Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Krampis, Konstantinos, Booth, Tim, Chapman, Brad, Tiwari, Bela, Bicak, Mesude, Field, Dawn, Nelson, Karen E
Published in BMC bioinformatics (19.03.2012)
Published in BMC bioinformatics (19.03.2012)
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Journal Article
Deep phenotyping of Alzheimer’s disease leveraging electronic medical records identifies sex-specific clinical associations
Tang, Alice S., Oskotsky, Tomiko, Havaldar, Shreyas, Mantyh, William G., Bicak, Mesude, Solsberg, Caroline Warly, Woldemariam, Sarah, Zeng, Billy, Hu, Zicheng, Oskotsky, Boris, Dubal, Dena, Allen, Isabel E., Glicksberg, Benjamin S., Sirota, Marina
Published in Nature communications (03.02.2022)
Published in Nature communications (03.02.2022)
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Journal Article
S247 Surveillance of Frameshift Neoantigen-Specific T Cells During Tumor Development in Patients With Lynch Syndrome and Mismatch Repair Deficient Colorectal Cancer
Brown, Matthew, Labiner, Arielle J., Velazquez, Leandra, Bozkus, Cansu Cimen, Habib, Juhana, Serebrenik, Joyce, Bicak, Mesude, Polydorides, Alexandros, Samstein, Robert, Bhardwaj, Nina, Lucas, Aimee
Published in The American journal of gastroenterology (01.10.2023)
Published in The American journal of gastroenterology (01.10.2023)
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Journal Article
138 Shared frameshift neoantigens are expressed throughout mismatch repair deficient cancer development and are recognized by tissue infiltrating T cells that are dysregulated in advanced lesions
Brown, Matthew, Velazquez, Leandra, Bicak, Mesude, Habib, Juhana, Holtzman, Sharonne, Saleh, Mona, Polydorides, Alexandros D, Bozkus, Cansu Cimen, Lucas, Aimee L, Samstein, Robert, Bhardwaj, Nina
Published in Journal for immunotherapy of cancer (01.11.2023)
Published in Journal for immunotherapy of cancer (01.11.2023)
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Journal Article
A call for an international network of genomic observatories (GOs)
Davies, Neil, Meyer, Chris, Gilbert, Jack A, Amaral-Zettler, Linda, Deck, John, Bicak, Mesude, Rocca-Serra, Philippe, Assunta-Sansone, Susanna, Willis, Kathy, Field, Dawn
Published in Gigascience (12.07.2012)
Published in Gigascience (12.07.2012)
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Journal Article
Checkpoint therapy in cancer treatment: progress, challenges, and future directions
Bicak, Mesude, Bozkus, Cansu Cimen, Bhardwaj, Nina
Published in The Journal of clinical investigation (17.09.2024)
Published in The Journal of clinical investigation (17.09.2024)
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Journal Article
Checkpoint therapy in cancer treatment: progress, challenges, and future directions
Bicak, Mesude, Cimen Bozkus, Cansu, Bhardwaj, Nina
Published in The Journal of clinical investigation (15.09.2024)
Published in The Journal of clinical investigation (15.09.2024)
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Journal Article
Mapping shared neoantigens and T-cell dysregulation in MSI-H endometrial cancer patients
Saleh, Mona, Holtzman, Sharonne, Brown, Matthew, Velazquez, Leandra, Bicak, Mesude, Bozkus, Cansu Cimen, Blank, Stephanie, Samstein, Robert, Bhardwaj, Nina
Published in Gynecologic oncology (01.11.2024)
Published in Gynecologic oncology (01.11.2024)
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Journal Article
Using Deep-Learning Algorithms to Simultaneously Identify Right and Left Ventricular Dysfunction From the Electrocardiogram
Vaid, Akhil, Johnson, Kipp W., Badgeley, Marcus A., Somani, Sulaiman S., Bicak, Mesude, Landi, Isotta, Russak, Adam, Zhao, Shan, Levin, Matthew A., Freeman, Robert S., Charney, Alexander W., Kukar, Atul, Kim, Bette, Danilov, Tatyana, Lerakis, Stamatios, Argulian, Edgar, Narula, Jagat, Nadkarni, Girish N., Glicksberg, Benjamin S.
Published in JACC. Cardiovascular imaging (01.03.2022)
Published in JACC. Cardiovascular imaging (01.03.2022)
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Journal Article
Federated Learning of Electronic Health Records to Improve Mortality Prediction in Hospitalized Patients With COVID-19: Machine Learning Approach
Vaid, Akhil, Jaladanki, Suraj K, Xu, Jie, Teng, Shelly, Kumar, Arvind, Lee, Samuel, Somani, Sulaiman, Paranjpe, Ishan, De Freitas, Jessica K, Wanyan, Tingyi, Johnson, Kipp W, Bicak, Mesude, Klang, Eyal, Kwon, Young Joon, Costa, Anthony, Zhao, Shan, Miotto, Riccardo, Charney, Alexander W, Böttinger, Erwin, Fayad, Zahi A, Nadkarni, Girish N, Wang, Fei, Glicksberg, Benjamin S
Published in JMIR medical informatics (27.01.2021)
Published in JMIR medical informatics (27.01.2021)
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Journal Article
Genome-wide Scan Identifies Role for AOX1 in Prostate Cancer Survival
Li, Weiqiang, Middha, Mridu, Bicak, Mesude, Sjoberg, Daniel D., Vertosick, Emily, Dahlin, Anders, Häggström, Christel, Hallmans, Göran, Rönn, Ann-Charlotte, Stattin, Pär, Melander, Olle, Ulmert, David, Lilja, Hans, Klein, Robert J.
Published in European urology (01.12.2018)
Published in European urology (01.12.2018)
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Journal Article
Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB
Bicak, Mesude, Wang, Xing, Gao, Xiaoni, Xu, Xing, Väänänen, Riina-Minna, Taimen, Pekka, Lilja, Hans, Pettersson, Kim, Klein, Robert J
Published in Human molecular genetics (27.06.2020)
Published in Human molecular genetics (27.06.2020)
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Journal Article
Genome‐wide association study identifies novel single nucleotide polymorphisms having age‐specific effect on prostate‐specific antigen levels
Li, Weiqiang, Bicak, Mesude, Sjoberg, Daniel D., Vertosick, Emily, Dahlin, Anders, Melander, Olle, Ulmert, David, Lilja, Hans, Klein, Robert J.
Published in The Prostate (01.12.2020)
Published in The Prostate (01.12.2020)
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Journal Article
BCI-838, an orally active mGluR2/3 receptor antagonist pro-drug, rescues learning behavior deficits in the PS19 MAPTP301S mouse model of tauopathy
Perez-Garcia, Georgina, Bicak, Mesude, Haure-Mirande, Jean-Vianney, Perez, Gissel M., Otero-Pagan, Alena, Gama Sosa, Miguel A., De Gasperi, Rita, Sano, Mary, Barlow, Carrolee, Gage, Fred H., Readhead, Benjamin, Ehrlich, Michelle E., Gandy, Sam, Elder, Gregory A.
Published in Neuroscience letters (16.02.2023)
Published in Neuroscience letters (16.02.2023)
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Journal Article
BCI-838, an orally active mGluR2/3 receptor antagonist pro-drug, rescues learning behavior deficits in the PS19 MAPT mouse model of tauopathy
Perez-Garcia, Georgina, Bicak, Mesude, Haure-Mirande, Jean-Vianney, Perez, Gissel M., Otero-Pagan, Alena, Gama Sosa, Miguel A., De Gasperi, Rita, Sano, Mary, Barlow, Carrolee, Gage, Fred H., Readhead, Benjamin, Ehrlich, Michelle E., Gandy, Sam, Elder, Gregory A.
Published in Neuroscience letters (16.02.2023)
Published in Neuroscience letters (16.02.2023)
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Journal Article
Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards
Ten Hoopen, Petra, Pesant, Stéphane, Kottmann, Renzo, Kopf, Anna, Bicak, Mesude, Claus, Simon, Deneudt, Klaas, Borremans, Catherine, Thijsse, Peter, Dekeyzer, Stefanie, Schaap, Dick Ma, Bowler, Chris, Glöckner, Frank Oliver, Cochrane, Guy
Published in Standards in genomic sciences (08.05.2015)
Published in Standards in genomic sciences (08.05.2015)
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Journal Article
Quantitative In Vivo Imaging of the Androgen Receptor Axis Reveals Degree of Prostate Cancer Radiotherapy Response
Storey, Claire M, Altai, Mohamed, Bicak, Mesude, Veach, Darren R, Lückerath, Katharina, Adrian, Gabriel, McDevitt, Michael R, Kalidindi, Teja, Park, Julie E, Herrmann, Ken, Abou, Diane, Zedan, Wahed, Peekhaus, Norbert, Klein, Robert J, Damoiseaux, Robert, Larson, Steven M, Lilja, Hans, Thorek, Daniel, Ulmert, David
Published in Molecular cancer research (01.04.2023)
Published in Molecular cancer research (01.04.2023)
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Journal Article
Genetic signature of prostate cancer mouse models resistant to optimized hK2 targeted α-particle therapy
Bicak, Mesude, Lückerath, Katharina, Kalidindi, Teja, Phelps, Michael E., Strand, Sven-Erik, Morris, Michael J., Radu, Caius G., Damoiseaux, Robert, Peltola, Mari T., Peekhaus, Norbert, Ho, Austin, Veach, Darren, Hager, Ann-Christin Malmborg, Larson, Steven M., Lilja, Hans, McDevitt, Michael R., Klein, Robert J., Ulmert, David
Published in Proceedings of the National Academy of Sciences - PNAS (30.06.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (30.06.2020)
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Journal Article
Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4 -related Alzheimer's disease
Taubes, Alice, Nova, Phil, Zalocusky, Kelly A, Kosti, Idit, Bicak, Mesude, Zilberter, Misha Y, Hao, Yanxia, Yoon, Seo Yeon, Oskotsky, Tomiko, Pineda, Silvia, Chen, Bin, Jones, Emily A Aery, Choudhary, Krishna, Grone, Brian, Balestra, Maureen E, Chaudhry, Fayzan, Paranjpe, Ishan, De Freitas, Jessica, Koutsodendris, Nicole, Chen, Nuo, Wang, Celine, Chang, William, An, Alice, Glicksberg, Benjamin S, Sirota, Marina, Huang, Yadong
Published in Nature aging (01.10.2021)
Published in Nature aging (01.10.2021)
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Journal Article