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2. Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Author

Setton, Jeremy, Hadi, Kevin, Choo, Zi-Ning, Kuchin, Katherine S., Tian, Huasong, Da Cruz Paula, Arnaud, Rosiene, Joel, Selenica, Pier, Behr, Julie, Yao, Xiaotong, Deshpande, Aditya, Sigouros, Michael, Manohar, Jyothi, Nauseef, Jones T., Mosquera, Juan-Miguel, Elemento, Olivier, Weigelt, Britta, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon N., and Imieliński, Marcin

Published
2023
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3. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Author

Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J, Ivanov, Nikolay A, Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T, Schenck, Edward J, Westover, Craig D, Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L, Granados, Andrea C, Santos, Yale A, Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M, Langhorst, Bradley W, Tanner, Nathan A, Kim, Youngmi, Reeves, Jason W, Hether, Tyler D, Warren, Sarah E, Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B, Rosenfeld, Jeffrey A, Chen, Ying, Steel, Peter AD, Shemesh, Amos J, Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R, Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M, Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F, Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E, Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, and Mason, Christopher E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Vaccine Related, Biodefense, Rare Diseases, Emerging Infectious Diseases, Clinical Research, Prevention, Lung, Pneumonia & Influenza, Aetiology, Development of treatments and therapeutic interventions, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Adult, Aged, Angiotensin Receptor Antagonists, Angiotensin-Converting Enzyme Inhibitors, Antiviral Agents, COVID-19, COVID-19 Nucleic Acid Testing, Drug Interactions, Female, Gene Expression Profiling, Genome, Viral, HLA Antigens, Host Microbial Interactions, Humans, Male, Middle Aged, Molecular Diagnostic Techniques, New York City, Nucleic Acid Amplification Techniques, Pandemics, RNA-Seq, SARS-CoV-2, COVID-19 Drug Treatment
Abstract

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Published
2021

4. Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer

Author

Webster, Andrew L. H., Sanders, Mathijs A., Patel, Krupa, Dietrich, Ralf, Noonan, Raymond J., Lach, Francis P., White, Ryan R., Goldfarb, Audrey, Hadi, Kevin, Edwards, Matthew M., Donovan, Frank X., Hoogenboezem, Remco M., Jung, Moonjung, Sridhar, Sunandini, Wiley, Tom F., Fedrigo, Olivier, Tian, Huasong, Rosiene, Joel, Heineman, Thomas, Kennedy, Jennifer A., Bean, Lorenzo, Rosti, Rasim O., Tryon, Rebecca, Gonzalez, Ashlyn-Maree, Rosenberg, Allana, Luo, Ji-Dung, Carroll, Thomas S., Shroff, Sanjana, Beaumont, Michael, Velleuer, Eunike, Rastatter, Jeff C., Wells, Susanne I., Surrallés, Jordi, Bagby, Grover, MacMillan, Margaret L., Wagner, John E., Cancio, Maria, Boulad, Farid, Scognamiglio, Theresa, Vaughan, Roger, Beaumont, Kristin G., Koren, Amnon, Imielinski, Marcin, Chandrasekharappa, Settara C., Auerbach, Arleen D., Singh, Bhuvanesh, Kutler, David I., Campbell, Peter J., and Smogorzewska, Agata

Published
2022
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5. System-wide transcriptome damage and tissue identity loss in COVID-19 patients

Author

Park, Jiwoon, Foox, Jonathan, Hether, Tyler, Danko, David C., Warren, Sarah, Kim, Youngmi, Reeves, Jason, Butler, Daniel J., Mozsary, Christopher, Rosiene, Joel, Shaiber, Alon, Afshin, Evan E., MacKay, Matthew, Rendeiro, André F., Bram, Yaron, Chandar, Vasuretha, Geiger, Heather, Craney, Arryn, Velu, Priya, Melnick, Ari M., Hajirasouliha, Iman, Beheshti, Afshin, Taylor, Deanne, Saravia-Butler, Amanda, Singh, Urminder, Wurtele, Eve Syrkin, Schisler, Jonathan, Fennessey, Samantha, Corvelo, André, Zody, Michael C., Germer, Soren, Salvatore, Steven, Levy, Shawn, Wu, Shixiu, Tatonetti, Nicholas P., Shapira, Sagi, Salvatore, Mirella, Westblade, Lars F., Cushing, Melissa, Rennert, Hanna, Kriegel, Alison J., Elemento, Olivier, Imielinski, Marcin, Rice, Charles M., Borczuk, Alain C., Meydan, Cem, Schwartz, Robert E., and Mason, Christopher E.

Published
2022
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8. Supplementary Figures from Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, primary, Xiang, Jenny Z., primary, Bhinder, Bhavneet, primary, Rosiene, Joel, primary, Abascal, Federico, primary, Maclachlan, Kylee H., primary, Eng, Kenneth Wha, primary, Uppal, Manik, primary, He, Feng, primary, Zhang, Wei, primary, Gao, Qi, primary, Yellapantula, Venkata D., primary, Trujillo-Alonso, Vicenta, primary, Park, Sunita I., primary, Oberley, Matthew J., primary, Ruckdeschel, Elizabeth, primary, Lim, Megan S., primary, Wertheim, Gerald B., primary, Barth, Matthew J., primary, Horton, Terzah M., primary, Derkach, Andriy, primary, Kovach, Alexandra E., primary, Forlenza, Christopher J., primary, Zhang, Yanming, primary, Landgren, Ola, primary, Moskowitz, Craig H., primary, Cesarman, Ethel, primary, Imielinski, Marcin, primary, Elemento, Olivier, primary, Roshal, Mikhail, primary, and Giulino-Roth, Lisa, primary

Published
2023
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9. Supplementary Data 2 from Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, primary, Xiang, Jenny Z., primary, Bhinder, Bhavneet, primary, Rosiene, Joel, primary, Abascal, Federico, primary, Maclachlan, Kylee H., primary, Eng, Kenneth Wha, primary, Uppal, Manik, primary, He, Feng, primary, Zhang, Wei, primary, Gao, Qi, primary, Yellapantula, Venkata D., primary, Trujillo-Alonso, Vicenta, primary, Park, Sunita I., primary, Oberley, Matthew J., primary, Ruckdeschel, Elizabeth, primary, Lim, Megan S., primary, Wertheim, Gerald B., primary, Barth, Matthew J., primary, Horton, Terzah M., primary, Derkach, Andriy, primary, Kovach, Alexandra E., primary, Forlenza, Christopher J., primary, Zhang, Yanming, primary, Landgren, Ola, primary, Moskowitz, Craig H., primary, Cesarman, Ethel, primary, Imielinski, Marcin, primary, Elemento, Olivier, primary, Roshal, Mikhail, primary, and Giulino-Roth, Lisa, primary

Published
2023
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10. Data from Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, primary, Xiang, Jenny Z., primary, Bhinder, Bhavneet, primary, Rosiene, Joel, primary, Abascal, Federico, primary, Maclachlan, Kylee H., primary, Eng, Kenneth Wha, primary, Uppal, Manik, primary, He, Feng, primary, Zhang, Wei, primary, Gao, Qi, primary, Yellapantula, Venkata D., primary, Trujillo-Alonso, Vicenta, primary, Park, Sunita I., primary, Oberley, Matthew J., primary, Ruckdeschel, Elizabeth, primary, Lim, Megan S., primary, Wertheim, Gerald B., primary, Barth, Matthew J., primary, Horton, Terzah M., primary, Derkach, Andriy, primary, Kovach, Alexandra E., primary, Forlenza, Christopher J., primary, Zhang, Yanming, primary, Landgren, Ola, primary, Moskowitz, Craig H., primary, Cesarman, Ethel, primary, Imielinski, Marcin, primary, Elemento, Olivier, primary, Roshal, Mikhail, primary, and Giulino-Roth, Lisa, primary

Published
2023
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11. Supplementary Tables from Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, primary, Xiang, Jenny Z., primary, Bhinder, Bhavneet, primary, Rosiene, Joel, primary, Abascal, Federico, primary, Maclachlan, Kylee H., primary, Eng, Kenneth Wha, primary, Uppal, Manik, primary, He, Feng, primary, Zhang, Wei, primary, Gao, Qi, primary, Yellapantula, Venkata D., primary, Trujillo-Alonso, Vicenta, primary, Park, Sunita I., primary, Oberley, Matthew J., primary, Ruckdeschel, Elizabeth, primary, Lim, Megan S., primary, Wertheim, Gerald B., primary, Barth, Matthew J., primary, Horton, Terzah M., primary, Derkach, Andriy, primary, Kovach, Alexandra E., primary, Forlenza, Christopher J., primary, Zhang, Yanming, primary, Landgren, Ola, primary, Moskowitz, Craig H., primary, Cesarman, Ethel, primary, Imielinski, Marcin, primary, Elemento, Olivier, primary, Roshal, Mikhail, primary, and Giulino-Roth, Lisa, primary

Published
2023
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12. Supplementary Data 1 from Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, primary, Xiang, Jenny Z., primary, Bhinder, Bhavneet, primary, Rosiene, Joel, primary, Abascal, Federico, primary, Maclachlan, Kylee H., primary, Eng, Kenneth Wha, primary, Uppal, Manik, primary, He, Feng, primary, Zhang, Wei, primary, Gao, Qi, primary, Yellapantula, Venkata D., primary, Trujillo-Alonso, Vicenta, primary, Park, Sunita I., primary, Oberley, Matthew J., primary, Ruckdeschel, Elizabeth, primary, Lim, Megan S., primary, Wertheim, Gerald B., primary, Barth, Matthew J., primary, Horton, Terzah M., primary, Derkach, Andriy, primary, Kovach, Alexandra E., primary, Forlenza, Christopher J., primary, Zhang, Yanming, primary, Landgren, Ola, primary, Moskowitz, Craig H., primary, Cesarman, Ethel, primary, Imielinski, Marcin, primary, Elemento, Olivier, primary, Roshal, Mikhail, primary, and Giulino-Roth, Lisa, primary

Published
2023
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13. Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

Author

Maura, Francesco, primary, Ziccheddu, Bachisio, additional, Xiang, Jenny Z., additional, Bhinder, Bhavneet, additional, Rosiene, Joel, additional, Abascal, Federico, additional, Maclachlan, Kylee H., additional, Eng, Kenneth Wha, additional, Uppal, Manik, additional, He, Feng, additional, Zhang, Wei, additional, Gao, Qi, additional, Yellapantula, Venkata D., additional, Trujillo-Alonso, Vicenta, additional, Park, Sunita I., additional, Oberley, Matthew J., additional, Ruckdeschel, Elizabeth, additional, Lim, Megan S., additional, Wertheim, Gerald B., additional, Barth, Matthew J., additional, Horton, Terzah M., additional, Derkach, Andriy, additional, Kovach, Alexandra E., additional, Forlenza, Christopher J., additional, Zhang, Yanming, additional, Landgren, Ola, additional, Moskowitz, Craig H., additional, Cesarman, Ethel, additional, Imielinski, Marcin, additional, Elemento, Olivier, additional, Roshal, Mikhail, additional, and Giulino-Roth, Lisa, additional

Published
2023
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14. Whole-genome characterization of myoepithelial carcinomas of the soft tissue

Author

Cyrta, Joanna, primary, Rosiene, Joel, additional, Bareja, Rohan, additional, Kudman, Sarah, additional, Al Zoughbi, Wael, additional, Motanagh, Samaneh, additional, Wilkes, David C., additional, Eng, Kenneth, additional, Zhang, Tuo, additional, Sticca, Evan, additional, Mathew, Susan, additional, Rubin, Mark A., additional, Sboner, Andrea, additional, Elemento, Olivier, additional, Rubin, Brian P., additional, Imielinski, Marcin, additional, and Mosquera, Juan Miguel, additional

Published
2022
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15. Sex-related characteristics and short-term outcomes of patients undergoing transcatheter tricuspid valve intervention for tricuspid regurgitation

Author

Scotti, Andrea, primary, Coisne, Augustin, additional, Taramasso, Maurizio, additional, Granada, Juan F, additional, Ludwig, Sebastian, additional, Rodés-Cabau, Josep, additional, Lurz, Philipp, additional, Hausleiter, Jörg, additional, Fam, Neil, additional, Kodali, Susheel K, additional, Rosiene, Joel, additional, Feinberg, Ari, additional, Pozzoli, Alberto, additional, Alessandrini, Hannes, additional, Biasco, Luigi, additional, Brochet, Eric, additional, Denti, Paolo, additional, Estévez-Loureiro, Rodrigo, additional, Frerker, Christian, additional, Ho, Edwin C, additional, Monivas, Vanessa, additional, Nickenig, Georg, additional, Praz, Fabien, additional, Puri, Rishi, additional, Sievert, Horst, additional, Tang, Gilbert H L, additional, Andreas, Martin, additional, Von Bardeleben, Ralph Stephan, additional, Rommel, Karl-Philipp, additional, Muntané-Carol, Guillem, additional, Gavazzoni, Mara, additional, Braun, Daniel, additional, Koell, Benedikt, additional, Kalbacher, Daniel, additional, Connelly, Kim A, additional, Juliard, Jean-Michel, additional, Harr, Claudia, additional, Pedrazzini, Giovanni, additional, Russo, Giulio, additional, Philippon, François, additional, Schofer, Joachim, additional, Thiele, Holger, additional, Unterhuber, Matthias, additional, Himbert, Dominique, additional, Alcázar, Marina Ureña, additional, Wild, Mirjam G, additional, Windecker, Stephan, additional, Jorde, Ulrich, additional, Maisano, Francesco, additional, Leon, Martin B, additional, Hahn, Rebecca T, additional, and Latib, Azeem, additional

Published
2022
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16. Trends in Collection and Utilization of Autologous Hematopoietic Stem Cells (APBHC) Intended for Transplant in Patients with Multiple Myeloma

Author

Samuel, Nina, primary, Laufer, Lauren, additional, Tanaguchi, Rodrigo, additional, Rosiene, Joel, additional, Palesi, Carlo, additional, Elkind, Richard, additional, Mantzaris, Ioannis, additional, Shastri, Aditi, additional, Kornblum, Noah, additional, Sica, R. Alejandro, additional, Shah, Urvi A, additional, Cooper, Dennis, additional, Verma, Amit, additional, and Shah, Nishi, additional

Published
2022
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17. Abstract 6196: Fanconi anemia pathway deficiency drives copy number variation in squamous cell carcinoma

Author

Webster, Andrew L., primary, Sanders, Mathijs A., additional, Patel, Krupa, additional, Dietrich, Ralf, additional, Noonan, Raymond J., additional, Lach, Francis P., additional, White, Ryan R., additional, Goldfarb, Audrey M., additional, Hadi, Kevin, additional, Edwards, Matthew M., additional, Donovan, Frank X., additional, Jung, Moonjung, additional, Sridhar, Sunandini, additional, Fedrigo, Olivier, additional, Tian, Huasong, additional, Rosiene, Joel, additional, Heineman, Thomas, additional, Kennedy, Jennifer, additional, Bean, Lorenzo, additional, Rosti, Rasim O., additional, Tryon, Rebecca, additional, Gonzalez, Ashlyn-Maree, additional, Rosenberg, Allana, additional, Luo, Ji-Dung, additional, Carrol, Thomas, additional, Velleuer, Eunike, additional, Rastatter, Jeff C., additional, Wells, Susanne I., additional, Surrallés, Jordi, additional, Bagby, Grover, additional, MacMillan, Margaret L., additional, Wagner, John E., additional, Cancio, Maria, additional, Boulad, Farid, additional, Scognamiglio, Theresa, additional, Vaughan, Roger, additional, Koren, Amnon, additional, Imielinski, Marcin, additional, Chandrasekharappa, Settara, additional, Auerbach, Arleen D., additional, Singh, Bhuvanesh, additional, Kutler, David, additional, Campbell, Peter J., additional, and Smogorzewska, Agata, additional

Published
2022
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18. Sex-related characteristics and short-term outcomes of patients undergoing transcatheter tricuspid valve intervention for tricuspid regurgitation.

Author

Scotti, Andrea, Coisne, Augustin, Taramasso, Maurizio, Granada, Juan F, Ludwig, Sebastian, Rodés-Cabau, Josep, Lurz, Philipp, Hausleiter, Jörg, Fam, Neil, Kodali, Susheel K, Rosiene, Joel, Feinberg, Ari, Pozzoli, Alberto, Alessandrini, Hannes, Biasco, Luigi, Brochet, Eric, Denti, Paolo, Estévez-Loureiro, Rodrigo, Frerker, Christian, and Ho, Edwin C

Subjects
TRICUSPID valve surgery, TRICUSPID valve, TREATMENT effectiveness
Abstract

Aims The impact of sexuality in patients with significant tricuspid regurgitation (TR) undergoing transcatheter tricuspid valve intervention (TTVI) is unknown. The aim of this study was to investigate sex-specific outcomes in patients with significant TR treated with TTVI vs. medical therapy alone. Methods and results The Transcatheter Tricuspid Valve Therapies (TriValve) registry collected data on patients with significant TR from 24 centres who underwent TTVI from 2016 to 2021. A control cohort was formed by medically managed patients with ≥severe isolated TR diagnosed in 2015–18. The primary endpoint was freedom from all-cause mortality. Secondary endpoints were heart failure (HF) hospitalization, New York Heart Association (NYHA) functional status, and TR severity. One-year outcomes were assessed for the TriValve cohort and compared with the control cohort with the inverse probability of treatment weighting (IPTW). A total of 556 and 2072 patients were included from the TriValve and control groups, respectively. After TTVI, there was no difference between women and men in 1-year freedom from all-cause mortality 80.9% vs. 77.9%, P = 0.56, nor in HF hospitalization (P = 0.36), NYHA Functional Classes III and IV (P = 0.17), and TR severity >2+ at last follow-up (P = 0.42). Multivariable Cox-regression weighted by IPTW showed improved 1-year survival after TTVI compared with medical therapy alone in both women (adjusted hazard ratio 0.45, 95% confidence interval 0.23–0.83, P = 0.01) and men (adjusted hazard ratio 0.42, 95% confidence interval 0.18–0.89, P = 0.03). Conclusion After TTVI in high-risk patients, there were no sex-related differences in terms of survival, HF hospitalization, functional status, and TR reduction up to 1 year. The IPTW analysis shows a survival benefit of TTVI over medical therapy alone in both women and men. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Genomic instability is enriched in localized prostate cancers from men of African ancestry.

Author

Nauseef, Jones T., primary, Shah, Yajas, additional, Shaiber, Alon, additional, Rosiene, Joel, additional, Wilkes, David, additional, Sigouros, Michael, additional, Manohar, Jyothi, additional, Vlachostergios, Panagiotis J., additional, Robinson, Brian D., additional, Elemento, Olivier, additional, Nanus, David M., additional, Mosquera, Juan Miguel, additional, and Imielinski, Marcin, additional

Published
2022
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20. Abstract P2-06-04: Pathognomonic long molecule footprints of backup repair pathways in homologous recombination deficient cancers

Author

Setton, Jeremy, primary, Hadi, Kevin, additional, Tian, Huasong, additional, Paula, Arnaud Da Cruz, additional, Rosiene, Joel, additional, Choo, Zi-Ning, additional, Behr, Julie, additional, Yao, Xiaotong, additional, Elemento, Olivier, additional, Weigelt, Britta, additional, Riaz, Nadeem, additional, Reis-Filho, Jorge S, additional, Imielinski, Marcin, additional, and Powell, Simon N, additional

Published
2022
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21. Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas

Author

Webster, Andrew L.H., primary, Sanders, Mathijs A., additional, Patel, Krupa, additional, Dietrich, Ralf, additional, Noonan, Raymond J., additional, Lach, Francis P., additional, White, Ryan R., additional, Goldfarb, Audrey, additional, Hadi, Kevin, additional, Edwards, Matthew M., additional, Donovan, Frank X., additional, Jung, Moonjung, additional, Sridhar, Sunandini, additional, Fedrigo, Olivier, additional, Tian, Huasong, additional, Rosiene, Joel, additional, Heineman, Thomas, additional, Kennedy, Jennifer A., additional, Bean, Lorenzo, additional, Rosti, Ozgur, additional, Tryon, Rebecca, additional, Gonzalez, Ashlyn-Maree, additional, Rosenberg, Allana, additional, Luo, Ji-Dung, additional, Carrol, Thomas, additional, Velleuer, Eunike, additional, Rastatter, Jeff C., additional, Wells, Susanne I., additional, Surrallés, Jordi, additional, Bagby, Grover, additional, MacMillan, Margaret L., additional, Wagner, John E., additional, Cancio, Maria, additional, Boulad, Farid, additional, Scognamiglio, Theresa, additional, Vaughan, Roger, additional, Koren, Amnon, additional, Imielinski, Marcin, additional, Chandrasekharappa, Settara, additional, Auerbach, Arleen D., additional, Singh, Bhuvanesh, additional, Kutler, David I., additional, Campbell, Peter J., additional, and Smogorzewska, Agata, additional

Published
2021
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22. Loose ends in cancer genome structure

Author

Behr, Julie M., primary, Yao, Xiaotong, additional, Hadi, Kevin, additional, Tian, Huasong, additional, Deshpande, Aditya, additional, Rosiene, Joel, additional, Lange, Titia de, additional, and Imieliński, Marcin, additional

Published
2021
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23. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

Author

Park, Jiwoon, primary, Foox, Jonathan, additional, Hether, Tyler, additional, Danko, David, additional, Warren, Sarah, additional, Kim, Youngmi, additional, Reeves, Jason, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Bram, Yaron, additional, Chandar, Vasuretha, additional, Geiger, Heather, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Beheshti, Afshin, additional, Taylor, Deanne, additional, Saravia-Butler, Amanda, additional, Singh, Urminder, additional, Wurtele, Eve Syrkin, additional, Schisler, Jonathan, additional, Fennessey, Samantha, additional, Corvelo, André, additional, Zody, Michael C., additional, Germer, Soren, additional, Salvatore, Steven, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Shapira, Sagi, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Rennert, Hanna, additional, Kriegel, Alison J., additional, Elemento, Olivier, additional, Imielinski, Marcin, additional, Borczuk, Alain C., additional, Meydan, Cem, additional, Schwartz, Robert E., additional, and Mason, Christopher E., additional

Published
2021
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25. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Author

Hadi, Kevin, primary, Yao, Xiaotong, additional, Behr, Julie M., additional, Deshpande, Aditya, additional, Xanthopoulakis, Charalampos, additional, Tian, Huasong, additional, Kudman, Sarah, additional, Rosiene, Joel, additional, Darmofal, Madison, additional, DeRose, Joseph, additional, Mortensen, Rick, additional, Adney, Emily M., additional, Shaiber, Alon, additional, Gajic, Zoran, additional, Sigouros, Michael, additional, Eng, Kenneth, additional, Wala, Jeremiah A., additional, Wrzeszczyński, Kazimierz O., additional, Arora, Kanika, additional, Shah, Minita, additional, Emde, Anne-Katrin, additional, Felice, Vanessa, additional, Frank, Mayu O., additional, Darnell, Robert B., additional, Ghandi, Mahmoud, additional, Huang, Franklin, additional, Dewhurst, Sally, additional, Maciejowski, John, additional, de Lange, Titia, additional, Setton, Jeremy, additional, Riaz, Nadeem, additional, Reis-Filho, Jorge S., additional, Powell, Simon, additional, Knowles, David A., additional, Reznik, Ed, additional, Mishra, Bud, additional, Beroukhim, Rameen, additional, Zody, Michael C., additional, Robine, Nicolas, additional, Oman, Kenji M., additional, Sanchez, Carissa A., additional, Kuhner, Mary K., additional, Smith, Lucian P., additional, Galipeau, Patricia C., additional, Paulson, Thomas G., additional, Reid, Brian J., additional, Li, Xiaohong, additional, Wilkes, David, additional, Sboner, Andrea, additional, Mosquera, Juan Miguel, additional, Elemento, Olivier, additional, and Imielinski, Marcin, additional

Published
2020
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26. Structural variant evolution after telomere crisis

Author

Dewhurst, S.M, primary, Yao, X, additional, Rosiene, Joel, additional, Tian, Huasong, additional, Behr, Julie, additional, Bosco, Nazario, additional, Takai, Kaori K., additional, de Lange, T, additional, and Imielinski, M, additional

Published
2020
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27. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

Author

Butler, Daniel J., primary, Mozsary, Christopher, additional, Meydan, Cem, additional, Danko, David, additional, Foox, Jonathan, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Sedlazeck, Fritz J., additional, Ivanov, Nikolay A., additional, Sierra, Maria, additional, Pohle, Diana, additional, Zietz, Michael, additional, Gisladottir, Undina, additional, Ramlall, Vijendra, additional, Westover, Craig D., additional, Ryon, Krista, additional, Young, Benjamin, additional, Bhattacharya, Chandrima, additional, Ruggiero, Phyllis, additional, Langhorst, Bradley W., additional, Tanner, Nathan, additional, Gawrys, Justyna, additional, Meleshko, Dmitry, additional, Xu, Dong, additional, Steel, Peter A. D., additional, Shemesh, Amos J., additional, Xiang, Jenny, additional, Thierry-Mieg, Jean, additional, Thierry-Mieg, Danielle, additional, Schwartz, Robert E., additional, Iftner, Angelika, additional, Bezdan, Daniela, additional, Sipley, John, additional, Cong, Lin, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Horner, Stacy M., additional, Iftner, Thomas, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Imielinski, Marcin, additional, Rennert, Hanna, additional, and Mason, Christopher E., additional

Published
2020
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28. Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

Author

Hadi, Kevin, primary, Yao, Xiaotong, additional, Behr, Julie M., additional, Deshpande, Aditya, additional, Xanthopoulakis, Charalampos, additional, Rosiene, Joel, additional, Darmofal, Madison, additional, Tian, Huasong, additional, DeRose, Joseph, additional, Mortensen, Rick, additional, Adney, Emily M., additional, Gajic, Zoran, additional, Eng, Kenneth, additional, Wala, Jeremiah A., additional, Wrzeszczyński, Kazimierz O., additional, Arora, Kanika, additional, Shah, Minita, additional, Emde, Anne-Katrin, additional, Felice, Vanessa, additional, Frank, Mayu O., additional, Darnell, Robert B., additional, Ghandi, Mahmoud, additional, Huang, Franklin, additional, Maciejowski, John, additional, De Lange, Titia, additional, Setton, Jeremy, additional, Riaz, Nadeem, additional, Reis-Filho, Jorge S., additional, Powell, Simon, additional, Knowles, David, additional, Reznik, Ed, additional, Mishra, Bud, additional, Beroukhim, Rameen, additional, Zody, Michael C., additional, Robine, Nicolas, additional, Oman, Kenji M., additional, Sanchez, Carissa A., additional, Kuhner, Mary K., additional, Smith, Lucian P., additional, Galipeau, Patricia C., additional, Paulson, Thomas G., additional, Reid, Brian J., additional, Li, Xiaohong, additional, Wilkes, David, additional, Sboner, Andrea, additional, Mosquera, Juan Miguel, additional, Elemento, Olivier, additional, and Imielinski, Marcin, additional

Published
2019
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33. Abstract 909: Single-cell transcriptomic profiling of non-small cell lung cancer uncovers inter- and intracell population structure across TCGA lung adenocarcinoma and lung squamous cancer subtypes

Author

Gyan, Kofi E., primary, Deshpande, Aditya, additional, Beg, Shaham, additional, Tian, Huasong, additional, Rosiene, Joel, additional, Stoeckius, Marlon, additional, Smibert, Peter, additional, Risso, Davide, additional, Mosquera, Juan Miguel, additional, and Imielinski, Marcin, additional

Published
2019
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38. Toward Objective Quantification of Perfusion-weighted Computed Tomography in Subarachnoid Hemorrhage: Quantification of Symmetry and Automated Delineation of Vascular Territories

Author

Imielinska, Celina Z., Liu, Sheena Xin, Rosiene, Joel, Sughrue, Michael E., Mocco, J., Komotar, Ricardo J., Ransom, Evan R., Lignelli-Dipple, Angela, Zacharia, Brad E., Connolly, Edward S., and D'Ambrosio, Anthony Louis

Subjects
Diagnostic imaging
Abstract

Rationale and Objectives: Perfusion-weighted computed tomography (CTP) is a relatively recent innovation that estimates a value for cerebral blood flow (CBF) using a series of axial head CT images tracking the time course of a signal from an intravenous contrast bolus. Materials and Methods: CTP images were obtained using a standard imaging protocol and were analyzed using commercially available software. A novel computer-based method was used for objective quantification of side-to-side asymmetries of CBF values calculated from CTP images. Results: Our method corrects for the inherent variability of the CTP methodology seen in the subarachnoid hemorrhage (SAH) patient population to potentially aid in the diagnosis of cerebral vasospasm (CVS). This method analyzes and quantifies side-to-side asymmetry of CBF and presents relative differences in a construct termed a Relative Difference Map (RDM). To further automate this process, we have developed a unique methodology that enables a computer to delineate vascular territories within a brain image, regardless of the size and shape of the brain. Conclusions: While both the quantification of image symmetry using RDMs and the automated assignment of vascular territories were initially designed for the analysis of CTP images, it is likely that they will be useful in a variety of applications.

Published
2005
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39. Tracking and transforming neocortical progenitors by CRISPR/ Cas9 gene targeting and piggyBac transposase lineage labeling.

Author

Fuyi Chen, Rosiene, Joel, Che, Alicia, Becker, Albert, and LoTurco, Joseph

Subjects
*CRISPRS, *ENDONUCLEASES, *TRANSPOSASES, *MUTAGENESIS, *NEURAL development, *NEOPLASTIC cell transformation, *PTEN protein
Abstract

The ability to induce targeted mutations in somatic cells in developing organisms and then track the fates of those cells is a powerful approach both for studying neural development and for modeling human disease. The CRISPR/Cas9 system allows for such targeted mutagenesis, and we therefore tested it in combination with a piggyBac transposase lineage labeling system to track the development of neocortical neural progenitors with targeted mutations in genes linked to neurodevelopmental disruptions and tumor formation. We show that sgRNAs designed to target PTEN successfully decreased PTEN expression, and led to neuronal hypertrophy and altered neuronal excitability. Targeting NF1, by contrast, caused increased astrocytogenesis at the expense of neurogenesis, and combined targeting of three tumor suppressors (PTEN, NF1 and P53) resulted in formation of glioblastoma tumors. Our results demonstrate that CRISPR/Cas9 combined with piggyBac transposase lineage labeling can produce unique models of neurodevelopmental disruption and tumors caused by somatic mutation in neural progenitors. [ABSTRACT FROM AUTHOR]

Published
2015
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42. A novel quantification method for determining previously undetected silent infarcts on MR-perfusion in patients following carotid endarterectomy

Author

Liu, Xin, primary, Imielinska, Celina, additional, Rosiene, Joel, additional, Rampersad, Anita, additional, Zurica, Joseph, additional, Wilson, David, additional, Halazun, Hadi, additional, Williams, Susan C., additional, Ligneli, Angela, additional, D'Ambrosio, Anthony, additional, Sughrue, Michael, additional, Connolly, Jr., E. S., additional, and Heyer, Eric J., additional

Published
2005
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43. Evaluation of ischemic stroke hybrid segmentation in a rat model of temporary middle cerebral artery occlusion using ground truth from histologic and MR data

Author

Imielinska, Celina, primary, Jin, Yinpeng, additional, Liu, Xin, additional, Rosiene, Joel, additional, Zacharia, Brad E., additional, Komotar, Ricardo J., additional, Mocco, J., additional, Sughrue, Michael E., additional, Grobelny, Bartosz, additional, Sisti, Alex, additional, Silverberg, Josh, additional, Khandji, Joyce, additional, Cohen, Hilary, additional, Connolly, Jr., Sander, additional, and D'Ambrosio, Anthony L., additional

Published
2005
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