N., primary, Brannon, A. Rose, primary, McDermott, Gregory C., primary, Pirun, Mono, primary, Ostrovnaya, Irina, primary, Kim, Philip, primary, Socci, Nicholas D., primary, Viale, Agnes, primary, Schwartz, Gary K., primary, Reuter, Victor, primary, Bochner, Bernard H., primary, Rosenberg, Jonathan E., primary, Bajorin, Dean F., primary, Berger, Michael F., primary, Petrini, John H.J., primary, Solit, David B., primary, and Taylor, Barry S., primary

Published
2023
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8. Supplementary Materials from Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

Author

Al-Ahmadie, Hikmat, primary, Iyer, Gopa, primary, Hohl, Marcel, primary, Asthana, Saurabh, primary, Inagaki, Akiko, primary, Schultz, Nikolaus, primary, Hanrahan, Aphrothiti J., primary, Scott, Sasinya N., primary, Brannon, A. Rose, primary, McDermott, Gregory C., primary, Pirun, Mono, primary, Ostrovnaya, Irina, primary, Kim, Philip, primary, Socci, Nicholas D., primary, Viale, Agnes, primary, Schwartz, Gary K., primary, Reuter, Victor, primary, Bochner, Bernard H., primary, Rosenberg, Jonathan E., primary, Bajorin, Dean F., primary, Berger, Michael F., primary, Petrini, John H.J., primary, Solit, David B., primary, and Taylor, Barry S., primary

Published
2023
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9. Supplementary Tables 1 - 6 from Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

Author

Al-Ahmadie, Hikmat, primary, Iyer, Gopa, primary, Hohl, Marcel, primary, Asthana, Saurabh, primary, Inagaki, Akiko, primary, Schultz, Nikolaus, primary, Hanrahan, Aphrothiti J., primary, Scott, Sasinya N., primary, Brannon, A. Rose, primary, McDermott, Gregory C., primary, Pirun, Mono, primary, Ostrovnaya, Irina, primary, Kim, Philip, primary, Socci, Nicholas D., primary, Viale, Agnes, primary, Schwartz, Gary K., primary, Reuter, Victor, primary, Bochner, Bernard H., primary, Rosenberg, Jonathan E., primary, Bajorin, Dean F., primary, Berger, Michael F., primary, Petrini, John H.J., primary, Solit, David B., primary, and Taylor, Barry S., primary

Published
2023
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14. Genome Sequencing Identifies a Basis for Everolimus Sensitivity

Author

Iyer, Gopa, Hanrahan, Aphrothiti J., Milowsky, Matthew I., Al-Ahmadie, Hikmat, Scott, Sasinya N., Janakiraman, Manickam, Pirun, Mono, Sander, Chris, Socci, Nicholas D., Ostrovnaya, Irina, Viale, Agnes, Heguy, Adriana, Peng, Luke, Chan, Timothy A., Bochner, Bernard, Bajorin, Dean F., Berger, Michael F., Taylor, Barry S., and Solit, David B.

Published
2012
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15. Tumor MHC Class I Expression Associates with Intralesional IL2 Response in Melanoma

Author

Pourmaleki, Maryam, primary, Jones, Caitlin J., additional, Ariyan, Charlotte E., additional, Zeng, Zheng, additional, Pirun, Mono, additional, Navarrete, Daniel A., additional, Li, Yanyun, additional, Zhang, Mianlei, additional, Nandakumar, Subhiksha, additional, Campos, Carl, additional, Nadeem, Saad, additional, Klimstra, David S., additional, Temple-Oberle, Claire F., additional, Brenn, Thomas, additional, Lipson, Evan J., additional, Schenk, Kara M., additional, Stein, Julie E., additional, Taube, Janis M., additional, White, Michael G., additional, Traweek, Raymond, additional, Wargo, Jennifer A., additional, Kirkwood, John M., additional, Gasmi, Billel, additional, Goff, Stephanie L., additional, Corwin, Alex D., additional, McDonough, Elizabeth, additional, Ginty, Fiona, additional, Callahan, Margaret K., additional, Schietinger, Andrea, additional, Socci, Nicholas D., additional, Mellinghoff, Ingo K., additional, and Hollmann, Travis J., additional

Published
2022
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16. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

Author

Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, McFadden, David Glenn, Bhutkar, Arjun, Chen, Frances K., Santiago, Philip M., Jacks, Tyler E., Politi, Katerina, Song, Xiaoling, Pirun, Mono, Kim-Kiselak, Caroline, Platt, James T., Lee, Emily, Hodges, Emily, Rosebrock, Adam P., Bronson, Roderick T., Socci, Nicholas D., Hannon, Gregory J., Varmus, Harold, Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, McFadden, David Glenn, Bhutkar, Arjun, Chen, Frances K., Santiago, Philip M., Jacks, Tyler E., Politi, Katerina, Song, Xiaoling, Pirun, Mono, Kim-Kiselak, Caroline, Platt, James T., Lee, Emily, Hodges, Emily, Rosebrock, Adam P., Bronson, Roderick T., Socci, Nicholas D., Hannon, Gregory J., and Varmus, Harold

Abstract

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity., United States. National Institutes of Health (NCI K08 160658)

Published
2017

17. The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma

Author

McFadden, David G., primary, Politi, Katerina, additional, Bhutkar, Arjun, additional, Chen, Frances K., additional, Song, Xiaoling, additional, Pirun, Mono, additional, Santiago, Philip M., additional, Kim, Caroline, additional, Platt, James T., additional, Lee, Emily, additional, Hodges, Emily, additional, Rosebrock, Adam P., additional, Bronson, Roderick, additional, Socci, Nicholas D., additional, Hannon, Gregory, additional, Jacks, Tyler, additional, and Varmus, Harold, additional

Published
2016
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19. Targeted massively parallel sequencing of angiosarcomas reveals frequent activation of the mitogen activated protein kinase pathway

Author

Murali, Rajmohan, primary, Chandramohan, Raghu, additional, Möller, Inga, additional, Scholz, Simone L., additional, Berger, Michael, additional, Huberman, Kety, additional, Viale, Agnes, additional, Pirun, Mono, additional, Socci, Nicholas D., additional, Bouvier, Nancy, additional, Bauer, Sebastian, additional, Artl, Monika, additional, Schilling, Bastian, additional, Schimming, Tobias, additional, Sucker, Antje, additional, Schwindenhammer, Benjamin, additional, Grabellus, Florian, additional, Speicher, Michael R., additional, Schaller, Jörg, additional, Hillen, Uwe, additional, Schadendorf, Dirk, additional, Mentzel, Thomas, additional, Cheng, Donavan T., additional, Wiesner, Thomas, additional, and Griewank, Klaus G., additional

Published
2015
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21. An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

Author

Höppner, Marc P., Lundquist, Andrew, Pirun, Mono, Meadows, Jennifer R. S., Zamani, Neda, Johnson, Jeremy, Sundström, Görel, Cook, April, FitzGerald, Michael G., Swofford, Ross, Mauceli, Evan, Moghadam, Behrooz Torabi, Greka, Anna, Alfoeldi, Jessica, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Berlin, Aaron, Brown, Adam, Gearin, Gary, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Shea, Terrance, Turner-Maier, Jason, Zimmer, Andrew, Lander, Eric S., di Palma, Federica, Lindblad-Toh, Kerstin, Grabherr, Manfred G., Höppner, Marc P., Lundquist, Andrew, Pirun, Mono, Meadows, Jennifer R. S., Zamani, Neda, Johnson, Jeremy, Sundström, Görel, Cook, April, FitzGerald, Michael G., Swofford, Ross, Mauceli, Evan, Moghadam, Behrooz Torabi, Greka, Anna, Alfoeldi, Jessica, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Berlin, Aaron, Brown, Adam, Gearin, Gary, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Shea, Terrance, Turner-Maier, Jason, Zimmer, Andrew, Lander, Eric S., di Palma, Federica, Lindblad-Toh, Kerstin, and Grabherr, Manfred G.

Abstract

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog similar to 175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional similar to 3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to,20,700 high-confidence protein coding loci, we found,4,600 antisense transcripts overlapping exons of protein coding genes, similar to 7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and,11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.

Published
2014
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22. An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

Author

Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Hoeppner, Marc P., Lundquist, Andrew, Pirun, Mono, Meadows, Jennifer R. S., Zamani, Neda, Johnson, Jeremy, Sundstrom, Gorel, Cook, April, FitzGerald, Michael G., Swofford, Ross, Mauceli, Evan, Moghadam, Behrooz Torabi, Greka, Anna, Alfoldi, Jessica, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Berlin, Aaron M., Brown, Adam, Gearin, Gary, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Shea, Terrance, Turner-Maier, Jason, Zimmer, Andrew, di Palma, Federica, Lindblad-Toh, Kerstin, Grabherr, Manfred G., Lander, Eric Steven, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Hoeppner, Marc P., Lundquist, Andrew, Pirun, Mono, Meadows, Jennifer R. S., Zamani, Neda, Johnson, Jeremy, Sundstrom, Gorel, Cook, April, FitzGerald, Michael G., Swofford, Ross, Mauceli, Evan, Moghadam, Behrooz Torabi, Greka, Anna, Alfoldi, Jessica, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Berlin, Aaron M., Brown, Adam, Gearin, Gary, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Shea, Terrance, Turner-Maier, Jason, Zimmer, Andrew, di Palma, Federica, Lindblad-Toh, Kerstin, Grabherr, Manfred G., and Lander, Eric Steven

Abstract

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ~175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ~3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ~20,700 high-confidence protein coding loci, we found ~4,600 antisense transcripts overlapping exons of protein coding genes, ~7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ~11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts., European Science Foundation (EURYI award), National Human Genome Research Institute (U.S.) (NHGRI (U54 HG003067)), Uppsala University, Swedish Medical Research Council, Swedish Research Council FORMAS, European Commission (FP7-LUPA, GA-201370), Science for Life Laboratory (Stockholm, Sweden) (Start-up grant)

Published
2014

23. Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy

Author

Al-Ahmadie, Hikmat, primary, Iyer, Gopa, additional, Hohl, Marcel, additional, Asthana, Saurabh, additional, Inagaki, Akiko, additional, Schultz, Nikolaus, additional, Hanrahan, Aphrothiti J., additional, Scott, Sasinya N., additional, Brannon, A. Rose, additional, McDermott, Gregory C., additional, Pirun, Mono, additional, Ostrovnaya, Irina, additional, Kim, Philip, additional, Socci, Nicholas D., additional, Viale, Agnes, additional, Schwartz, Gary K., additional, Reuter, Victor, additional, Bochner, Bernard H., additional, Rosenberg, Jonathan E., additional, Bajorin, Dean F., additional, Berger, Michael F., additional, Petrini, John H.J., additional, Solit, David B., additional, and Taylor, Barry S., additional

Published
2014
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24. A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations

Author

Kohsaka, Shinji, primary, Shukla, Neerav, additional, Ameur, Nabahet, additional, Ito, Tatsuo, additional, Ng, Charlotte K Y, additional, Wang, Lu, additional, Lim, Diana, additional, Marchetti, Angela, additional, Viale, Agnes, additional, Pirun, Mono, additional, Socci, Nicholas D, additional, Qin, Li-Xuan, additional, Sciot, Raf, additional, Bridge, Julia, additional, Singer, Samuel, additional, Meyers, Paul, additional, Wexler, Leonard H, additional, Barr, Frederic G, additional, Dogan, Snjezana, additional, Fletcher, Jonathan A, additional, Reis-Filho, Jorge S, additional, and Ladanyi, Marc, additional

Published
2014
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25. An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

Author

Hoeppner, Marc P., primary, Lundquist, Andrew, additional, Pirun, Mono, additional, Meadows, Jennifer R. S., additional, Zamani, Neda, additional, Johnson, Jeremy, additional, Sundström, Görel, additional, Cook, April, additional, FitzGerald, Michael G., additional, Swofford, Ross, additional, Mauceli, Evan, additional, Moghadam, Behrooz Torabi, additional, Greka, Anna, additional, Alföldi, Jessica, additional, Abouelleil, Amr, additional, Aftuck, Lynne, additional, Bessette, Daniel, additional, Berlin, Aaron, additional, Brown, Adam, additional, Gearin, Gary, additional, Lui, Annie, additional, Macdonald, J. Pendexter, additional, Priest, Margaret, additional, Shea, Terrance, additional, Turner-Maier, Jason, additional, Zimmer, Andrew, additional, Lander, Eric S., additional, di Palma, Federica, additional, Lindblad-Toh, Kerstin, additional, and Grabherr, Manfred G., additional

Published
2014
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26. The genomic basis of adaptive evolution in threespine sticklebacks

Author

Jones, Felicity C., Grabherr, Manfred G., Chan, Yingguang Frank, Russell, Pamela, Mauceli, Evan, Johnson, Jeremy, Swofford, Ross, Pirun, Mono, Zody, Michael C., White, Simon, Birney, Ewan, Searle, Stephen, Schmutz, Jeremy, Grimwood, Jane, Dickson, Mark C., Myers, Richard M., Miller, Craig T., Summers, Brian R., Knecht, Anne K., Brady, Shannon D., Zhang, Haili, Pollen, Alex A., Howes, Timothy, Amemiya, Chris, Lander, Eric S., Di Palma, Federica, Lindblad-Toh, Kerstin, Kingsley, David M., Jones, Felicity C., Grabherr, Manfred G., Chan, Yingguang Frank, Russell, Pamela, Mauceli, Evan, Johnson, Jeremy, Swofford, Ross, Pirun, Mono, Zody, Michael C., White, Simon, Birney, Ewan, Searle, Stephen, Schmutz, Jeremy, Grimwood, Jane, Dickson, Mark C., Myers, Richard M., Miller, Craig T., Summers, Brian R., Knecht, Anne K., Brady, Shannon D., Zhang, Haili, Pollen, Alex A., Howes, Timothy, Amemiya, Chris, Lander, Eric S., Di Palma, Federica, Lindblad-Toh, Kerstin, and Kingsley, David M.

Abstract

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature., De två sista författarna delar sistaförfattarskapet. (Kingsley och Lindblad-Toh)

Published
2012
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27. Next-Generation Sequencing Suggests Complex, Heterogeneous Pathogenesis In Peripheral T-Cell Lymphoma Unspecified

Author

Schatz, Jonathan H., primary, Horwitz, Steven M., additional, Lunning, Matthew A., additional, Dolgalev, Igor, additional, Huberman, Kety, additional, Heguy, Adriana, additional, Viale, Agnes, additional, Socci, Nicholas D., additional, Pirun, Mono, additional, Teruya-Feldstein, Julie, additional, and Wendel, Hans-Guido, additional

Published
2013
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29. Germline mutations in BAP1 predispose to melanocytic tumors

Author

Wiesner, Thomas, primary, Obenauf, Anna C, additional, Murali, Rajmohan, additional, Fried, Isabella, additional, Griewank, Klaus G, additional, Ulz, Peter, additional, Windpassinger, Christian, additional, Wackernagel, Werner, additional, Loy, Shea, additional, Wolf, Ingrid, additional, Viale, Agnes, additional, Lash, Alex E, additional, Pirun, Mono, additional, Socci, Nicholas D, additional, Rütten, Arno, additional, Palmedo, Gabriele, additional, Abramson, David, additional, Offit, Kenneth, additional, Ott, Arthur, additional, Becker, Jürgen C, additional, Cerroni, Lorenzo, additional, Kutzner, Heinz, additional, Bastian, Boris C, additional, and Speicher, Michael R, additional

Published
2011
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30. Abstract LB-125: Germline mutations in BAP1 predispose to melanocytic nevi and melanoma

Author

Wiesner, Thomas, primary, Obenauf, Anna, additional, Murali, Rajmohan, additional, Fried, Isabella, additional, Griewank, Klaus, additional, Ulz, Peter, additional, Windpassinger, Christian, additional, Loy, Shea, additional, Wackernagel, Werner, additional, Wolf, Ingrid, additional, Becker, Juergen, additional, Viale, Agnes, additional, Lash, Alex, additional, Pirun, Mono, additional, Socci, Nick, additional, Ruetten, Arno, additional, Palmedo, Gabrielle, additional, Ott, Arthur, additional, Abramson, David, additional, Offit, Kenneth, additional, Cerroni, Lorenzo, additional, Kutzner, Heinz, additional, Bastian, Boris, additional, and Speicher, Michael, additional

Published
2011
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31. Abstract LB-151: Targeted gene resequencing in a K-ras-dependent mouse model of metastatic lung adenocarcinoma

Author

McFadden, David G., primary, Xuan, Zhenyu, additional, Rosebrock, Adam, additional, Politi, Katerina, additional, Santiago, Philip, additional, Hodges, Emily, additional, Winslow, Monte, additional, Hiramatsu, Nobuhito, additional, Pirun, Mono, additional, Crowley, Denise, additional, Bronson, Roderick, additional, Socci, Nicholas, additional, Varmus, Harold, additional, Hannon, Greg, additional, and Jacks, Tyler, additional

Published
2010
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34. Osteogenic Differentiation of Human Bone Marrow Stromal Cells on Partially Demineralized Bone Scaffolds in Vitro

Author

Mauney, Joshua R., Blumberg, Jeff, Pirun, Mono, Volloch, Vladimir, Vunjak-Novakovic, Gordana, and Kaplan, David L.

Abstract

Tissue engineering has been used to enhance the utility of biomaterials for clinical bone repair by the incorporation of an osteogenic cell source into a scaffold followed by the in vitro promotion of osteogenic differentiation before host implantation. In this study, three-dimensional, partially demineralized bone scaffolds were investigated for their ability to support osteogenic differentiation of human bone marrow stromal cells (BMSCs) in vitro. Dynamic cell seeding resulted in homogeneous cell attachment and infiltration within the matrix and produced significantly higher seeding efficiencies when compared with a conventional static seeding method. Dynamically seeded scaffolds were cultured for 7 and 14 days in the presence of dexamethasone and evaluated on biochemical, molecular, and morphological levels for osteogenic differentiation. Significant elevation in alkaline phosphatase activity was observed versus controls over the 14-day culture, with a transient peak indicative of early mineralization on day 7. On the basis of RT-PCR, dexamethasone-treated samples showed elevations in alkaline phosphatase and osteocalcin expression levels at 7 and 14 days over nontreated controls, while bone sialoprotein was produced only in the presence of dexamethasone at 14 days. Scanning electron microscopy evaluation of dexamethasone-treated samples at 14 days revealed primarily cuboidal cells indicative of mature osteoblasts, in contrast to nontreated controls displaying a majority of cells with a fibroblastic cell morphology. These results demonstrate that partially demineralized bone can be successfully used with human BMSCs to support osteogenic differentiation in vitro. This osseous biomaterial may offer new potential benefits as a tool for clinical bone replacement.

Published
2004
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