FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA
Liu, Yaping, Reed, Sarah C., Lo, Christopher, Choudhury, Atish D., Parsons, Heather A., Stover, Daniel G., Ha, Gavin, Gydush, Gregory, Rhoades, Justin, Rotem, Denisse, Freeman, Samuel, Katz, David W., Bandaru, Ravi, Zheng, Haizi, Fu, Hailu, Adalsteinsson, Viktor A., Kellis, Manolis
Published in Nature communications (30.03.2024)
Published in Nature communications (30.03.2024)
Get full text
Journal Article
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing
Viswanathan, Srinivas R., Ha, Gavin, Hoff, Andreas M., Wala, Jeremiah A., Carrot-Zhang, Jian, Whelan, Christopher W., Haradhvala, Nicholas J., Freeman, Samuel S., Reed, Sarah C., Rhoades, Justin, Polak, Paz, Cipicchio, Michelle, Wankowicz, Stephanie A., Wong, Alicia, Kamath, Tushar, Zhang, Zhenwei, Gydush, Gregory J., Rotem, Denisse, Love, J. Christopher, Getz, Gad, Gabriel, Stacey, Zhang, Cheng-Zhong, Dehm, Scott M., Nelson, Peter S., Van Allen, Eliezer M., Choudhury, Atish D., Adalsteinsson, Viktor A., Beroukhim, Rameen, Taplin, Mary-Ellen, Meyerson, Matthew
Published in Cell (12.07.2018)
Published in Cell (12.07.2018)
Get full text
Journal Article
Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush, Gregory, Nguyen, Erica, Bae, Jin H., Blewett, Timothy, Rhoades, Justin, Reed, Sarah C., Shea, Douglas, Xiong, Kan, Liu, Ruolin, Yu, Fangyan, Leong, Ka Wai, Choudhury, Atish D., Stover, Daniel G., Tolaney, Sara M., Krop, Ian E., Christopher Love, J., Parsons, Heather A., Mike Makrigiorgos, G., Golub, Todd R., Adalsteinsson, Viktor A.
Published in Nature biomedical engineering (01.03.2022)
Published in Nature biomedical engineering (01.03.2022)
Get full text
Journal Article
Tumor fraction in cell-free DNA as a biomarker in prostate cancer
Choudhury, Atish D, Werner, Lillian, Francini, Edoardo, Wei, Xiao X, Ha, Gavin, Freeman, Samuel S, Rhoades, Justin, Reed, Sarah C, Gydush, Gregory, Rotem, Denisse, Lo, Christopher, Taplin, Mary-Ellen, Harshman, Lauren C, Zhang, Zhenwei, O'Connor, Edward P, Stover, Daniel G, Parsons, Heather A, Getz, Gad, Meyerson, Matthew, Love, J Christopher, Hahn, William C, Adalsteinsson, Viktor A
Published in JCI insight (02.11.2018)
Published in JCI insight (02.11.2018)
Get full text
Journal Article
Circulating Cell-Free DNA as Biomarker of Taxane Resistance in Metastatic Castration-Resistant Prostate Cancer
Francini, Edoardo, Ou, Fang-Shu, Rhoades, Justin, Wolfe, Eric G., O’Connor, Edward P., Ha, Gavin, Gydush, Gregory, Kelleher, Kaitlin M., Bhatt, Rupal S., Balk, Steven P., Sweeney, Christopher J., Adalsteinsson, Viktor A., Taplin, Mary-Ellen, Choudhury, Atish D.
Published in Cancers (12.08.2021)
Published in Cancers (12.08.2021)
Get full text
Journal Article
Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer
Stover, Daniel G, Parsons, Heather A, Ha, Gavin, Freeman, Samuel S, Barry, William T, Guo, Hao, Choudhury, Atish D, Gydush, Gregory, Reed, Sarah C, Rhoades, Justin, Rotem, Denisse, Hughes, Melissa E, Dillon, Deborah A, Partridge, Ann H, Wagle, Nikhil, Krop, Ian E, Getz, Gad, Golub, Todd R, Love, J Christopher, Winer, Eric P, Tolaney, Sara M, Lin, Nancy U, Adalsteinsson, Viktor A
Published in Journal of clinical oncology (20.02.2018)
Published in Journal of clinical oncology (20.02.2018)
Get full text
Journal Article
Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Parsons, Heather A, Rhoades, Justin, Reed, Sarah C, Gydush, Gregory, Ram, Priyanka, Exman, Pedro, Xiong, Kan, Lo, Christopher C, Li, Tianyu, Fleharty, Mark, Kirkner, Gregory J, Rotem, Denisse, Cohen, Ofir, Yu, Fangyan, Fitarelli-Kiehl, Mariana, Leong, Ka Wai, Hughes, Melissa E, Rosenberg, Shoshana M, Collins, Laura C, Miller, Kathy D, Blumenstiel, Brendan, Trippa, Lorenzo, Cibulskis, Carrie, Neuberg, Donna S, DeFelice, Matthew, Freeman, Samuel S, Lennon, Niall J, Wagle, Nikhil, Ha, Gavin, Stover, Daniel G, Choudhury, Atish D, Getz, Gad, Winer, Eric P, Meyerson, Matthew, Lin, Nancy U, Krop, Ian, Love, J Christopher, Makrigiorgos, G Mike, Partridge, Ann H, Mayer, Erica L, Golub, Todd R, Adalsteinsson, Viktor A
Published in Clinical cancer research (01.06.2020)
Published in Clinical cancer research (01.06.2020)
Get full text
Journal Article
Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine
Pagès, Mélanie, Rotem, Denisse, Gydush, Gregory, Reed, Sarah, Rhoades, Justin, Ha, Gavin, Lo, Christopher, Fleharty, Mark, Duran, Madeleine, Jones, Robert, Becker, Sarah, Haller, Michaela, Sinai, Claire E, Goumnerova, Liliana, Golub, Todd R, Love, J Christopher, Ligon, Keith L, Wright, Karen D, Adalsteinsson, Viktor A, Beroukhim, Rameen, Bandopadhayay, Pratiti
Published in Neuro-oncology (Charlottesville, Va.) (01.08.2022)
Published in Neuro-oncology (Charlottesville, Va.) (01.08.2022)
Get full text
Journal Article
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity
Bae, Jin H., Liu, Ruolin, Roberts, Eugenia, Nguyen, Erica, Tabrizi, Shervin, Rhoades, Justin, Blewett, Timothy, Xiong, Kan, Gydush, Gregory, Shea, Douglas, An, Zhenyi, Patel, Sahil, Cheng, Ju, Sridhar, Sainetra, Liu, Mei Hong, Lassen, Emilie, Skytte, Anne-Bine, Grońska-Pęski, Marta, Shoag, Jonathan E., Evrony, Gilad D., Parsons, Heather A., Mayer, Erica L., Makrigiorgos, G. Mike, Golub, Todd R., Adalsteinsson, Viktor A.
Published in Nature genetics (01.05.2023)
Published in Nature genetics (01.05.2023)
Get full text
Journal Article
A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
Leong, Ka Wai, Yu, Fangyan, Adalsteinsson, Viktor A, Reed, Sarah, Gydush, Gregory, Ladas, Ioannis, Li, Jiang, Tantisira, Kelan G, Makrigiorgos, Gerassimos Mike
Published in Nucleic acids research (16.12.2019)
Published in Nucleic acids research (16.12.2019)
Get full text
Journal Article
Regulation of fibrin-mediated tumor cell adhesion to the endothelium using anti-thrombin aptamer
Gaddes, Erin R., Lee, Deborah, Gydush, Gregory, Wang, Yong, Dong, Cheng
Published in Experimental cell research (10.12.2015)
Published in Experimental cell research (10.12.2015)
Get full text
Journal Article
Circulating-free DNA (cfDNA) as biomarker of taxane resistance in metastatic castration-resistant prostate cancer (mCRPC)
Francini, Edoardo, Ou, Fang-Shu, Rhoades, Justin, Wolfe, Eric G., O'Connor, Edward, Ha, Gavin, Gregory, Gydush, Kelleher, Kaitlin, Bhatt, Rupal Satish, Balk, Steven P., Sweeney, Christopher, Adalsteinsson, Viktor, Taplin, Mary-Ellen, Choudhury, Atish Dipankar
Published in Journal of clinical oncology (20.02.2020)
Published in Journal of clinical oncology (20.02.2020)
Get full text
Journal Article
Abstract 5689: Identify tissue-of-origin in cancer cfDNA by whole genome sequencing
Liu, Yaping, Reed, Sarah, Choudhury, Atish D., Parsons, Heather A., Stover, Daniel G., Ha, Gavin, Gydush, Gregory, Rhoades, Justin, Rotem, Denisse, Freeman, Samuel, Adalsteinsson, Viktor, Kellis, Manolis
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Get full text
Journal Article
GENE-07. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL-FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE
Pagès, Mélanie, Rotem, Denisse, Gydush, Gregory, Reed, Sarah, Rhoades, Justin, Ha, Gavin, Lo, Chris, Tracy, Adam, Jones, Robert, Becker, Sarah, Haller, Michaela, Chi, Susan, Kieran, Mark, Goumnerova, Liliana, Love, Christopher, Ligon, Keith, Wright, Karen, Adalsteinsson, Viktor, Beroukhim, Rameen, Bandopadhayay, Pratiti
Published in Neuro-oncology (Charlottesville, Va.) (23.04.2019)
Published in Neuro-oncology (Charlottesville, Va.) (23.04.2019)
Get full text
Journal Article
Detection of Leptomeningeal Disease Using Cell-Free DNA From Cerebrospinal Fluid
White, Michael D, Klein, Robert H, Shaw, Brian, Kim, Albert, Subramanian, Megha, Mora, Joana L, Giobbie-Hurder, Anita, Nagabhushan, Deepika, Jain, Aarushi, Singh, Mohini, Kuter, Benjamin M, Nayyar, Naema, Bertalan, Mia S, Stocking, Jackson H, Markson, Samuel C, Lastrapes, Matthew, Alvarez-Breckenridge, Christopher, Cahill, Daniel P, Gydush, Gregory, Rhoades, Justin, Rotem, Denisse, Adalsteinsson, Viktor A, Mahar, Maura, Kaplan, Alexander, Oh, Kevin, Sullivan, Ryan J, Gerstner, Elizabeth, Carter, Scott L, Brastianos, Priscilla K
Published in JAMA network open (02.08.2021)
Published in JAMA network open (02.08.2021)
Get full text
Journal Article
Abstract 3001: Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services
Getz, Gad, Cibulskis, Carrie, Leshchiner, Ignaty, Hanna, Megan, Livitz, Dimitri, Slowik, Kara, Levovitz, Chaya, Utro, Filippo, Rhrissorrakrai, Kahn, Rotem, Denisse, Gydush, Gregory, Reed, Sarah C., Rhoades, Justin, Ha, Gavin, Freeman, Samuel S., Lo, Christopher, Fleharty, Mark, Abreu, Justin, Larkin, Katie, Cipicchio, Michelle, Blumenstiel, Brendan, DeFelice, Matt, Grimsby, Jonna, Hamilton, Susanna, Lennon, Niall, Adalsteinsson, Viktor A., Parida, Laxmi
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Get full text
Journal Article
Abstract LB-225: Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient
Freeman, Samuel S., Lin, Ziao, Ha, Gavin, Leshchiner, Ignaty, Rhoades, Justin, Livitz, Dimitri, Rosebrock, Daniel, Reed, Sarah C., Gydush, Gregory, Lo, Christopher, Rotem, Denisse, Choudhury, Atish D., Stover, Daniel G., Parsons, Heather A., Boehm, Jesse S., Love, J Christopher, Meyerson, Matthew, Grandgenett, Paul, Hollingsworth, Michael A., Adalsteinsson, Viktor A., Getz, Gad
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Get full text
Journal Article
Aptamer-Based Polyvalent Ligands for Regulated Cell Attachment on the Hydrogel Surface
Gaddes, Erin R, Gydush, Gregory, Li, Shihui, Chen, Niancao, Dong, Cheng, Wang, Yong
Published in Biomacromolecules (13.04.2015)
Published in Biomacromolecules (13.04.2015)
Get full text
Journal Article
INNV-22. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE
Pages, Mélanie, Rotem, Denisse, Gydush, Gregory, Reed, Sarah, Rhoades, Justin, Ha, Gavin, Lo, Chris, Tracy, Adam, Jones, Robert, Becker, Sarah, Haller, Michaela, Chi, Susan, Kieran, Mark, Goumnerova, Liliana, Love, J Christopher, Ligon, Keith, Bandopadhayay, Pratiti, Wright, Karen, Adalsteinsson, Viktor A, Beroukhim, Rameen
Published in Neuro-oncology (Charlottesville, Va.) (05.11.2018)
Published in Neuro-oncology (Charlottesville, Va.) (05.11.2018)
Get full text
Journal Article
TBIO-18. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE
Pages, Melanie, Rotem, Denisse, Gydush, Gregory, Reed, Sarah, Rhoades, Justin, Ha, Gavin, Lo, Chris, Tracy, Adam, Jones, Robert, Becker, Sarah, Haller, Michaela, Chi, Susan, Kieran, Mark, Goumnerova, Liliana, Love, J Christopher, Ligon, Keith L, Bandopadhayay, Pratiti, Wright, Karen, Adalsteinsson, Viktor A, Beroukhim, Rameen
Published in Neuro-oncology (Charlottesville, Va.) (22.06.2018)
Published in Neuro-oncology (Charlottesville, Va.) (22.06.2018)
Get full text
Journal Article