Gene variants of coagulation related proteins that interact with SARS-CoV-2
Holcomb, David, Alexaki, Aikaterini, Hernandez, Nancy, Hunt, Ryan, Laurie, Kyle, Kames, Jacob, Hamasaki-Katagiri, Nobuko, Komar, Anton A, DiCuccio, Michael, Kimchi-Sarfaty, Chava
Published in PLoS computational biology (17.03.2021)
Published in PLoS computational biology (17.03.2021)
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Journal Article
Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Alexaki, Aikaterini, Hettiarachchi, Gaya K., Athey, John C., Katneni, Upendra K., Simhadri, Vijaya, Hamasaki-Katagiri, Nobuko, Nanavaty, Puja, Lin, Brian, Takeda, Kazuyo, Freedberg, Darón, Monroe, Dougald, McGill, Joseph R., Peters, Robert, Kames, Jacob M., Holcomb, David D., Hunt, Ryan C., Sauna, Zuben E., Gelinas, Amy, Janjic, Nebojsa, DiCuccio, Michael, Bar, Haim, Komar, Anton A., Kimchi-Sarfaty, Chava
Published in Scientific reports (29.10.2019)
Published in Scientific reports (29.10.2019)
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Journal Article
A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Hunt, Ryan, Hettiarachchi, Gaya, Katneni, Upendra, Hernandez, Nancy, Holcomb, David, Kames, Jacob, Alnifaidy, Redab, Lin, Brian, Hamasaki-Katagiri, Nobuko, Wesley, Aaron, Kafri, Tal, Morris, Christina, Bouché, Laura, Panico, Maria, Schiller, Tal, Ibla, Juan, Bar, Haim, Ismail, Amra, Morris, Howard, Komar, Anton, Kimchi-Sarfaty, Chava
Published in International journal of molecular sciences (15.11.2019)
Published in International journal of molecular sciences (15.11.2019)
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Journal Article
Translational and transcriptional responses in human primary hepatocytes under hypoxia
Hettiarachchi, Gaya K, Katneni, Upendra K, Hunt, Ryan C, Kames, Jacob M, Athey, John C, Bar, Haim, Sauna, Zuben E, McGill, Joseph R, Ibla, Juan C, Kimchi-Sarfaty, Chava
Published in American journal of physiology: Gastrointestinal and liver physiology (01.06.2019)
Published in American journal of physiology: Gastrointestinal and liver physiology (01.06.2019)
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Journal Article
Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage
Meyer, Douglas, Kames, Jacob, Bar, Haim, Komar, Anton A, Alexaki, Aikaterini, Ibla, Juan, Hunt, Ryan C, Santana-Quintero, Luis V, Golikov, Anton, DiCuccio, Michael, Kimchi-Sarfaty, Chava
Published in Genome medicine (28.07.2021)
Published in Genome medicine (28.07.2021)
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Journal Article
Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer
Clavé, Sergi, Jackson, Jennifer B, Salido, Marta, Kames, Jacob, Gerding, Kelly M R, Verner, Ellen L, Kong, Eric F, Weingartner, Elizabeth, Gibert, Joan, Hardy-Werbin, Max, Rocha, Pedro, Riera, Xènia, Torres, Erica, Hernandez, James, Cerqueira, Gustavo, Nichol, Donna, Simmons, John, Taus, Álvaro, Pijuan, Lara, Bellosillo, Beatriz, Arriola, Edurne
Published in Frontiers in oncology (20.10.2023)
Published in Frontiers in oncology (20.10.2023)
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Journal Article
Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX [version 2; peer review: 3 approved]
Alexaki, Aikaterini, Kames, Jacob, Hettiarachchi, Gaya K, Athey, John C, Katneni, Upendra K, Hunt, Ryan C, Hamasaki-Katagiri, Nobuko, Holcomb, David D, DiCuccio, Michael, Bar, Haim, Komar, Anton A, Kimchi-Sarfaty, Chava
Published in F1000 research (2020)
Published in F1000 research (2020)
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Journal Article
Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins
Holcomb, David D., Jankowska, Katarzyna I., Hernandez, Nancy, Laurie, Kyle, Kames, Jacob, Hamasaki-Katagiri, Nobuko, Komar, Anton A., DiCuccio, Michael, Kimchi-Sarfaty, Chava
Published in STAR protocols (16.09.2022)
Published in STAR protocols (16.09.2022)
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Journal Article
Structural, functional, and immunogenicity implications of F9 gene recoding
Katneni, Upendra K., Alexaki, Aikaterini, Hunt, Ryan C., Hamasaki-Katagiri, Nobuko, Hettiarachchi, Gaya K., Kames, Jacob M., McGill, Joseph R., Holcomb, David D., Athey, John C., Lin, Brian, Parunov, Leonid A., Kafri, Tal, Lu, Qi, Peters, Robert, Ovanesov, Mikhail V., Freedberg, Darón I., Bar, Haim, Komar, Anton A., Sauna, Zuben E., Kimchi-Sarfaty, Chava
Published in Blood advances (12.07.2022)
Published in Blood advances (12.07.2022)
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Journal Article
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Kames, Jacob, Holcomb, David D., Kimchi, Ofer, DiCuccio, Michael, Hamasaki-Katagiri, Nobuko, Wang, Tony, Komar, Anton A., Alexaki, Aikaterini, Kimchi-Sarfaty, Chava
Published in Scientific reports (24.09.2020)
Published in Scientific reports (24.09.2020)
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Journal Article
Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design
Alexaki, Aikaterini, Kames, Jacob, Holcomb, David D., Athey, John, Santana-Quintero, Luis V., Lam, Phuc Vihn Nguyen, Hamasaki-Katagiri, Nobuko, Osipova, Ekaterina, Simonyan, Vahan, Bar, Haim, Komar, Anton A., Kimchi-Sarfaty, Chava
Published in Journal of molecular biology (14.06.2019)
Published in Journal of molecular biology (14.06.2019)
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Journal Article
New approaches to predict the effect of co-occurring variants on protein characteristics
Holcomb, David, Hamasaki-Katagiri, Nobuko, Laurie, Kyle, Katneni, Upendra, Kames, Jacob, Alexaki, Aikaterini, Bar, Haim, Kimchi-Sarfaty, Chava
Published in American journal of human genetics (05.08.2021)
Published in American journal of human genetics (05.08.2021)
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Journal Article
TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression
Kames, Jacob, Alexaki, Aikaterini, Holcomb, David D., Santana-Quintero, Luis V., Athey, John C., Hamasaki-Katagiri, Nobuko, Katneni, Upendra, Golikov, Anton, Ibla, Juan C., Bar, Haim, Kimchi-Sarfaty, Chava
Published in Journal of molecular biology (15.05.2020)
Published in Journal of molecular biology (15.05.2020)
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Journal Article
Abstract 5452: Complimentary use of DNA- and RNA-based NGS assays optimizes detection of clinically relevant translocations for comprehensive genomic profiling
Ren, Rongqin, Jackson, Jennifer, Kames, Jacob, Riles, David, Coldren, Christopher, Wheeler, Scott, Chandra, Pranil, Shiller, Michelle
Published in Cancer research (Chicago, Ill.) (04.04.2023)
Published in Cancer research (Chicago, Ill.) (04.04.2023)
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Journal Article
Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
Jankowska, Katarzyna I, Meyer, Douglas, Holcomb, David Dillon, Kames, Jacob, Hamasaki-Katagiri, Nobuko, Katneni, Upendra K., Hunt, Ryan C., Ibla, Juan C., Kimchi-Sarfaty, Chava
Published in Blood advances (27.09.2022)
Published in Blood advances (27.09.2022)
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Journal Article
Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX [version 1; peer review: 3 approved with reservations]
Alexaki, Aikaterini, Kames, Jacob, Hettiarachchi, Gaya K, Athey, John C, Katneni, Upendra K, Hunt, Ryan C, Hamasaki-Katagiri, Nobuko, Holcomb, David D, DiCuccio, Michael, Bar, Haim, Komar, Anton A, Kimchi-Sarfaty, Chava
Published in F1000 research (2020)
Published in F1000 research (2020)
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Journal Article
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2
Holcomb, David, Alexaki, Aikaterini, Hernandez, Nancy, Laurie, Kyle, Kames, Jacob, Hamasaki-Katagiri, Nobuko, Komar, Anton A, DiCuccio, Michael, Kimchi-Sarfaty, Chava
Published in bioRxiv (18.09.2020)
Published in bioRxiv (18.09.2020)
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Paper
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Kames, Jacob, Holcomb, David D, Kimchi, Ofer, DiCuccio, Michael, Hamasaki-Katagiri, Nobuko, Wang, Tony, Komar, Anton A, Alexaki, Aikaterini, Kimchi-Sarfaty, Chava
Published in bioRxiv (31.03.2020)
Published in bioRxiv (31.03.2020)
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