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1. Circulating Immune Cell and Outcome Analysis from the Phase 2 Study of PD-L1 Blockade with Durvalumab for Newly Diagnosed and Recurrent GlioblastomaPD-L1 blockade with durvalumab for glioblastoma

Author

Nayak, Lakshmi, Standifer, Nathan, Dietrich, Jorg, Clarke, Jennifer L, Dunn, Gavin P, Lim, Michael, Cloughesy, Timothy, Gan, Hui K, Flagg, Elizabeth, George, Elizabeth, Gaffey, Sarah, Hayden, Julia, Holcroft, Christina, Wen, Patrick Y, Macri, Mary, Park, Andrew J, Ricciardi, Toni, Ryan, Aileen, Schwarzenberger, Paul, Venhaus, Ralph, de los Reyes, Melissa, Durham, Nicholas M, Creasy, Todd, Huang, Raymond Y, Kaley, Thomas, and Reardon, David A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Brain Disorders, Brain Cancer, Clinical Research, Rare Diseases, Cancer, Antibodies, Monoclonal, B7-H1 Antigen, Bevacizumab, Biomarkers, Tumor, Dexamethasone, Glioblastoma, Humans, Ki-67 Antigen, Neoplasm Recurrence, Local, Oncology & Carcinogenesis, Clinical sciences, Oncology and carcinogenesis
Abstract

PurposePD-L1 is upregulated in glioblastoma and supports immunosuppression. We evaluated PD-L1 blockade with durvalumab among glioblastoma cohorts and investigated potential biomarkers.Patients and methodsMGMT unmethylated newly diagnosed patients received radiotherapy plus durvalumab (cohort A; n = 40). Bevacizumab-naïve, recurrent patients received durvalumab alone (cohort B; n = 31) or in combination with standard bevacizumab (cohort B2; n = 33) or low-dose bevacizumab (cohort B3; n = 33). Bevacizumab-refractory patients received durvalumab plus bevacizumab (cohort C; n = 22). Primary endpoints were: OS-12 (A), PFS-6 (B, B2, B3), and OS-6 (C). Exploratory biomarkers included: a systematic, quantitative, and phenotypic evaluation of circulating immune cells; tumor mutational burden (TMB); and tumor immune activation signature (IAS).ResultsNo cohort achieved the primary efficacy endpoint. Outcome was comparable among recurrent, bevacizumab-naïve cohorts. No unexpected toxicities were observed. A widespread reduction of effector immune cell subsets was noted among recurrent patients compared with newly diagnosed patients that was partially due to dexamethasone use. A trend of increased CD8+Ki67+ T cells at day 15 was noted among patients who achieved the primary endpoint and were not on dexamethasone. Neither TMB nor IAS predicted outcome.ConclusionsPatients with recurrent glioblastoma have markedly lower baseline levels of multiple circulating immune cell subsets compared with newly diagnosed patients. An early increase in systemic Ki67+CD8+ cells may warrant further evaluation as a potential biomarker of therapeutic benefit among patients with glioblastoma undergoing checkpoint therapy. Dexamethasone decreased immune cell subsets. PD-L1 blockade and combination with standard or reduced dose bevacizumab was ineffective.

Published
2022

4. Comparative Genomics of Trypanosomatid Parasitic Protozoa

Author

El-Sayed, Najib M., Myler, Peter J., Blandin, Gaëlle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Björn, Stuart, Kenneth D., and Hall, Neil

Published
2005

5. Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes

Author

Gardner, Malcolm J., Bishop, Richard, Shah, Trushar, de Villiers, Etienne P., Carlton, Jane M., Hall, Neil, Ren, Qinghu, Paulsen, Ian T., Pain, Arnab, Berriman, Matthew, Sato, Shigeharu, Ralph, Stuart A., Mann, David J., Xiong, Zikai, Shallom, Shamira J., Weidman, Janice, Jiang, Lingxia, Lynn, Jeffery, Weaver, Bruce, Shoaibi, Azadeh, Domingo, Alexander R., Wasawo, Delia, Crabtree, Jonathan, Wortman, Jennifer R., Haas, Brian, Angiuoli, Samuel V., Creasy, Todd H., Lu, Charles, Suh, Bernard, Silva, Joana C., Utterback, Teresa R., Feldblyum, Tamara V., Pertea, Mihaela, Allen, Jonathan, Nierman, William C., Salzberg, Steven L., White, Owen R., Fitzhugh, Henry A., Morzaria, Subhash, Venter, J. Craig, Fraser, Claire M., and Nene, Vishvanath

Published
2005

7. EQUIPPED FOR THE TRIP.

Author

Creasy, Todd

Subjects
CAREER development, ORGANIZATIONAL behavior, EXECUTIVES, PERSONALITY, CONFLICT management
Abstract

The article emphasizes the significance of considering conflict management style, self-monitoring, and change orientation when selecting managers for improvement projects like Six Sigma or lean initiatives. Topics include the importance of personality traits in project success, the impact of self-monitoring, change orientation, and conflict management on project outcomes, and the implications for selecting the right improvement manager.

Published
2024

10. Supplementary Data from Circulating Immune Cell and Outcome Analysis from the Phase II Study of PD-L1 Blockade with Durvalumab for Newly Diagnosed and Recurrent Glioblastoma

Author

Nayak, Lakshmi, primary, Standifer, Nathan, primary, Dietrich, Jorg, primary, Clarke, Jennifer L., primary, Dunn, Gavin P., primary, Lim, Michael, primary, Cloughesy, Timothy, primary, Gan, Hui K., primary, Flagg, Elizabeth, primary, George, Elizabeth, primary, Gaffey, Sarah, primary, Hayden, Julia, primary, Holcroft, Christina, primary, Wen, Patrick Y., primary, Macri, Mary, primary, Park, Andrew J., primary, Ricciardi, Toni, primary, Ryan, Aileen, primary, Schwarzenberger, Paul, primary, Venhaus, Ralph, primary, Reyes, Melissa de los, primary, Durham, Nicholas M., primary, Creasy, Todd, primary, Huang, Raymond Y., primary, Kaley, Thomas, primary, and Reardon, David A., primary

Published
2023
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11. Supplementary Figure from Circulating Immune Cell and Outcome Analysis from the Phase II Study of PD-L1 Blockade with Durvalumab for Newly Diagnosed and Recurrent Glioblastoma

Author

Nayak, Lakshmi, primary, Standifer, Nathan, primary, Dietrich, Jorg, primary, Clarke, Jennifer L., primary, Dunn, Gavin P., primary, Lim, Michael, primary, Cloughesy, Timothy, primary, Gan, Hui K., primary, Flagg, Elizabeth, primary, George, Elizabeth, primary, Gaffey, Sarah, primary, Hayden, Julia, primary, Holcroft, Christina, primary, Wen, Patrick Y., primary, Macri, Mary, primary, Park, Andrew J., primary, Ricciardi, Toni, primary, Ryan, Aileen, primary, Schwarzenberger, Paul, primary, Venhaus, Ralph, primary, Reyes, Melissa de los, primary, Durham, Nicholas M., primary, Creasy, Todd, primary, Huang, Raymond Y., primary, Kaley, Thomas, primary, and Reardon, David A., primary

Published
2023
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12. The tumor inflammation signature (TIS) is associated with anti-PD-1 treatment benefit in the CERTIM pan-cancer cohort

Author

Damotte, Diane, Warren, Sarah, Arrondeau, Jennifer, Boudou-Rouquette, Pascaline, Mansuet-Lupo, Audrey, Biton, Jérôme, Ouakrim, Hanane, Alifano, Marco, Gervais, Claire, Bellesoeur, Audrey, Kramkimel, Nora, Tlemsani, Camille, Burroni, Barbara, Duche, Angéline, Letourneur, Franck, Si, Han, Halpin, Rebecca, Creasy, Todd, Herbst, Ronald, Ren, Xing, Morel, Pascale, Cesano, Alessandra, Goldwasser, François, and Leroy, Karen

Published
2019
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13. Circulating Immune Cell and Outcome Analysis from the Phase II Study of PD-L1 Blockade with Durvalumab for Newly Diagnosed and Recurrent Glioblastoma.

Author

Nayak, Lakshmi, Nayak, Lakshmi, Standifer, Nathan, Dietrich, Jorg, Clarke, Jennifer L, Dunn, Gavin P, Lim, Michael, Cloughesy, Timothy, Gan, Hui K, Flagg, Elizabeth, George, Elizabeth, Gaffey, Sarah, Hayden, Julia, Holcroft, Christina, Wen, Patrick Y, Macri, Mary, Park, Andrew J, Ricciardi, Toni, Ryan, Aileen, Schwarzenberger, Paul, Venhaus, Ralph, Reyes, Melissa de Los, Durham, Nicholas M, Creasy, Todd, Huang, Raymond Y, Kaley, Thomas, Reardon, David A, Nayak, Lakshmi, Nayak, Lakshmi, Standifer, Nathan, Dietrich, Jorg, Clarke, Jennifer L, Dunn, Gavin P, Lim, Michael, Cloughesy, Timothy, Gan, Hui K, Flagg, Elizabeth, George, Elizabeth, Gaffey, Sarah, Hayden, Julia, Holcroft, Christina, Wen, Patrick Y, Macri, Mary, Park, Andrew J, Ricciardi, Toni, Ryan, Aileen, Schwarzenberger, Paul, Venhaus, Ralph, Reyes, Melissa de Los, Durham, Nicholas M, Creasy, Todd, Huang, Raymond Y, Kaley, Thomas, and Reardon, David A

Abstract

PurposePD-L1 is upregulated in glioblastoma and supports immunosuppression. We evaluated PD-L1 blockade with durvalumab among glioblastoma cohorts and investigated potential biomarkers.Patients and methodsMGMT unmethylated newly diagnosed patients received radiotherapy plus durvalumab (cohort A; n = 40). Bevacizumab-naïve, recurrent patients received durvalumab alone (cohort B; n = 31) or in combination with standard bevacizumab (cohort B2; n = 33) or low-dose bevacizumab (cohort B3; n = 33). Bevacizumab-refractory patients received durvalumab plus bevacizumab (cohort C; n = 22). Primary endpoints were: OS-12 (A), PFS-6 (B, B2, B3), and OS-6 (C). Exploratory biomarkers included: a systematic, quantitative, and phenotypic evaluation of circulating immune cells; tumor mutational burden (TMB); and tumor immune activation signature (IAS).ResultsNo cohort achieved the primary efficacy endpoint. Outcome was comparable among recurrent, bevacizumab-naïve cohorts. No unexpected toxicities were observed. A widespread reduction of effector immune cell subsets was noted among recurrent patients compared with newly diagnosed patients that was partially due to dexamethasone use. A trend of increased CD8+Ki67+ T cells at day 15 was noted among patients who achieved the primary endpoint and were not on dexamethasone. Neither TMB nor IAS predicted outcome.ConclusionsPatients with recurrent glioblastoma have markedly lower baseline levels of multiple circulating immune cell subsets compared with newly diagnosed patients. An early increase in systemic Ki67+CD8+ cells may warrant further evaluation as a potential biomarker of therapeutic benefit among patients with glioblastoma undergoing checkpoint therapy. Dexamethasone decreased immune cell subsets. PD-L1 blockade and combination with standard or reduced dose bevacizumab was ineffective.

Published
2022

14. Circulating Immune Cell and Outcome Analysis from the Phase II Study of PD-L1 Blockade with Durvalumab for Newly Diagnosed and Recurrent Glioblastoma

Author

Nayak, Lakshmi, primary, Standifer, Nathan, additional, Dietrich, Jorg, additional, Clarke, Jennifer L., additional, Dunn, Gavin P., additional, Lim, Michael, additional, Cloughesy, Timothy, additional, Gan, Hui K., additional, Flagg, Elizabeth, additional, George, Elizabeth, additional, Gaffey, Sarah, additional, Hayden, Julia, additional, Holcroft, Christina, additional, Wen, Patrick Y., additional, Macri, Mary, additional, Park, Andrew J., additional, Ricciardi, Toni, additional, Ryan, Aileen, additional, Schwarzenberger, Paul, additional, Venhaus, Ralph, additional, Reyes, Melissa de los, additional, Durham, Nicholas M., additional, Creasy, Todd, additional, Huang, Raymond Y., additional, Kaley, Thomas, additional, and Reardon, David A., additional

Published
2022
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15. Draft Genome of the Filarial Nematode Parasite Brugia malayi

Author

Ghedin, Elodie, Wang, Shiliang, Spiro, David, Caler, Elisabet, Zhao, Qi, Crabtree, Jonathan, Allen, Jonathan E., Delcher, Arthur L., Guiliano, David B., Miranda-Saavedra, Diego, Angiuoli, Samuel V., Creasy, Todd, Amedeo, Paolo, Haas, Brian, El-Sayed, Najib M., Wortman, Jennifer R., Feldblyum, Tamara, Tallon, Luke, Schatz, Michael, Shumway, Martin, Koo, Hean, Salzberg, Steven L., Schobel, Seth, Pertea, Mihaela, Pop, Mihai, White, Owen, Barton, Geoffrey J., Carlow, Clotilde K. S., Crawford, Michael J., Daub, Jennifer, Dimmic, Matthew W., Estes, Chris F., Foster, Jeremy M., Ganatra, Mehul, Gregory, William F., Johnson, Nicholas M., Jin, Jinming, Komuniecki, Richard, Korf, Ian, Kumar, Sanjay, Laney, Sandra, Li, Ben-Wen, Li, Wen, Lindblom, Tim H., Lustigman, Sara, Ma, Dong, Maina, Claude V., Martin, David M. A., McCarter, James P., McReynolds, Larry, Mitreva, Makedonka, Nutman, Thomas B., Parkinson, John, Peregrín-Alvarez, José M., Poole, Catherine, Ren, Qinghu, Saunders, Lori, Sluder, Ann E., Smith, Katherine, Stanke, Mario, Unnasch, Thomas R., Ware, Jenna, Wei, Aguan D., Weil, Gary, Williams, Deryck J., Zhang, Yinhua, Williams, Steven A., Fraser-Liggett, Claire, Slatko, Barton, Blaxter, Mark L., and Scott, Alan L.

Published
2007
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19. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition

Author

Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., Daugherty, Sean C., DeBoy, Robert, Durkin, A. Scott, Giglio, Michelle Gwinn, Madupu, Ramana, Nelson, William C., Rosovitz, M.J., Sullivan, Steven, Crabtree, Jonathan, Creasy, Todd, Davidsen, Tanja, Haft, Dan H., Zafar, Nikhat, Zhou, Liwei, Halpin, Rebecca, Holley, Tara, Khouri, Hoda, Feldblyum, Tamara, White, Owen, Fraser, Claire M., Chatterjee, Arun K., Cartinhour, Sam, Schneider, David J., Mansfield, John, Collmer, Alan, and Buell, C. Robin

Subjects
Genomics -- Comparative analysis, Genetic research -- Comparative analysis, Biological sciences
Abstract

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

Published
2005

20. Comparative genomics of trypanosomatid parasitic protozoa

Author

Sayed, Najib M. El-, Myler, Peter J., Blandin, Gaelle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Alsmark, U. Cecilia M., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Bjorn, Stuart, Kenneth D., and Hall, Neil

Subjects
Leishmaniasis -- Genetic aspects, Trypanosoma cruzi -- Genetic aspects, Trypanosoma brucei -- Genetic aspects, Science and technology, Genetic aspects
Abstract

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that--along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions--have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont., The protozoan pamogens Leishmania major, Trypanosoma cruzi, and Trypanosoma brucei (family Trypanosomatidae, order Kinetoplastida) collectively cause disease and death in millions of humans and countless infections in other mammals, primarily [...]

Published
2005

21. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana

Author

Theologis, Athanasios, Ecker, Joseph R., Palm, Curtis J., Federspiel, Nancy A., Kaul, Samir, White, Owen, Alonso, Jose, Altafi, Hootan, Araujo, Rina, Bowman, Cheryl L., Brooks, Shelise Y., Buehler, Eugen, Chan, April, Chao, Qimin, Chen, Huaming, Cheuk, Rosa F., Chin, Christina W., Chung, Mike K., Conn, Lane, Conway, Aaron B., Conway, Andrew R., Creasy, Todd H., Dewar, Ken, Dunn, Patrick, Etgu, Pelin, Feldblyum, Tamara V., Feng, JiDong, Fong, Betty, Fujii, Claire Y., Gill, John E., Goldsmith, Andrew D., Haas, Brian, Hansen, Nancy F., Hughes, Beth, Huizar, Lucas, Hunter, Jonathan L., Jenkins, Jennifer, Johnson-Hopson, Chanda, Khan, Shehnaz, Khaykin, Elizabeth, Kim, Christopher J., Koo, Hean L., Kremenetskaia, Irina, Kurtz, David B., Kwan, Andrea, Lam, Bao, Langin-Hooper, Stephanie, Lee, Andrew, Lee, Jeong M., Lenz, Catherine A., Li, Joycelyn. H., Li, YaPing, Lin, Xiaoying, Liu, Shirley X., Liu, Zhaoying A., Luros, Jason S., Maiti, Rama, Marziali, Andre, Militscher, Jennifer, Miranda, Molly, Nguyen, Michelle, Nierman, William C., Osborne, Brian I., Pai, Grace, Peterson, Jeremy, Pham, Paul K., Rizzo, Michael, Rooney, Timothy, Rowley, Don, Sakano, Hitomi, Salzberg, Steven L., Schwartz, Jody R., Shinn, Paul, Southwick, Audrey M., Sun, Hui, Tallon, Luke J., Tambunga, Gabriel, Toriumi, Mitsue J., Town, Christopher D., Utterback, Teresa, Van Aken, Susan, Vaysberg, Maria, Vysotskaia, Valentina S., Walker, Michelle, Wu, Dongying, Yu, Guixia, Fraser, Claire M., Venter, J. Craig, and Davis, Ronald W.

Published
2000
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22. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Author

Wells, Daniel K., primary, van Buuren, Marit M., additional, Dang, Kristen K., additional, Hubbard-Lucey, Vanessa M., additional, Sheehan, Kathleen C.F., additional, Campbell, Katie M., additional, Lamb, Andrew, additional, Ward, Jeffrey P., additional, Sidney, John, additional, Blazquez, Ana B., additional, Rech, Andrew J., additional, Zaretsky, Jesse M., additional, Comin-Anduix, Begonya, additional, Ng, Alphonsus H.C., additional, Chour, William, additional, Yu, Thomas V., additional, Rizvi, Hira, additional, Chen, Jia M., additional, Manning, Patrice, additional, Steiner, Gabriela M., additional, Doan, Xengie C., additional, Merghoub, Taha, additional, Guinney, Justin, additional, Kolom, Adam, additional, Selinsky, Cheryl, additional, Ribas, Antoni, additional, Hellmann, Matthew D., additional, Hacohen, Nir, additional, Sette, Alessandro, additional, Heath, James R., additional, Bhardwaj, Nina, additional, Ramsdell, Fred, additional, Schreiber, Robert D., additional, Schumacher, Ton N., additional, Kvistborg, Pia, additional, Defranoux, Nadine A., additional, Khan, Aly A., additional, Lugade, Amit, additional, Lazic, Ana M. Mijalkovic, additional, Frentzen, Angela A. Elizabeth, additional, Tadmor, Arbel D., additional, Sasson, Ariella S., additional, Rao, Arjun A., additional, Pei, Baikang, additional, Schrörs, Barbara, additional, Berent-Maoz, Beata, additional, Carreno, Beatriz M., additional, Song, Bin, additional, Peters, Bjoern, additional, Li, Bo, additional, Higgs, Brandon W., additional, Stevenson, Brian J., additional, Iseli, Christian, additional, Miller, Christopher A., additional, Morehouse, Christopher A., additional, Melief, Cornelis J.M., additional, Puig-Saus, Cristina, additional, van Beek, Daphne, additional, Balli, David, additional, Gfeller, David, additional, Haussler, David, additional, Jäger, Dirk, additional, Cortes, Eduardo, additional, Esaulova, Ekaterina, additional, Sherafat, Elham, additional, Arcila, Francisco, additional, Bartha, Gabor, additional, Liu, Geng, additional, Coukos, George, additional, Richard, Guilhem, additional, Chang, Han, additional, Si, Han, additional, Zörnig, Inka, additional, Xenarios, Ioannis, additional, Mandoiu, Ion, additional, Kooi, Irsan, additional, Conway, James P., additional, Kessler, Jan H., additional, Greenbaum, Jason A., additional, Perera, Jason F., additional, Harris, Jason, additional, Hundal, Jasreet, additional, Shelton, Jennifer M., additional, Wang, Jianmin, additional, Wang, Jiaqian, additional, Greshock, Joel, additional, Blake, Jonathon, additional, Szustakowski, Joseph, additional, Kodysh, Julia, additional, Forman, Juliet, additional, Wei, Lei, additional, Lee, Leo J., additional, Fanchi, Lorenzo F., additional, Slagter, Maarten, additional, Lang, Maren, additional, Mueller, Markus, additional, Lower, Martin, additional, Vormehr, Mathias, additional, Artyomov, Maxim N., additional, Kuziora, Michael, additional, Princiotta, Michael, additional, Bassani-Sternberg, Michal, additional, Macabali, Mignonette, additional, Kojicic, Milica R., additional, Yang, Naibo, additional, Raicevic, Nevena M. Ilic, additional, Guex, Nicolas, additional, Robine, Nicolas, additional, Halama, Niels, additional, Skundric, Nikola M., additional, Milicevic, Ognjen S., additional, Gellert, Pascal, additional, Jongeneel, Patrick, additional, Charoentong, Pornpimol, additional, Srivastava, Pramod K., additional, Tanden, Prateek, additional, Shah, Priyanka, additional, Hu, Qiang, additional, Gupta, Ravi, additional, Chen, Richard, additional, Petit, Robert, additional, Ziman, Robert, additional, Hilker, Rolf, additional, Shukla, Sachet A., additional, Al Seesi, Sahar, additional, Boyle, Sean M., additional, Qiu, Si, additional, Sarkizova, Siranush, additional, Salama, Sofie, additional, Liu, Song, additional, Wu, Song, additional, Sridhar, Sriram, additional, Ketelaars, Steven L.C., additional, Jhunjhunwala, Suchit, additional, Shcheglova, Tatiana, additional, Schuepbach, Thierry, additional, Creasy, Todd H., additional, Josipovic, Veliborka, additional, Kovacevic, Vladimir B., additional, Fu, Weixuan, additional, Krebber, Willem-Jan, additional, Hsu, Yi-Hsiang, additional, Sebastian, Yinong, additional, Yalcin, Zeynep Kosaloglu-, additional, and Huang, Zhiqin, additional

Published
2020
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23. Abstract 5544: Newcastle Disease Virus in human derived tumors: Understanding immune recruitment and activation via virally delivered IL-12

Author

Durham, Nicholas M., primary, McGlinchey, Kelly, additional, Burke, Shannon, additional, Creasy, Todd, additional, Rath, Nicola, additional, Monks, Noel, additional, Tammali, Ravinder, additional, Schifferli, Kevin, additional, Holoweckyj, Nick, additional, Hayes, Susie, additional, Jones, Emma, additional, Kelly, Elizabeth J., additional, Carroll, Danielle, additional, Harper, James, additional, and Streicher, Katie, additional

Published
2020
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24. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Author

Lin, Xiaoying, Kaul, Samir, Rounsley, Steve, Shea, Terrance P., Benito, Maria-Ines, Town, Christopher D., Fujii, claire Y., Mason, Tanya, Bowman, Cheryl L., Barnstead, Mary, Feldblyum, Tamara V., Buell, C. Robin, Ketchum, Karen A., Lee, John, Ronning, Catherine M., Koo, Hean L., Moffat, Kelly S., Cronin, Lisa A., Shen, Mian, Pai, Grace, Aken, Susan Van, Umayam, Lowell, Tallon, Luke J., Gill, John E., Adams, Mark D., Carrera, Ana J., Creasy, Todd H., Goodman, Howard M., Somerville, Chris R., Copenhaver, Greg P., Preuss, Daphne, Nierman, William C., White, Owen, Eisen, Jonathan A., Salzberg, Steven L., Fraser, Claire M., and Venter, J. Craig

Subjects
Arabidopsis thaliana -- Genetic aspects, Plant chromosomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It has been possible to identify the sequence of chromosome 2 from the Columbia ecotype of Arabidopsis thaliana in two gap-free assemblies of 3.6 Mb and 16 Mb. The two assemblies terminate in blocks of 180-bp repeats, with the repeats representing the inner boundaries of the completed sequence. Within the genetically defined centromere, there is a stretch of 270 kb of sequence that is almost identical to that of the Arabidopsis mitochondrial gene. It cannot be established whether the observed sequence polymorphisms are the result of divergence of the insertion from the mitochondrial genome or of differences among ecotypes.

Published
1999

25. Pyramid power

Author

Creasy, Todd

Subjects
Quality control -- Methods, Six Sigma (Quality control) -- Usage, Lean manufacturing -- Usage, Quality control, Business, Economics, Engineering and manufacturing industries
Abstract

6TOC is the next step for Six Sigma, combining the principles of the theory of constraints with lean Six Sigma for bottom line results. 6TOC's metrics pyramids and communications offer businesses a way of monitoring benefits and maintaining gains. How to apply 6TOC is explained.

Published
2009

26. MOESM4 of The tumor inflammation signature (TIS) is associated with anti-PD-1 treatment benefit in the CERTIM pan-cancer cohort

Author

Damotte, Diane, Warren, Sarah, Arrondeau, Jennifer, Boudou-Rouquette, Pascaline, Mansuet-Lupo, Audrey, JÊrôMe Biton, Ouakrim, Hanane, Alifano, Marco, Gervais, Claire, Bellesoeur, Audrey, Kramkimel, Nora, Tlemsani, Camille, Burroni, Barbara, AngÊline Duche, Letourneur, Franck, Si, Han, Halpin, Rebecca, Creasy, Todd, Herbst, Ronald, Ren, Xing, Morel, Pascale, Cesano, Alessandra, FrançOis Goldwasser, and Leroy, Karen

Subjects
neoplasms, respiratory tract diseases
Abstract

Additional file 4: Table S4. Clinical characteristics of the NSCLC patients with TMB data.

Published
2019
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27. Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer

Author

Kumar Nikhil, Creasy Todd, Sun Yezhou, Flowers Melissa, Tallon Luke J, and Dunning Hotopp Julie C

Subjects
Wolbachia, Drosophila ananassae, RNASeq, Transcriptomics, Lateral gene transfer, Horizontal gene transfer, Endosymbiont, Insect vector, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background Numerous methods exist for enriching bacterial or mammalian mRNA prior to transcriptome experiments. Yet there persists a need for methods to enrich for mRNA in non-mammalian animal systems. For example, insects contain many important and interesting obligate intracellular bacteria, including endosymbionts and vector-borne pathogens. Such obligate intracellular bacteria are difficult to study by traditional methods. Therefore, genomics has greatly increased our understanding of these bacteria. Efficient subtraction methods are needed for removing both bacteria and insect rRNA in these systems to enable transcriptome-based studies. Findings A method is described that efficiently removes >95% of insect rRNA from total RNA samples, as determined by microfluidics and transcriptome sequencing. This subtraction yielded a 6.2-fold increase in mRNA abundance. Such a host rRNA-depletion strategy, in combination with bacterial rRNA depletion, is necessary to analyze transcription of obligate intracellular bacteria. Here, transcripts were identified that arise from a lateral gene transfer of an entire Wolbachia bacterial genome into a Drosophila ananassae chromosome. In this case, an rRNA depletion strategy is preferred over polyA-based enrichment since transcripts arising from bacteria-to-animal lateral gene transfer may not be poly-adenylated. Conclusions This enrichment method yields a significant increase in mRNA abundance when poly-A selection is not suitable. It can be used in combination with bacterial rRNA subtraction to enable experiments to simultaneously measure bacteria and insect mRNA in vector and endosymbiont biology experiments.

Published
2012
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28. Impaired Tumor-Infiltrating T Cells in Patients with Chronic Obstructive Pulmonary Disease Impact Lung Cancer Response to PD-1 Blockade

Author

Biton, Jérôme, primary, Ouakrim, Hanane, additional, Dechartres, Agnès, additional, Alifano, Marco, additional, Mansuet-Lupo, Audrey, additional, Si, Han, additional, Halpin, Rebecca, additional, Creasy, Todd, additional, Bantsimba-Malanda, Claudie, additional, Arrondeau, Jennifer, additional, Goldwasser, François, additional, Boudou-Rouquette, Pascaline, additional, Fournel, Ludovic, additional, Roche, Nicolas, additional, Burgel, Pierre-Régis, additional, Goc, Jeremy, additional, Devi-Marulkar, Priyanka, additional, Germain, Claire, additional, Dieu-Nosjean, Marie-Caroline, additional, Cremer, Isabelle, additional, Herbst, Ronald, additional, and Damotte, Diane, additional

Published
2018
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31. Abstract 5390: microRNA signature of T cell exhaustion

Author

Greenlees, Lydia M., primary, Kuziora, Michael, additional, Sebastian, Yinong, additional, Creasy, Todd, additional, Lee, Young S., additional, Pilataxi, Fernanda, additional, Holoweckyj, Nick, additional, Cheng, Li, additional, Higgs, Brandon W., additional, Ranade, Koustubh, additional, and Streicher, Katie, additional

Published
2018
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33. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils

Author

Ward, Naomi L., Challacombe, Jean F., Janssen, Peter H., Henrissat, Bernard, Coutinho, Pedro M., Martin Wu, Xie, Gary, Haft, Daniel H., Sait, Michelle, Badger, Jonathan, Barabote, Ravi D., Bradley, Brent, Brettin, Thomas S., Brinkac, Lauren M., Bruce, David, Creasy, Todd, Daugherty, Sean C., Davidsen, Tanja M., DeBoy, Robert T., Detter, J. Chris, Dodson, Robert J., Durkin, A. Scott, Ganapathy, Anuradha, Gwinn-Giglio, Michelle, Han, Cliff S., Khouri, Hoda, Kiss, Hajnalka, Kothari, Sagar P., Madupu, Ramana, Nelson, Karen E., Nelson, William C., Paulsen, Ian, Penn, Kevin, Qinghu Ren, Rosovitz, M.J., Selengut, Jeremy D., Shrivastava, Susmita, Sullivan, Steven A., Tapia, Roxanne, Thompson, L. Sue, Watkins, Kisha L., Qi Yang, Chunhui Yu, Zafar, Nikhat, Zhou, Liwei, and Kuske, Cherly R.

Subjects
Bacterial genetics -- Research, Cyanobacteria -- Physiological aspects, Cyanobacteria -- Genetic aspects, Hydration (Chemistry) -- Analysis, Soil microbiology -- Research, Biological sciences
Abstract

The result from the comparison of complete genomes of three strains from the phylum Acidobacteria which share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi are presented. The cells of the isolates of Acidobacteria strains are found to be long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions and are well equipped to tolerate fluctuations in soil hydration.

Published
2009

36. TEAMS RESEARCH IN PROJECT MANAGEMENT AND ORGANIZATIONAL BEHAVIOR: Leveraging One Discipline to Propel Another.

Author

CARNES, ANDREW, CREASY, TODD, and JOHNSON, NATHAN

Subjects
ORGANIZATIONAL behavior, RESEARCH teams, RESEARCH management, PROJECT management, PROJECT management software, THEORY-practice relationship, VIRTUAL work teams
Abstract

Teams and team related concepts have been investigated in the organizational behavior (OB) and project management (PM) disciplines for a century and nearly halfcentury respectfully. A five-decade, interdisciplinary examination of the OB and PM team literatures suggests areas for expeditiously incorporating OB concepts into PM research thus reducing an average 25-year "thematic lag" between OB's and PM's similar, team-centric research initiations. Adoption of a shared agenda, as done previously in other fields (e.g. Selznick, 1948), would allow PM researchers to leverage prior OB studies while focusing sharply on PM-specific team issues thus propelling research in theory and practice. [ABSTRACT FROM AUTHOR]

Published
2019
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37. Understanding employee-level dynamics within the merger and acquisition process

Author

Creasy, Todd, Stull, Michael, and Peck, Simon

Subjects
Acquisitions and mergers -- Research, Labor relations -- Research, Business, Business, general
Abstract

A model exploring the potential determinants of success in the acculturation process du ring mergers and acquisitions is presented. The effects of employee-level factors and perceptions of managerial behaviors during the process are investigated.

Published
2009

38. The Power of 'Lean Crushing'

Author

Creasy, Todd

Subjects
Six Sigma (Quality control) -- Comparative analysis, Six Sigma (Quality control) -- Methods, Lean manufacturing -- Comparative analysis, Business, Petroleum, energy and mining industries
Abstract

Not long ago, I happened upon a list of the manufacturers of the engines that power the 200+ mph cars at the Indianapolis 500 race. Of the 20 or so [...]

Published
2008

39. BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data

Author

Zhu, Wei, primary, Kuziora, Michael, additional, Creasy, Todd, additional, Lai, Zhongwu, additional, Morehouse, Christopher, additional, Guo, Xiang, additional, Sebastian, Yinong, additional, Shen, Dong, additional, Huang, Jiaqi, additional, Dry, Jonathan R., additional, Xue, Feng, additional, Jiang, Liyan, additional, Yao, Yihong, additional, and Higgs, Brandon W., additional

Published
2015
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41. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys

Author

Ioannidis, Panagiotis, Ioannidis, Panagiotis, Lu, Yong, Kumar, Nikhil, Creasy, Todd, Daugherty, Sean, Chibucos, Marcus C, Orvis, Joshua, Shetty, Amol, Ott, Sandra, Flowers, Melissa, Sengamalay, Naomi, Tallon, Luke J, Pick, Leslie, Dunning Hotopp, Julie C, Ioannidis, Panagiotis, Ioannidis, Panagiotis, Lu, Yong, Kumar, Nikhil, Creasy, Todd, Daugherty, Sean, Chibucos, Marcus C, Orvis, Joshua, Shetty, Amol, Ott, Sandra, Flowers, Melissa, Sengamalay, Naomi, Tallon, Luke J, Pick, Leslie, and Dunning Hotopp, Julie C

Abstract

Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of the mid-Atlantic region of the United States, causing economically important damage to a wide range of crops. Native to Asia, BMSB was first observed in Allentown, PA, USA, in 1996, and this pest is now well-established throughout the US mid-Atlantic region and beyond. In addition to the serious threat BMSB poses to agriculture, BMSB has become a nuisance to homeowners, invading home gardens and congregating in large numbers in human-made structures, including homes, to overwinter. Despite its significance as an agricultural pest with limited control options, only 100 bp of BMSB sequence data was available in public databases when this project began. Transcriptome sequencing was undertaken to provide a molecular resource to the research community to inform the development of pest control strategies and to provide molecular data for population genetics studies of BMSB. Using normalized, strand-specific libraries, we sequenced pools of all BMSB life stages on the Illumina HiSeq. Trinity was used to assemble 200,000 putative transcripts in >100,000 components. A novel bioinformatic method that analyzed the strand-specificity of the data reduced this to 53,071 putative transcripts from 18,573 components. By integrating multiple other data types, we narrowed this further to 13,211 representative transcripts. Bacterial endosymbiont genes were identified in this dataset, some of which have a copy number consistent with being lateral gene transfers between endosymbiont genomes and Hemiptera, including ankyrin-repeat related proteins, lysozyme, and mannanase. Such genes and endosymbionts may provide novel targets for BMSB-specific biocontrol. This study demonstrates the utility of strand-specific sequencing in generating shotgun transcriptomes and that rapid sequencing shotgun transcriptomes is possible without the need for extensive inbr

Published
2014

42. Hard Wired.

Author

Creasy, Todd

Subjects
SIX Sigma, COMMUNICATIVE competence, SELF-evaluation
Abstract

The article offers information on the importance to select leaders who are innovative with good communication skills for lean Six Sigma projects. Carlotta Walker suggested to administer self-evaluations during team leader selection in improving the likelihood of engagement of team member, that would improve lean Six Sigma project results. Self-assessments were used in determining levels of innovativeness and communication apprehension with CA measured by the survey of James McCroskey.

Published
2017

43. SUBJECT TO REVIEW.

Author

Creasy, Todd

Subjects
SIX Sigma, MEDICAL quality control, HEALTH care industry, LEAN management, HEALTH outcome assessment
Abstract

The article discusses the implementation of the Six Sigma (SS) in the healthcare setting for project improvements, wherein it mentions several reports showing how project opportunities fall short of expectations. Topics discussed include the classification of the SS projects, the importance of leadership for achieving success, and the improvement of patient outcomes.

Published
2017

45. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys

Author

Ioannidis, Panagiotis, primary, Lu, Yong, additional, Kumar, Nikhil, additional, Creasy, Todd, additional, Daugherty, Sean, additional, Chibucos, Marcus C, additional, Orvis, Joshua, additional, Shetty, Amol, additional, Ott, Sandra, additional, Flowers, Melissa, additional, Sengamalay, Naomi, additional, Tallon, Luke J, additional, Pick, Leslie, additional, and Hotopp, Julie C Dunning, additional

Published
2014
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46. Correction: Corrigendum: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Author

Veluchamy, Alaguraj, primary, Lin, Xin, additional, Maumus, Florian, additional, Rivarola, Maximo, additional, Bhavsar, Jaysheel, additional, Creasy, Todd, additional, O’Brien, Kimberly, additional, Sengamalay, Naomi A., additional, Tallon, Luke J., additional, Smith, Andrew D., additional, Rayko, Edda, additional, Ahmed, Ikhlak, additional, Crom, Stéphane Le, additional, Farrant, Gregory K., additional, Sgro, Jean-Yves, additional, Olson, Sue A., additional, Bondurant, Sandra Splinter, additional, Allen, Andrew E., additional, Rabinowicz, Pablo D., additional, Sussman, Michael R., additional, Bowler, Chris, additional, and Tirichine, Leïla, additional

Published
2014
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47. Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

Author

Humphrys, Michael S., primary, Creasy, Todd, additional, Sun, Yezhou, additional, Shetty, Amol C., additional, Chibucos, Marcus C., additional, Drabek, Elliott F., additional, Fraser, Claire M., additional, Farooq, Umar, additional, Sengamalay, Naomi, additional, Ott, Sandy, additional, Shou, Huizhong, additional, Bavoil, Patrik M., additional, Mahurkar, Anup, additional, and Myers, Garry S. A., additional

Published
2013
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49. Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Author

Veluchamy, Alaguraj, primary, Lin, Xin, additional, Maumus, Florian, additional, Rivarola, Maximo, additional, Bhavsar, Jaysheel, additional, Creasy, Todd, additional, O’Brien, Kimberly, additional, Sengamalay, Naomi A., additional, Tallon, Luke J., additional, Smith, Andrew D., additional, Rayko, Edda, additional, Ahmed, Ikhlak, additional, Crom, Stéphane Le, additional, Farrant, Gregory K., additional, Sgro, Jean-Yves, additional, Olson, Sue A., additional, Bondurant, Sandra Splinter, additional, Allen, Andrew E., additional, Rabinowicz, Pablo D., additional, Sussman, Michael R., additional, Bowler, Chris, additional, and Tirichine, Leïla, additional

Published
2013
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50. Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells

Author

Kimaro Mlacha, Sheila Z, primary, Romero-Steiner, Sandra, additional, Dunning Hotopp, Julie C, additional, Kumar, Nikhil, additional, Ishmael, Nadeeza, additional, Riley, David R, additional, Farooq, Umar, additional, Creasy, Todd H, additional, Tallon, Luke J, additional, Liu, Xinyue, additional, Goldsmith, Cynthia S, additional, Sampson, Jacquelyn, additional, Carlone, George M, additional, Hollingshead, Susan K, additional, Scott, J Anthony G, additional, and Tettelin, Hervé, additional

Published
2013
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