Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes
Peng, Quan, Vijaya Satya, Ravi, Lewis, Marcus, Randad, Pranay, Wang, Yexun
Published in BMC genomics (07.08.2015)
Published in BMC genomics (07.08.2015)
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Journal Article
A new strategy to reduce allelic bias in RNA-Seq readmapping
Satya, Ravi Vijaya, Zavaljevski, Nela, Reifman, Jaques
Published in Nucleic acids research (01.09.2012)
Published in Nucleic acids research (01.09.2012)
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Journal Article
A high-throughput pipeline for the design of real-time PCR signatures
Vijaya Satya, Ravi, Kumar, Kamal, Zavaljevski, Nela, Reifman, Jaques
Published in BMC bioinformatics (23.06.2010)
Published in BMC bioinformatics (23.06.2010)
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Journal Article
Thermodynamic basis for the emergence of genomes during prebiotic evolution
Woo, Hyung-June, Vijaya Satya, Ravi, Reifman, Jaques
Published in PLoS computational biology (01.05.2012)
Published in PLoS computational biology (01.05.2012)
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Journal Article
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
Vijaya Satya, Ravi, Zavaljevski, Nela, Kumar, Kamal, Reifman, Jaques
Published in BMC bioinformatics (10.04.2008)
Published in BMC bioinformatics (10.04.2008)
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Journal Article
Comparison of somatic mutation calling methods in amplicon and whole exome sequence data
Xu, Huilei, DiCarlo, John, Satya, Ravi Vijaya, Peng, Quan, Wang, Yexun
Published in BMC genomics (28.03.2014)
Published in BMC genomics (28.03.2014)
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Journal Article
In silico microarray probe design for diagnosis of multiple pathogens
Vijaya Satya, Ravi, Zavaljevski, Nela, Kumar, Kamal, Bode, Elizabeth, Padilla, Susana, Wasieloski, Leonard, Geyer, Jeanne, Reifman, Jaques
Published in BMC genomics (21.10.2008)
Published in BMC genomics (21.10.2008)
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Journal Article
Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer
Janku, Filip, Zhang, Shile, Waters, Jill, Liu, Li, Huang, Helen J, Subbiah, Vivek, Hong, David S, Karp, Daniel D, Fu, Siqing, Cai, Xuyu, Ramzanali, Nishma M, Madwani, Kiran, Cabrilo, Goran, Andrews, Debra L, Zhao, Yue, Javle, Milind, Kopetz, E Scott, Luthra, Rajyalakshmi, Kim, Hyunsung J, Gnerre, Sante, Satya, Ravi Vijaya, Chuang, Han-Yu, Kruglyak, Kristina M, Toung, Jonathan, Zhao, Chen, Shen, Richard, Heymach, John V, Meric-Bernstam, Funda, Mills, Gordon B, Fan, Jian-Bing, Salathia, Neeraj S
Published in Clinical cancer research (15.09.2017)
Published in Clinical cancer research (15.09.2017)
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Journal Article
16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles
Hang, Jun, Desai, Valmik, Zavaljevski, Nela, Yang, Yu, Lin, Xiaoxu, Satya, Ravi Vijaya, Martinez, Luis J, Blaylock, Jason M, Jarman, Richard G, Thomas, Stephen J, Kuschner, Robert A
Published in Microbiome (16.09.2014)
Published in Microbiome (16.09.2014)
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Journal Article
AGeS: a software system for microbial genome sequence annotation
Kumar, Kamal, Desai, Valmik, Cheng, Li, Khitrov, Maxim, Grover, Deepak, Satya, Ravi Vijaya, Yu, Chenggang, Zavaljevski, Nela, Reifman, Jaques
Published in PloS one (07.03.2011)
Published in PloS one (07.03.2011)
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Journal Article
SNIT: SNP identification for strain typing
Vijaya Satya, Ravi, Zavaljevski, Nela, Reifman, Jaques
Published in Source code for biology and medicine (08.09.2011)
Published in Source code for biology and medicine (08.09.2011)
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Journal Article
Constructing Near-Perfect Phylogenies with multiple homoplasy events
Satya, Ravi Vijaya, Mukherjee, Amar, Alexe, Gabriela, Parida, Laxmi, Bhanot, Gyan
Published in Bioinformatics (15.07.2006)
Published in Bioinformatics (15.07.2006)
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Journal Article
Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines
Wallqvist, Anders, Yu, Chenggang, Reifman, Jaques, Zavaljevski, Nela, Vijaya Satya, Ravi, Bondugula, Rajkumar, Desai, Valmik, Hu, Xin, Kumar, Kamal, Lee, Michael S., Yeh, In-Chul
Published in Computing in science & engineering (01.09.2010)
Published in Computing in science & engineering (01.09.2010)
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Journal Article
Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA
Liu, M.C., Klein, E.A., Swanton, C., Seiden, M.V., Klein, Eric A., Yeatman, Timothy J., Cohn, Allen L., Lapham, Rosanna, Parker, Alexander S., McIntyre, Kristi, Sekeres, Mikkael A., Siegel, Robert, Wang, Xuezhong, Cosgrove, David P., Trent, Jonathan, Thiel, David D., Garbo, Lawrence E., Giguere, Jeffrey K., Michels, Ross M., Harris, Ronald P., Richey, Stephen L., McCarthy, Timothy A., Couch, Fergus J., Wilks, Sharon T., Krie, Amy K., Balaraman, Rama, Rieger-Christ, Kimberly, Sullivan, Travis, Greenwald, Daniel R., Oh, William, Tsao, Che-Kai, Kennecke, Hagen F., Manhas, Atisha P., Ulrich, Brian K., Kovoor, Philip A., Stokoe, Christopher, Courtright, Jay G., Larson, Timothy G., Seiden, Michael V., Cummings, Steven R., Absalan, Farnaz, Alexander, Gregory, Allen, Brian, Aravanis, Alexander M., Beausang, John F., Berman, Jennifer, Bredno, Joerg, Calef, Robert, Cann, Gordon, Carter, Jeremy, Chen, Xiaoji, Chien, Tom C., Davydov, Konstantin, Demas, Vasiliki, Fields, Alexander P., Freese, Peter, Gnerre, Sante, Gross, Samuel, Hall, Megan P., Hartman, Anne-Renee, Hou, Chenlu, Hubbell, Earl, Jiang, Roger, Kim, TaeHyung, Klausner, Richard D., Kurtzman, Kathryn N., Lee, Mark, Lin, Wendy, Lipson, Jafi, Maddala, Tara, Maher, M. Cyrus, Melton, Collin, Mich, Andrea, Newman, Joshua, Nicula, Virgil, Nikolic, Ongjen, Patel, Shilpen, Rava, Richard, Schellenberger, Jan, Scott, Eric, Sehnert, Amy J., Shaknovich, Rita, Shanmugam, Avinash, Shashidhar, K.C., Shenoy, Archana, Shojaee, Seyedmehdi, Tang, Susan, Valouev, Anton, Venn, Oliver, Williams, Richard T., Wu, Tony, Yakym, Christopher, Yang, Xiao, Yecies, Jessica, Yip, Alexander S., Yue, Jeanne, Zhang, Lily, Zhang, Lori (Quan), Curtis, Christina, Berry, Donald A.
Published in Annals of oncology (01.06.2020)
Published in Annals of oncology (01.06.2020)
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Journal Article
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
Razavi, Pedram, Li, Bob T, Brown, David N, Jung, Byoungsok, Hubbell, Earl, Shen, Ronglai, Abida, Wassim, Juluru, Krishna, De Bruijn, Ino, Hou, Chenlu, Venn, Oliver, Lim, Raymond, Anand, Aseem, Maddala, Tara, Gnerre, Sante, Vijaya Satya, Ravi, Liu, Qinwen, Shen, Ling, Eattock, Nicholas, Yue, Jeanne, Blocker, Alexander W, Lee, Mark, Sehnert, Amy, Xu, Hui, Hall, Megan P, Santiago-Zayas, Angie, Novotny, William F, Isbell, James M, Rusch, Valerie W, Plitas, George, Heerdt, Alexandra S, Ladanyi, Marc, Hyman, David M, Jones, David R, Morrow, Monica, Riely, Gregory J, Scher, Howard I, Rudin, Charles M, Robson, Mark E, Diaz, Jr, Luis A, Solit, David B, Aravanis, Alexander M, Reis-Filho, Jorge S
Published in Nature medicine (01.12.2019)
Published in Nature medicine (01.12.2019)
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Journal Article
PTAP motif duplication in the p6 Gag protein confers a replication advantage on HIV-1 subtype C
Sharma, Shilpee, Arunachalam, Prabhu S., Menon, Malini, Ragupathy, Viswanath, Satya, Ravi Vijaya, Jebaraj, Joshua, Aralaguppe, Shambhu Ganeshappa, Rao, Chaitra, Pal, Sreshtha, Saravanan, Shanmugam, Murugavel, Kailapuri G., Balakrishnan, Pachamuthu, Solomon, Suniti, Hewlett, Indira, Ranga, Udaykumar
Published in The Journal of biological chemistry (27.07.2018)
Published in The Journal of biological chemistry (27.07.2018)
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Journal Article
Abstract 3404: Landscape and genomic correlates of ctDNA-based tumor mutational burden across six solid tumor types
Quinn, Katie, Helman, Elena, Nance, Tracy, Yen, Jennifer, Latham, John, Gleitsman, Kristin, Vijaya-Satya, Ravi, Artieri, Carlo, Artyomenko, Alex, Sikora, Marcin, Chudova, Darya, Lanman, Richard B., Talasaz, AmirAli
Published in Cancer research (Chicago, Ill.) (01.07.2019)
Published in Cancer research (Chicago, Ill.) (01.07.2019)
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Journal Article
Abstract 3656: Target enrichment of methylated circulating tumor DNA for colorectal cancer detection
Huang, Hsiao-Yun, Satya, Ravi Vijaya, Chan, Wen-Ching, Atolia, Esha, Babiarz, Joshua, Zimmermann, Bernhard, Kawli, Trupti
Published in Cancer research (Chicago, Ill.) (22.03.2024)
Published in Cancer research (Chicago, Ill.) (22.03.2024)
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Journal Article