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1. Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis

Author

Liu, Jiangang, Cho, Yong Beom, Hong, Hye Kyung, Wu, Song, Ebert, Philip J., Bray, Steven M., Wong, Swee Seong, Ting, Jason C., Calley, John N., Whittington, Catherine F., Bhagwat, Shripad V., Reinhard, Christoph, Wild, Robert, Nam, Do-Hyun, Aggarwal, Amit, Lee, Woo Yong, and Peng, Sheng-Bin

Published
2020
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2. Genomic characterization of intrinsic and acquired resistance to cetuximab in colorectal cancer patients

Author

Bray, Steven M., Lee, Jeeyun, Kim, Seung Tae, Hur, Joon Young, Ebert, Philip J., Calley, John N., Wulur, Isabella H., Gopalappa, Thejaswini, Wong, Swee Seong, Qian, Hui-Rong, Ting, Jason C., Liu, Jiangang, Willard, Melinda D., Novosiadly, Ruslan D., Park, Young Suk, Park, Joon Oh, Lim, Ho Yeong, Kang, Won Ki, Aggarwal, Amit, Kim, Hee Cheol, and Reinhard, Christoph

Published
2019
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3. BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders

Author

Schubert, Christian R., O’Donnell, Patricio, Quan, Jie, Wendland, Jens R., Xi, Hualin S., Winslow, Ashley R., Domenici, Enrico, Essioux, Laurent, Kam-Thong, Tony, Airey, David C., Calley, John N., Collier, David A., Wang, Hong, Eastwood, Brian, Ebert, Philip, Liu, Yushi, Nisenbaum, Laura, Ruble, Cara, Scherschel, James E., Smith, Ryan Matthew, Qian, Hui-Rong, Merchant, Kalpana, Didriksen, Michael, Matsumoto, Mitsuyuki, Saito, Takeshi, Brandon, Nicholas J., Cross, Alan J., Wang, Qi, Manji, Husseini, Kolb, Hartmuth, Furey, Maura, Drevets, Wayne C., Shin, Joo Heon, Jaffe, Andrew E., Jia, Yankai, Straub, Richard E., Deep-Soboslay, Amy, Hyde, Thomas M., Kleinman, Joel E., and Weinberger, Daniel R.

Published
2015
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7. Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

Author

Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, Mangravite, Lara M., Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, and Mangravite, Lara M.

Abstract

© 2020, The Author(s). The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).

Published
2022

15. Abstract 2586: PI3K/AKT signaling pathway is transcriptionally elevated in prexasertib-resistant TNBC PDX models

Author

Ding, Yan, primary, Liu, Jiangang, additional, Calley, John N., additional, Qian, Hui-Rong, additional, Iversen, Philip W., additional, Ebert, Philip J., additional, Beckmann, Richard P., additional, Donoho, Gregory P., additional, Martinez, Ricardo, additional, Wu, Wenjuan, additional, Lin, Aimee Bence, additional, Bowden, Emma, additional, and Aggarwal, Amit, additional

Published
2018
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18. Genomic Characterization of Intrinsic and Acquired Resistance to Cetuximab in Colorectal Cancer Patients

Author

Bray, Steven M, primary, Lee, Jeeyun, additional, Kim, Seung Tae, additional, Young Kim, Sun, additional, Young Hur, Joon, additional, Ebert, Philip J, additional, Calley, John N, additional, Wulur, Isabella H, additional, Gopalappa, Thejaswini, additional, Seong Wong, Swee, additional, Qian, Hui-Rong, additional, Ting, Jason C, additional, Liu, Jiangang, additional, Willard, Melinda D, additional, Novosiadly, Ruslan D, additional, Park, Young Suk, additional, Park, Joon Oh, additional, Lim, Ho Yeong, additional, Ki Kang, Won, additional, Aggarwal, Amit, additional, Cheol Kim, Hee, additional, and Reinhard, Christoph, additional

Published
2018
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19. Additional file 3: Figure S3. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
fungi
Abstract

Reads mapped at the 5â UTR of human HTR2A and predicted transcription start sites, visualized using IGV. (PDF 102Â kb)

Published
2016
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20. Additional file 9: Figure S6. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
body regions, nervous system, fungi
Abstract

Revised gene model for mouse Htr2a. (PDF 93Â kb)

Published
2016
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21. Additional file 18: Figure S8. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

Author

Smith, Aaron, Calley, John, Mathur, Sachin, Qian, Hui-Rong, Wu, Han, Farmen, Mark, Caiment, Florian, Bushel, Pierre, Jianying Li, Fisher, Craig, Kirby, Patrick, Koenig, Erik, Hall, David, and Watson, David

Abstract

qPCR of pancreas enriched miRNAs. Total RNA from the pancreas tissue of each individual rat was normalized by mass and examined by qPCR for expression of miRs-216a-5p, 375-3p and 148a-3p. Ct values are indicated on the Y-axis and the rat pancreas samples are indicated on the X-axis. Each miRNA appears to be expressed at approximately the same Ct value indicating they are present at roughly the same quantity in the pancreas. (PDF 32Â kb)

Published
2016
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22. Additional file 2: Figure S2. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
fungi
Abstract

Predicted splice donor, splice acceptor, branch site, and polypyrimidine tract scores for annotated vs. novel HTR2A exons. (PDF 144Â kb)

Published
2016
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23. Additional file 13: Figure S9. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
body regions, nervous system, fungi
Abstract

Putative transcription factor binding sites at the rs6311 locus in human HTR2A. (PDF 106Â kb)

Published
2016
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24. Additional file 4: Figure S4. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
body regions, genetic structures, nervous system, fungi
Abstract

Reads mapped at the 3â UTR of human HTR2A and predicted polyadenylation signals, visualized using IGV. (PDF 108Â kb)

Published
2016
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25. Additional file 5: Figure S5. of Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara, Smith, Ryan, Calley, John, Munsie, Leanne, Airey, David, Gao, Yuan, Shin, Joo, Hyde, Thomas, Straub, Richard, Weinberger, Daniel, and Nisenbaum, Laura

Subjects
body regions, genetic structures, nervous system, fungi
Abstract

Reads mapped at exon 3b of human HTR2A and predicted polyadenylation signals, visualized using IGV. (PDF 105Â kb)

Published
2016
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26. Additional file 5: Figure S1. of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

Author

Smith, Aaron, Calley, John, Mathur, Sachin, Qian, Hui-Rong, Wu, Han, Farmen, Mark, Caiment, Florian, Bushel, Pierre, Jianying Li, Fisher, Craig, Kirby, Patrick, Koenig, Erik, Hall, David, and Watson, David

Abstract

Tissue specific and enriched miRNAs identified by Lilly. Tissue specific and enriched miRNAs identified by Eli Lilly are displayed in a heat map with tissues listed on the X-axis and miRNAs listed on the Y-axis. Expression levels are indicated by a range of colors with blue indicating low expression and red indicating high expression. P-values are included next to each miRNA indicating the degree of tissue specificity and/or enrichment. Some miRNAs may be enriched in several tissues resulting in a high p-value. (PDF 88Â kb)

Published
2016
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27. Additional file 1: of The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

Author

Smith, Aaron, Calley, John, Mathur, Sachin, Qian, Hui-Rong, Wu, Han, Farmen, Mark, Caiment, Florian, Bushel, Pierre, Jianying Li, Fisher, Craig, Kirby, Patrick, Koenig, Erik, Hall, David, and Watson, David

Abstract

Supplementary Methods. Eli Lilly miRDeep 2 novel miRNA identification (DOCX 13Â kb)

Published
2016
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28. Abstract 1446: Super-enhancer identification via Bru/BrUV-Seq and H3K27Ac ChIP-Seq

Author

Tang, Chunlao, primary, Yadav, Vipin, additional, Qian, Hui-Rong, additional, Cunningham, Jason B., additional, Gao, Hong, additional, Liu, Yushi, additional, Ting, Jason C., additional, Bray, Steven M., additional, Ebert, Philip J., additional, Lin, Yuhao, additional, Aggarwal, Amit, additional, Calley, John N., additional, and Patel, Bharvin K., additional

Published
2017
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29. Abstract 4104: Intrinsic and acquired resistance to cetuximab in colorectal cancer patients

Author

Bray, Steven M., primary, Lee, Jeeyun, additional, Kim, Seung Tae, additional, Ebert, Philip J., additional, Calley, John N., additional, Wulur, Isabella H., additional, Gopalappa, Thejaswini, additional, Wong, Swee Seong, additional, Qian, Hui-Rong, additional, Ting, Jason C., additional, Liu, Jiangang, additional, Willard, Melinda D., additional, Aggarwal, Amit, additional, Novosiadly, Ruslan D., additional, Kim, Hee-Cheol, additional, and Reinhard, Christoph, additional

Published
2017
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30. Abstract 849: Molecular characterization of primary tumor & the paired liver metastatic biopsies of colorectal cancer reveals a critical role of immunosuppression, EMT & angiogenesis in cancer metastasis

Author

Liu, Jiangang, primary, Cho, Yong Beom, additional, Hong, Hye kyung, additional, Wu, Song, additional, Ebert, Philip J., additional, Bray, Steven M., additional, Wong, Swee Seong, additional, Ting, Jason C., additional, Calley, John N., additional, Whittington, Catherine F., additional, Bhagwat, Shripad, additional, Bowden, Emma, additional, Aggarwal, Amit, additional, Reinhard, Christoph, additional, Wild, Robert, additional, Nam, Do-Hyun, additional, Lee, Woo Yong, additional, and Peng, Sheng-Bin, additional

Published
2017
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31. The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

Author

Smith, Aaron, primary, Calley, John, additional, Mathur, Sachin, additional, Qian, Hui-Rong, additional, Wu, Han, additional, Farmen, Mark, additional, Caiment, Florian, additional, Bushel, Pierre R., additional, Li, Jianying, additional, Fisher, Craig, additional, Kirby, Patrick, additional, Koenig, Erik, additional, Hall, David G., additional, and Watson, David E, additional

Published
2016
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32. Abstract 2647: Merestinib (LY2801653), targeting several oncokinases including NTRK1/2/3, shows potent anti-tumor effect in colorectal cell line- and patient-derived xenograft (PDX) model bearing TPM3-NTRK1 fusion

Author

Konicek, Bruce W., primary, Bray, Steve M., additional, Capen, Andrew R., additional, Calley, John N., additional, Credille, Kelly M., additional, Ebert, Philip J., additional, Heady, Gary, additional, Patel, Bharvin K., additional, Peek, Victoria L., additional, Stephens, Jennifer R., additional, Um, Suzane L., additional, Willard, Melinda D., additional, Wulur, Isabella H., additional, Zeng, Yi, additional, Walgren, Richard A., additional, and Yan, Sau-Chi Betty, additional

Published
2016
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33. Genomic structure and expression of the human serotonin 2A receptor gene (HTR2A) locus: identification of novel HTR2A and antisense (HTR2A-AS1) exons

Author

Ruble, Cara L., primary, Smith, Ryan M., additional, Calley, John, additional, Munsie, Leanne, additional, Airey, David C., additional, Gao, Yuan, additional, Shin, Joo Heon, additional, Hyde, Thomas M., additional, Straub, Richard E., additional, Weinberger, Daniel R., additional, and Nisenbaum, Laura K., additional

Published
2016
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35. Abstract LB-048: Copy number and loss of heterozygosity (LOH) analysis in 52 breast cancer FFPE samples using molecular Inversion probe array: detailed analysis of reproducibility and performance compared to NGS platforms

Author

Horn, Candice L., primary, Nunes, Fabio, additional, Calley, John, additional, Bray, Steven, additional, Wulur, Isabella, additional, Farmen, Mark, additional, Gallavan, Robert, additional, Halfpenny, Iris, additional, Medlow, Paul, additional, McGreeghan-Crosby, Keith, additional, and Jellema, Gera, additional

Published
2015
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38. P3‐024: An unbiased approach to identifying tau kinases that phosphorylate tau at sites associated with early Alzheimer's disease

Author

Bose, Suchira, primary, Cavallini, Annalisa, additional, Brewerton, Suzanne, additional, Bell, Amanda, additional, Sargent, Samantha, additional, Glover, Sarah, additional, Hardy, Clare, additional, Moore, Roger, additional, Calley, John, additional, Ramachandran, Devaki, additional, Poidinger, Michael, additional, Davies, Peter, additional, Hutton, Michael, additional, and Szekeres, Phillip, additional

Published
2012
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42. The Drosophila maternal-effect mutantcappuccino and its interactors

Author

Calley, John Nels, 1961 and Calley, John Nels, 1961

Abstract

cappuccino (capu) is a Drosophila melanogaster gene required for establishing the dorsal-ventral and anterior-posterior axes of the developing egg and embryo. Egg chambers mutant for capu exhibit cytoplasmic streaming during mid-oogenesis that does not normally occur until late oogenesis. All known capu alleles stream at the same speed. Since capu alleles do differ in their effects on the dorsal-ventral axis, it is unlikely that premature streaming is a cause of the dorsal-ventral defects. Premature streaming may, however, cause the posterior defects. Streaming occurs at the same speed if isolated egg chambers are treated with the actin depolymerizing drug cytochalasin D, which suggests that CAPU may act in the actin cytoskeleton. A screen for proteins which physically interact with CAPU identified profilin, a regulator of the actin cytoskeleton as a probable partner of CAPU. This again suggests that CAPU acts in the actin cytoskeleton. CAPU is a member of the formin homology (FH) family of proteins. Sequence analysis of this family makes it possible to multiply align all family members throughout their carboxy-terminal halves. This makes possible better predictions of secondary structure, phylogenetic analysis, and identification of novel regions of conserved sequence. Analysis of the amino-terminal halves suggests that significant alignment is also possible in these more highly divergent regions. Members of the rho family of small GTPases have been implicated in the regulation of the actin cytoskeleton. They physically associate with members of the FH family, including CAPU. All four rho-like proteins tested associate with CAPU in the Interaction Trap system. There are also indications of genetic interactions between capu and the rho-like genes dcdc42 and drac1.

Published
1998

43. Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization

Author

King, Michael W., primary, Nguyen, Trent, additional, Calley, John, additional, Harty, Mark W., additional, Muzinich, Michael C., additional, Mescher, Anthony L., additional, Chalfant, Chris, additional, N'Cho, Mathias, additional, McLeaster, Kevin, additional, McEntire, Jacquelyn, additional, Stocum, David, additional, Smith, Rosamund C., additional, and Neff, Anton W., additional

Published
2003
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46. Assessment of Diet-induced Obese Rats as an Obesity Model by Comparative Functional Genomics.

Author

Shuyu Li, Hong-Yan Zhang, Hu, Charlie C., Lawrence, Frank, Gallagher, Kelly E., Surapaneni, Anupama, Estrem, Shawn T., Calley, John N., Varga, Gabor, Dow, Ernst R., and Chen, Yanyun

Subjects
GENOMICS, LABORATORY rats, DIET, OBESITY, GENE expression, FAT cells
Abstract

The article presents a study on the use of comparative functional genomics in the assessment of diet-induced (DIO) obese rats as an obesity model. In the study, gene-expression profiles of epididymal fat from DIO and lean rats were taken and compared with human subcutaneous adipocytes. The researchers conclude that caloric intake and fuel efficiency were higher in DIO rats resulting in high body weight and adiposity.

Published
2008
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47. Expression of Xenopus XlSALL4 during limb development and regeneration

Author

Neff, Anton W., King, Michael W., Harty, Mark W., Nguyen, Trent, Calley, John, Smith, Rosamund C., and Mescher, Anthony L.

Abstract

The multi‐C2H2 zinc‐finger domain containing transcriptional regulators of the spalt (SAL) family plays important developmental regulatory roles. In a competitive subtractive hybridization screen of genes expressed in Xenopus laevis hindlimb regeneration blastemas, we identified a SAL family member that, by phylogenetic analysis, falls in the same clade as human SALL4 and have designated it as XlSALL4. Mutations of human SALL4 have been linked to Okihiro syndrome, which includes preaxial (anterior) limb defects. The expression pattern of XlSALL4 transcripts during normal forelimb and hindlimb development and during hindlimb regeneration at the regeneration‐competent and regeneration‐incompetent stages is temporally and regionally dynamic. We show for the first time that a SAL family member (XlSALL4) is expressed at the right place and time to play a role regulating both digit identity along the anterior/posterior axis and epimorphic limb regeneration. Developmental Dynamics 233:356–367, 2005. © 2005 Wiley‐Liss, Inc.

Published
2005
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48. Identification of genes expressed during <TOGGLE>Xenopus laevis</TOGGLE> limb regeneration by using subtractive hybridization

Author

King, Michael W., Nguyen, Trent, Calley, John, Harty, Mark W., Muzinich, Michael C., Mescher, Anthony L., Chalfant, Chris, N'Cho, Mathias, McLeaster, Kevin, and McEntire, Jacquelyn

Abstract

Suppression polymerase chain reaction–based subtractive hybridization was used to identify genes that are expressed during Xenopus laevis hindlimb regeneration. Subtractions were done by using RNAs extracted from the regeneration-competent stage (stage 53) and regeneration-incompetent stage (stage 59) of limb development. Forward and reverse subtractions were done between stage 53 7-day blastema and stage 53 contralateral limb (competent stage), stage 59 7-day pseudoblastema and stage 59 contralateral limb (incompetent stage), and stage 53 7-day blastema and stage 59 7-day pseudoblastema. Several thousand clones were analyzed from the various subtracted libraries, either by random selection and sequencing (1,920) or by screening subtracted cDNA clones (6,150), arrayed on nylon membranes, with tissue-specific probes. Several hundred clones were identified from the array screens whose expression levels were at least twofold higher in experimental tissue vs. control tissue (e.g., blastema vs. limb) and selected for sequencing. In addition, primers were designed to assay several of the randomly selected clones and used to assess the level of expression of these genes during regeneration and normal limb development. Approximately half of the selected clones were differentially expressed, as expected, including several that demonstrate blastema-specific enhancement of expression. Three distinct categories of expression were identified in our screens: (1) clones that are expressed in both regeneration-competent blastemas and -incompetent pseudoblastemas, (2) clones that are expressed at highest levels in regeneration-competent blastemas, and (3) clones that are expressed at highest levels in regeneration-incompetent pseudoblastemas. Characterizing the role of each of these three categories of genes will be important in furthering our understanding of the process of tissue regeneration. Developmental Dynamics 226:398–409, 2003. © 2003 Wiley-Liss, Inc.

Published
2003
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49. Spire contains actin binding domains and is related to ascidian posterior end mark-5

Author

Wellington, Andrea, Emmons, Steve, James, Brian, Calley, John, Grover, Melissa, Tolias, Peter, and Manseau, Lynn

Abstract

Spire is a maternal effect locus that affects both the dorsal- ventral and anterior-posterior axes of the Drosophila egg and embryo. It is required for localization of determinants within the developing oocyte to the posterior pole and to the dorsal anterior corner. During mid-oogenesis, spire mutants display premature microtubule-dependent cytoplasmic streaming, a phenotype that can be mimicked by pharmacological disruption of the actin cytoskeleton with cytochalasin D. Spire has been cloned by transposon tagging and is related to posterior end mark-5, a gene from sea squirts that encodes a posteriorly localized mRNA. Spire mRNA is not, however, localized to the posterior pole. SPIRE also contains two domains with similarity to the actin monomer-binding WH2 domain, and we demonstrate that SPIRE binds to actin in the interaction trap system and in vitro. In addition, SPIRE interacts with the rho family GTPases RHOA, RAC1 and CDC42 in the interaction trap system. Thus, our evidence supports the model that SPIRE links rho family signaling to the actin cytoskeleton.

Published
1999
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50. Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.

Author

Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, The CommonMind Consortium (CMC), Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, and Browne, Andrew

Subjects
NUCLEOTIDE sequence, GENOTYPES, AUTOPSY, ALZHEIMER'S disease, META-analysis, CEREBRAL cortex, CEREBELLUM
Abstract

The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer's Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975). [ABSTRACT FROM AUTHOR]

Published
2020
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