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1. Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations

Author

Szczesny, Brooke, Boorgula, Meher Preethi, Chavan, Sameer, Campbell, Monica, Johnson, Randi K., Kammers, Kai, Thompson, Emma E., Cox, Madison S., Shankar, Gautam, Cox, Corey, Morin, Andréanne, Lorizio, Wendy, Daya, Michelle, Kelada, Samir N. P., Beaty, Terri H., Doumatey, Ayo P., Cruz, Alvaro A., Watson, Harold, Naureckas, Edward T., Giles, B. Louise, Arinola, Ganiyu A., Sogaolu, Olumide, Falade, Adegoke G., Hansel, Nadia N., Yang, Ivana V., Olopade, Christopher O., Rotimi, Charles N., Landis, R. Clive, Figueiredo, Camila A., Altman, Matthew C., Kenny, Eimear, Ruczinski, Ingo, Liu, Andrew H., Ober, Carole, Taub, Margaret A., Barnes, Kathleen C., and Mathias, Rasika A.

Published
2024
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2. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program

Author

Wheeler, Marsha M, Stilp, Adrienne M, Rao, Shuquan, Halldórsson, Bjarni V, Beyter, Doruk, Wen, Jia, Mihkaylova, Anna V, McHugh, Caitlin P, Lane, John, Jiang, Min-Zhi, Raffield, Laura M, Jun, Goo, Sedlazeck, Fritz J, Metcalf, Ginger, Yao, Yao, Bis, Joshua B, Chami, Nathalie, de Vries, Paul S, Desai, Pinkal, Floyd, James S, Gao, Yan, Kammers, Kai, Kim, Wonji, Moon, Jee-Young, Ratan, Aakrosh, Yanek, Lisa R, Almasy, Laura, Becker, Lewis C, Blangero, John, Cho, Michael H, Curran, Joanne E, Fornage, Myriam, Kaplan, Robert C, Lewis, Joshua P, Loos, Ruth JF, Mitchell, Braxton D, Morrison, Alanna C, Preuss, Michael, Psaty, Bruce M, Rich, Stephen S, Rotter, Jerome I, Tang, Hua, Tracy, Russell P, Boerwinkle, Eric, Abecasis, Goncalo R, Blackwell, Thomas W, Smith, Albert V, Johnson, Andrew D, Mathias, Rasika A, Nickerson, Deborah A, Conomos, Matthew P, Li, Yun, Þorsteinsdóttir, Unnur, Magnússon, Magnús K, Stefansson, Kari, Pankratz, Nathan D, Bauer, Daniel E, Auer, Paul L, and Reiner, Alex P

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Hematology, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Cardiovascular, Good Health and Well Being, Humans, Genome-Wide Association Study, Whole Genome Sequencing, Blood Cells
Abstract

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.

Published
2022

3. Linking open-source code commits and MOOC grades to evaluate massive online open peer review

Author

Wang, Siruo, Jager, Leah R., Kammers, Kai, Hadavand, Aboozar, and Leek, Jeffrey T.

Subjects
Computer Science - Computers and Society, Statistics - Applications
Abstract

Massive Open Online Courses (MOOCs) have been used by students as a low-cost and low-touch educational credential in a variety of fields. Understanding the grading mechanisms behind these course assignments is important for evaluating MOOC credentials. A common approach to grading free-response assignments is massive scale peer-review, especially used for assignments that are not easy to grade programmatically. It is difficult to assess these approaches since the responses typically require human evaluation. Here we link data from public code repositories on GitHub and course grades for a large massive-online open course to study the dynamics of massive scale peer review. This has important implications for understanding the dynamics of difficult to grade assignments. Since the research was not hypothesis-driven, we described the results in an exploratory framework. We find three distinct clusters of repeated peer-review submissions and use these clusters to study how grades change in response to changes in code submissions. Our exploration also leads to an important observation that massive scale peer-review scores are highly variable, increase, on average, with repeated submissions, and changes in scores are not closely tied to the code changes that form the basis for the re-submissions.

Published
2021

5. Genome sequencing unveils a regulatory landscape of platelet reactivity.

Author

Keramati, Ali R, Chen, Ming-Huei, Rodriguez, Benjamin AT, Yanek, Lisa R, Bhan, Arunoday, Gaynor, Brady J, Ryan, Kathleen, Brody, Jennifer A, Zhong, Xue, Wei, Qiang, NHLBI Trans-Omics for Precision (TOPMed) Consortium, Kammers, Kai, Kanchan, Kanika, Iyer, Kruthika, Kowalski, Madeline H, Pitsillides, Achilleas N, Cupples, L Adrienne, Li, Bingshan, Schlaeger, Thorsten M, Shuldiner, Alan R, O'Connell, Jeffrey R, Ruczinski, Ingo, Mitchell, Braxton D, Faraday, Nauder, Taub, Margaret A, Becker, Lewis C, Lewis, Joshua P, Mathias, Rasika A, and Johnson, Andrew D

Subjects
NHLBI Trans-Omics for Precision (TOPMed) Consortium, Blood Platelets, K562 Cells, Humans, Thrombosis, GTP-Binding Proteins, RGS Proteins, Receptors, Cell Surface, Platelet Function Tests, Chromosome Mapping, Base Sequence, Platelet Aggregation, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, HEK293 Cells, Whole Genome Sequencing
Abstract

Platelet aggregation at the site of atherosclerotic vascular injury is the underlying pathophysiology of myocardial infarction and stroke. To build upon prior GWAS, here we report on 16 loci identified through a whole genome sequencing (WGS) approach in 3,855 NHLBI Trans-Omics for Precision Medicine (TOPMed) participants deeply phenotyped for platelet aggregation. We identify the RGS18 locus, which encodes a myeloerythroid lineage-specific regulator of G-protein signaling that co-localizes with expression quantitative trait loci (eQTL) signatures for RGS18 expression in platelets. Gene-based approaches implicate the SVEP1 gene, a known contributor of coronary artery disease risk. Sentinel variants at RGS18 and PEAR1 are associated with thrombosis risk and increased gastrointestinal bleeding risk, respectively. Our WGS findings add to previously identified GWAS loci, provide insights regarding the mechanism(s) by which genetics may influence cardiovascular disease risk, and underscore the importance of rare variant and regulatory approaches to identifying loci contributing to complex phenotypes.

Published
2021

6. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Author

Baumann, Alexander, Rula, Andrew, Kovalsy, Anton, Bernard, Clare, Caetano-Anollés, Derek, Van der Auwera, Geraldine A., Canas, Justin, Yuksel, Kaan, Herman, Kate, Taylor, M. Morgan, Simeon, Marianie, Baumann, Michael, Wang, Qi, Title, Robert, Munshi, Ruchi, Chaluvadi, Sushma, Reeves, Valerie, Disman, William, Thomas, Salin, Hajian, Allie, Kiernan, Elizabeth, Gupta, Namrata, Vosburg, Trish, Geistlinger, Ludwig, Ramos, Marcel, Oh, Sehyun, Rogers, Dave, McDade, Frances, Hastie, Mim, Turaga, Nitesh, Ostrovsky, Alexander, Mahmoud, Alexandru, Baker, Dannon, Clements, Dave, Cox, Katherine E.L., Suderman, Keith, Kucher, Nataliya, Golitsynskiy, Sergey, Zarate, Samantha, Wheelan, Sarah J., Kammers, Kai, Stevens, Ana, Hutter, Carolyn, Wellington, Christopher, Ghanaim, Elena M., Wiley, Ken L., Jr., Sen, Shurjo K., Di Francesco, Valentina, s Yuen, Deni, Walsh, Brian, Sargent, Luke, Jalili, Vahid, Chilton, John, Shepherd, Lori, Stubbs, B.J., O’Farrell, Ash, Vizzier, Benton A., Jr., Overbeck, Charles, Reid, Charles, Steinberg, David Charles, Sheets, Elizabeth A., Lucas, Julian, Blauvelt, Lon, Cabansay, Louise, Warren, Noah, Hannafious, Brian, Harris, Tim, Reddy, Radhika, Torstenson, Eric, Banasiewicz, M. Katie, Abel, Haley J., Walker, Jason, Schatz, Michael C., Philippakis, Anthony A., Afgan, Enis, Banks, Eric, Carey, Vincent J., Carroll, Robert J., Culotti, Alessandro, Ellrott, Kyle, Goecks, Jeremy, Grossman, Robert L., Hall, Ira M., Hansen, Kasper D., Lawson, Jonathan, Leek, Jeffrey T., Luria, Anne O’Donnell, Mosher, Stephen, Morgan, Martin, Nekrutenko, Anton, O’Connor, Brian D., Osborn, Kevin, Paten, Benedict, Patterson, Candace, Tan, Frederick J., Taylor, Casey Overby, Vessio, Jennifer, Waldron, Levi, Wang, Ting, and Wuichet, Kristin

Published
2022
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7. Deconvoluting virome-wide antibody epitope reactivity profiles

Author

Monaco, Daniel R., Kottapalli, Sanjay V., Breitwieser, Florian P., Anderson, Danielle E., Wijaya, Limin, Tan, Kevin, Chia, Wan Ni, Kammers, Kai, Caturegli, Patrizio, Waugh, Kathleen, Roederer, Mario, Petri, Michelle, Goldman, Daniel W., Rewers, Marian, Wang, Lin-Fa, and Larman, H. Benjamin

Published
2022
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8. Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment

Author

Grant-McAuley, Wendy, Laeyendecker, Oliver, Monaco, Daniel, Chen, Athena, Hudelson, Sarah E., Klock, Ethan, Brookmeyer, Ron, Morrison, Douglas, Piwowar-Manning, Estelle, Morrison, Charles S., Hayes, Richard, Ayles, Helen, Bock, Peter, Kosloff, Barry, Shanaube, Kwame, Mandla, Nomtha, van Deventer, Anneen, Ruczinski, Ingo, Kammers, Kai, Larman, H. Benjamin, and Eshleman, Susan H.

Published
2022
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11. Gene and protein expression in human megakaryocytes derived from induced pluripotent stem cells

Author

Kammers, Kai, Taub, Margaret A., Mathias, Rasika A., Yanek, Lisa R., Kanchan, Kanika, Venkatraman, Vidya, Sundararaman, Niveda, Martin, Joshua, Liu, Senquan, Hoyle, Dixie, Raedschelders, Koen, Holewinski, Ronald, Parker, Sarah, Dardov, Victoria, Faraday, Nauder, Becker, Diane M., Cheng, Linzhao, Wang, Zack Z., Leek, Jeffrey T., Van Eyk, Jennifer E., and Becker, Lewis C.

Published
2021
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13. Identification of antibody targets associated with lower HIV viral load and viremic control.

Author

Grant-McAuley, Wendy, Morgenlander, William R., Ruczinski, Ingo, Kammers, Kai, Laeyendecker, Oliver, Hudelson, Sarah E., Thakar, Manjusha, Piwowar-Manning, Estelle, Clarke, William, Breaud, Autumn, Ayles, Helen, Bock, Peter, Moore, Ayana, Kosloff, Barry, Shanaube, Kwame, Meehan, Sue-Ann, van Deventer, Anneen, Fidler, Sarah, Hayes, Richard, and Larman, H. Benjamin

Subjects
HIV antibodies, HIV infections, VIRAL load, HIV prevention, HUMORAL immunity
Abstract

Background: High HIV viral loads (VL) are associated with increased morbidity, mortality, and on-going transmission. HIV controllers maintain low VLs in the absence of antiretroviral therapy (ART). We previously used a massively multiplexed antibody profiling assay (VirScan) to compare antibody profiles in HIV controllers and persons living with HIV (PWH) who were virally suppressed on ART. In this report, we used VirScan to evaluate whether antibody reactivity to specific HIV targets and broad reactivity across the HIV genome was associated with VL and controller status 1–2 years after infection. Methods: Samples were obtained from participants who acquired HIV infection in a community-randomized trial in Africa that evaluated an integrated strategy for HIV prevention (HPTN 071 PopART). Controller status was determined using VL and antiretroviral (ARV) drug data obtained at the seroconversion visit and 1 year later. Viremic controllers had VLs <2,000 copies/mL at both visits; non-controllers had VLs >2,000 copies/mL at both visits. Both groups had no ARV drugs detected at either visit. VirScan testing was performed at the second HIV-positive visit (1–2 years after HIV infection). Results: The study cohort included 13 viremic controllers and 64 non-controllers. We identified ten clusters of homologous peptides that had high levels of antibody reactivity (three in gag, three in env, two in integrase, one in protease, and one in vpu). Reactivity to 43 peptides (eight unique epitopes) in six of these clusters was associated with lower VL; reactivity to six of the eight epitopes was associated with HIV controller status. Higher aggregate antibody reactivity across the eight epitopes (more epitopes targeted, higher mean reactivity across all epitopes) and across the HIV genome was also associated with lower VL and controller status. Conclusions: We identified HIV antibody targets associated with lower VL and HIV controller status 1–2 years after infection. Robust aggregate responses to these targets and broad antibody reactivity across the HIV genome were also associated with lower VL and controller status. These findings provide novel insights into the relationship between humoral immunity and viral containment that could help inform the design of antibody-based approaches for reducing HIV VL. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Long-term quality of life after preoperative radiochemotherapy in patients with localized and locally advanced breast cancer

Author

Haussmann, Jan, Nestle-Kraemling, Carolin, Bölke, Edwin, Wollandt, Sylvia, Speer, Vanessa, Djiepmo Njanang, Freddy-Joel, Tamaskovics, Bálint, Gerber, Peter Arne, Orth, Klaus, Ruckhaeberle, Eugen, Fehm, Tanja, Corradini, Stefanie, Lammering, Guido, Mohrmann, Svjetlana, Audretsch, Werner, Maas, Kitti, Roth, Stephan, Kammers, Kai, Budach, Wilfried, and Matuschek, Christiane

Published
2020
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15. Comprehensive Profiling of HIV Antibody Evolution

Author

Eshleman, Susan H., Laeyendecker, Oliver, Kammers, Kai, Chen, Athena, Sivay, Mariya V., Kottapalli, Sanjay, Sie, Brandon M., Yuan, Tiezheng, Monaco, Daniel R., Mohan, Divya, Wansley, Daniel, Kula, Tomasz, Morrison, Charles, Elledge, Stephen J., Brookmeyer, Ron, Ruczinski, Ingo, and Larman, H. Benjamin

Published
2019
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19. Long-term cosmetic outcome after preoperative radio-/chemotherapy in locally advanced breast cancer patients

Author

Matuschek, Christiane, Nestle-Kraemling, Carolin, Haussmann, Jan, Bölke, Edwin, Wollandt, Sylvia, Speer, Vanessa, Djiepmo Njanang, Freddy Joel, Tamaskovics, Bálint, Gerber, Peter Arne, Orth, Klaus, Ruckhaeberle, Eugen, Fehm, Tanja, Corradini, Stefanie, Lammering, Guido, Mohrmann, Svjetlana, Audretsch, Werner, Roth, Stephan, Kammers, Kai, and Budach, Wilfried

Published
2019
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20. Comprehensive profiling of pre-infection antibodies identifies HIV targets associated with viremic control and viral load

Author

Grant-McAuley, Wendy, primary, Morgenlander, William, additional, Hudelson, Sarah E., additional, Thakar, Manjusha, additional, Piwowar-Manning, Estelle, additional, Clarke, William, additional, Breaud, Autumn, additional, Blankson, Joel, additional, Wilson, Ethan, additional, Ayles, Helen, additional, Bock, Peter, additional, Moore, Ayana, additional, Kosloff, Barry, additional, Shanaube, Kwame, additional, Meehan, Sue-Ann, additional, van Deventer, Anneen, additional, Fidler, Sarah, additional, Hayes, Richard, additional, Ruczinski, Ingo, additional, Kammers, Kai, additional, Laeyendecker, Oliver, additional, Larman, H. Benjamin, additional, and Eshleman, Susan H., additional

Published
2023
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25. β3AR-Dependent BDNF (Brain-Derived Neurotrophic Factor) Generation Limits Chronic Postischemic Heart Failure

Author

Cannavo, Alessandro, primary, Jun, Seungho, additional, Rengo, Giuseppe, additional, Marzano, Federica, additional, Agrimi, Jacopo, additional, Liccardo, Daniela, additional, Elia, Andrea, additional, Keceli, Gizem, additional, Altobelli, Giovanna G., additional, Marcucci, Lorenzo, additional, Megighian, Aram, additional, Gao, Erhe, additional, Feng, Ning, additional, Kammers, Kai, additional, Ferrara, Nicola, additional, Finos, Livio, additional, Koch, Walter J., additional, and Paolocci, Nazareno, additional

Published
2023
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30. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program

Author

Wheeler, Marsha M., Stilp, Adrienne M., Rao, Shuquan, Halldórsson, Bjarni V., Beyter, Doruk, Wen, Jia, Mihkaylova, Anna V., McHugh, Caitlin P., Lane, John, Jiang, Min Zhi, Raffield, Laura M., Jun, Goo, Sedlazeck, Fritz J., Metcalf, Ginger, Yao, Yao, Bis, Joshua B., Chami, Nathalie, de Vries, Paul S., Desai, Pinkal, Floyd, James S., Gao, Yan, Kammers, Kai, Kim, Wonji, Moon, Jee Young, Ratan, Aakrosh, Yanek, Lisa R., Almasy, Laura, Becker, Lewis C., Blangero, John, Cho, Michael H., Curran, Joanne E., Fornage, Myriam, Kaplan, Robert C., Lewis, Joshua P., Loos, Ruth J.F., Mitchell, Braxton D., Morrison, Alanna C., Preuss, Michael, Psaty, Bruce M., Rich, Stephen S., Rotter, Jerome I., Tang, Hua, Tracy, Russell P., Boerwinkle, Eric, Abecasis, Goncalo R., Blackwell, Thomas W., Smith, Albert V., Johnson, Andrew D., Mathias, Rasika A., Nickerson, Deborah A., Conomos, Matthew P., Li, Yun, Þorsteinsdóttir, Unnur, Magnússon, Magnús K., Stefansson, Kari, Pankratz, Nathan D., Bauer, Daniel E., Auer, Paul L., Reiner, Alex P., Wheeler, Marsha M., Stilp, Adrienne M., Rao, Shuquan, Halldórsson, Bjarni V., Beyter, Doruk, Wen, Jia, Mihkaylova, Anna V., McHugh, Caitlin P., Lane, John, Jiang, Min Zhi, Raffield, Laura M., Jun, Goo, Sedlazeck, Fritz J., Metcalf, Ginger, Yao, Yao, Bis, Joshua B., Chami, Nathalie, de Vries, Paul S., Desai, Pinkal, Floyd, James S., Gao, Yan, Kammers, Kai, Kim, Wonji, Moon, Jee Young, Ratan, Aakrosh, Yanek, Lisa R., Almasy, Laura, Becker, Lewis C., Blangero, John, Cho, Michael H., Curran, Joanne E., Fornage, Myriam, Kaplan, Robert C., Lewis, Joshua P., Loos, Ruth J.F., Mitchell, Braxton D., Morrison, Alanna C., Preuss, Michael, Psaty, Bruce M., Rich, Stephen S., Rotter, Jerome I., Tang, Hua, Tracy, Russell P., Boerwinkle, Eric, Abecasis, Goncalo R., Blackwell, Thomas W., Smith, Albert V., Johnson, Andrew D., Mathias, Rasika A., Nickerson, Deborah A., Conomos, Matthew P., Li, Yun, Þorsteinsdóttir, Unnur, Magnússon, Magnús K., Stefansson, Kari, Pankratz, Nathan D., Bauer, Daniel E., Auer, Paul L., and Reiner, Alex P.

Abstract

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.

Published
2022

31. Gluconate-Lactobionate-Dextran Perfusion Solutions Attenuate Ischemic Injury and Improve Function in a Murine Cardiac Transplant Model

Author

Guo, Yinan, primary, Messner, Franka, additional, Beck, Sarah E., additional, Iglesias Lozano, Marcos, additional, Schwelberger, Hubert, additional, Zhang, Yichuan, additional, Kammers, Kai, additional, Oh, Byoung Chol, additional, Greene, Elizabeth D., additional, Brandacher, Gerald, additional, and Brockbank, Kelvin G. M., additional

Published
2022
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32. Additional file 1 of Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment

Author

Grant-McAuley, Wendy, Laeyendecker, Oliver, Monaco, Daniel, Chen, Athena, Hudelson, Sarah E., Klock, Ethan, Brookmeyer, Ron, Morrison, Douglas, Piwowar-Manning, Estelle, Morrison, Charles S., Hayes, Richard, Ayles, Helen, Bock, Peter, Kosloff, Barry, Shanaube, Kwame, Mandla, Nomtha, van Deventer, Anneen, Ruczinski, Ingo, Kammers, Kai, Larman, H. Benjamin, and Eshleman, Susan H.

Abstract

Additional file 1. Development of the LAg + PepPair MAA.

Published
2022
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36. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Author

Schatz, Michael C., primary, Philippakis, Anthony A., additional, Afgan, Enis, additional, Banks, Eric, additional, Carey, Vincent J., additional, Carroll, Robert J., additional, Culotti, Alessandro, additional, Ellrott, Kyle, additional, Goecks, Jeremy, additional, Grossman, Robert L., additional, Hall, Ira M., additional, Hansen, Kasper D., additional, Lawson, Jonathan, additional, Leek, Jeffrey T., additional, Luria, Anne O’Donnell, additional, Mosher, Stephen, additional, Morgan, Martin, additional, Nekrutenko, Anton, additional, O’Connor, Brian D., additional, Osborn, Kevin, additional, Paten, Benedict, additional, Patterson, Candace, additional, Tan, Frederick J., additional, Taylor, Casey Overby, additional, Vessio, Jennifer, additional, Waldron, Levi, additional, Wang, Ting, additional, Wuichet, Kristin, additional, Baumann, Alexander, additional, Rula, Andrew, additional, Kovalsy, Anton, additional, Bernard, Clare, additional, Caetano-Anollés, Derek, additional, Van der Auwera, Geraldine A., additional, Canas, Justin, additional, Yuksel, Kaan, additional, Herman, Kate, additional, Taylor, M. Morgan, additional, Simeon, Marianie, additional, Baumann, Michael, additional, Wang, Qi, additional, Title, Robert, additional, Munshi, Ruchi, additional, Chaluvadi, Sushma, additional, Reeves, Valerie, additional, Disman, William, additional, Thomas, Salin, additional, Hajian, Allie, additional, Kiernan, Elizabeth, additional, Gupta, Namrata, additional, Vosburg, Trish, additional, Geistlinger, Ludwig, additional, Ramos, Marcel, additional, Oh, Sehyun, additional, Rogers, Dave, additional, McDade, Frances, additional, Hastie, Mim, additional, Turaga, Nitesh, additional, Ostrovsky, Alexander, additional, Mahmoud, Alexandru, additional, Baker, Dannon, additional, Clements, Dave, additional, Cox, Katherine E.L., additional, Suderman, Keith, additional, Kucher, Nataliya, additional, Golitsynskiy, Sergey, additional, Zarate, Samantha, additional, Wheelan, Sarah J., additional, Kammers, Kai, additional, Stevens, Ana, additional, Hutter, Carolyn, additional, Wellington, Christopher, additional, Ghanaim, Elena M., additional, Wiley, Ken L., additional, Sen, Shurjo K., additional, Di Francesco, Valentina, additional, s Yuen, Deni, additional, Walsh, Brian, additional, Sargent, Luke, additional, Jalili, Vahid, additional, Chilton, John, additional, Shepherd, Lori, additional, Stubbs, B.J., additional, O’Farrell, Ash, additional, Vizzier, Benton A., additional, Overbeck, Charles, additional, Reid, Charles, additional, Steinberg, David Charles, additional, Sheets, Elizabeth A., additional, Lucas, Julian, additional, Blauvelt, Lon, additional, Cabansay, Louise, additional, Warren, Noah, additional, Hannafious, Brian, additional, Harris, Tim, additional, Reddy, Radhika, additional, Torstenson, Eric, additional, Banasiewicz, M. Katie, additional, Abel, Haley J., additional, and Walker, Jason, additional

Published
2022
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39. Comparison of Different Systemic Therapeutic Regimes in Resectable Soft-Tissue Sarcoma—Results of a Network Meta-Analysis

Author

Haussmann, Jan, primary, Matuschek, Christiane, additional, Bölke, Edwin, additional, Tamaskovics, Balint, additional, Corradini, Stefanie, additional, Wessalowski, Rüdiger, additional, Maas, Kitti, additional, Schmidt, Livia, additional, Orth, Klaus, additional, Peiper, Matthias, additional, Keitel, Verena, additional, Feldt, Torsten, additional, Jensen, Björn-Erik Ole, additional, Luedde, Tom, additional, Fischer, Johannes, additional, Knoefel, Wolfram Trudo, additional, Ashmawy, Hany, additional, Pedotoa, Alessia, additional, Kammers, Kai, additional, and Budach, Wilfried, additional

Published
2021
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40. 86: Predictive Factors of Survival After Neoadjuvant Radiotherapy and Chemotherapy in High-Risk Breast Cancer

Author

Matuschek, Christiane, primary, Budach, Wilfried, additional, Tamaskovics, Balint, additional, Fischer, Johannes, additional, Boelke, Edwin, additional, Corradini, Stefanie, additional, Kammers, Kai, additional, Kraemling, Carolin Nestle, additional, Fehm, Tanja, additional, Wollandt, Sylvia, additional, Speer, Vanessa, additional, and Haussmann, Jan, additional

Published
2021
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41. HIV Antibody Profiles in HIV Controllers and Persons With Treatment-Induced Viral Suppression

Author

Kammers, Kai, primary, Chen, Athena, additional, Monaco, Daniel R., additional, Hudelson, Sarah E., additional, Grant-McAuley, Wendy, additional, Moore, Richard D., additional, Alter, Galit, additional, Deeks, Steven G., additional, Morrison, Charles S., additional, Eller, Leigh A., additional, Blankson, Joel N., additional, Laeyendecker, Oliver, additional, Ruczinski, Ingo, additional, Eshleman, Susan H., additional, and Larman, H. Benjamin, additional

Published
2021
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42. Comparing Local and Systemic Control between Partial- and Whole-Breast Radiotherapy in Low-Risk Breast Cancer—A Meta-Analysis of Randomized Trials

Author

Haussmann, Jan, primary, Budach, Wilfried, additional, Strnad, Vratislav, additional, Corradini, Stefanie, additional, Krug, David, additional, Schmidt, Livia, additional, Tamaskovics, Balint, additional, Bölke, Edwin, additional, Simiantonakis, Ioannis, additional, Kammers, Kai, additional, and Matuschek, Christiane, additional

Published
2021
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46. No Difference in Overall Survival and Non-Breast Cancer Deaths after Partial Breast Radiotherapy Compared to Whole Breast Radiotherapy—A Meta-Analysis of Randomized Trials

Author

Haussmann, Jan, primary, Budach, Wilfried, additional, Corradini, Stefanie, additional, Krug, David, additional, Tamaskovics, Balint, additional, Bölke, Edwin, additional, Djiepmo-Njanang, Freddy-Joel, additional, Simiantonakis, Ioannis, additional, Kammers, Kai, additional, and Matuschek, Christiane, additional

Published
2020
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47. Abstract 330: Expression of Glycolytic Enzymes in Induced Pluripotent Stem Cells, Derived Megakaryocytes, and Endothelial Cells

Author

Chandra, Arun, primary, Vaidya, Dhananjay, additional, Chang, Rui, additional, Knowles, Josh, additional, Carcamo-oribe, Ivan, additional, Kammers, Kai, additional, Martin, Joshua, additional, Taub, Margaret, additional, Hoyle, Dixie, additional, Gao, Yongxing, additional, Yanek, Lisa, additional, Kral, Brian, additional, Faraday, Nauder, additional, Becker, Diane, additional, Mathias, Rasika, additional, Cheng, Linzhao, additional, Leek, Jeffrey, additional, Wang, Zack, additional, and Becker, Lewis, additional

Published
2020
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49. Survival models with preclustered gene groups as covariates

Author

Kammers Kai, Lang Michel, Hengstler Jan G, Schmidt Marcus, and Rahnenführer Jörg

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the typically large number of genes compared to the number of observations (individuals). Feature selection procedures can generate predictive models with high prediction accuracy and at the same time low model complexity. However, interpretability of the resulting models is still limited due to little knowledge on many of the remaining selected genes. Thus, we summarize genes as gene groups defined by the hierarchically structured Gene Ontology (GO) and include these gene groups as covariates in the hazard regression models. Since expression profiles within GO groups are often heterogeneous, we present a new method to obtain subgroups with coherent patterns. We apply preclustering to genes within GO groups according to the correlation of their gene expression measurements. Results We compare Cox models for modeling disease free survival times of breast cancer patients. Besides classical clinical covariates we consider genes, GO groups and preclustered GO groups as additional genomic covariates. Survival models with preclustered gene groups as covariates have similar prediction accuracy as models built only with single genes or GO groups. Conclusions The preclustering information enables a more detailed analysis of the biological meaning of covariates selected in the final models. Compared to models built only with single genes there is additional functional information contained in the GO annotation, and compared to models using GO groups as covariates the preclustering yields coherent representative gene expression profiles.

Published
2011
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50. Targeting mitochondrial translation by inhibiting DDX3 : A novel radiosensitization strategy for cancer treatment

Author

Heerma Van Voss, M. R., Vesuna, F., Bol, G. M., Afzal, J., Tantravedi, Saritha, Bergman, Y., Kammers, Kai, Lehar, M., Malek, Reem, Ballew, M., ter Hoeve, N., Abou, D., Thorek, D., Berlinicke, Cynthia, Yazdankhah, M., Sinha, D., le Couteur, A., Abrahams, R., Tran, Phuoc T., Van Diest, P. J., Raman, V., Heerma Van Voss, M. R., Vesuna, F., Bol, G. M., Afzal, J., Tantravedi, Saritha, Bergman, Y., Kammers, Kai, Lehar, M., Malek, Reem, Ballew, M., ter Hoeve, N., Abou, D., Thorek, D., Berlinicke, Cynthia, Yazdankhah, M., Sinha, D., le Couteur, A., Abrahams, R., Tran, Phuoc T., Van Diest, P. J., and Raman, V.

Published
2018

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