SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data
Davis, Eric M, Sun, Yu, Liu, Yanling, Kolekar, Pandurang, Shao, Ying, Szlachta, Karol, Mulder, Heather L, Ren, Dongren, Rice, Stephen V, Wang, Zhaoming, Nakitandwe, Joy, Gout, Alexander M, Shaner, Bridget, Hall, Salina, Robison, Leslie L, Pounds, Stanley, Klco, Jeffery M, Easton, John, Ma, Xiaotu
Published in Genome Biology (25.01.2021)
Published in Genome Biology (25.01.2021)
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A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing
Chen, Wenan, Zhang, Silu, Williams, Justin, Ju, Bensheng, Shaner, Bridget, Easton, John, Wu, Gang, Chen, Xiang
Published in Computational and structural biotechnology journal (01.01.2020)
Published in Computational and structural biotechnology journal (01.01.2020)
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Journal Article
Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)
Shaw, Timothy I, Dong, Li, Tian, Liqing, Qian, Chenxi, Liu, Yu, Ju, Bensheng, High, Anthony, Kavdia, Kanisha, Pagala, Vishwajeeth R, Shaner, Bridget, Pei, Deqing, Easton, John, Janke, Laura J, Porter, Shaina N, Ma, Xiaotu, Cheng, Cheng, Pruett-Miller, Shondra M, Choi, John, Yu, Jiyang, Peng, Junmin, Gu, Wei, Look, A Thomas, Downing, James R, Zhang, Jinghui
Published in Scientific reports (04.03.2021)
Published in Scientific reports (04.03.2021)
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Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor
Arunachalam, Sasi, Szlachta, Karol, Brady, Samuel W, Ma, Xiaotu, Ju, Bensheng, Shaner, Bridget, Mulder, Heather L, Easton, John, Raphael, Benjamin J, Myers, Matthew, Tinkle, Christopher, Allen, Sariah J, Orr, Brent A, Wetmore, Cynthia J, Baker, Suzanne J, Zhang, Jinghui
Published in Acta neuropathologica communications (31.05.2022)
Published in Acta neuropathologica communications (31.05.2022)
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Accurate genomic variant detection in single cells with primary template-directed amplification
Gonzalez-Pena, Veronica, Natarajan, Sivaraman, Xia, Yuntao, Klein, David, Carter, Robert, Pang, Yakun, Shaner, Bridget, Annu, Kavya, Putnam, Daniel, Chen, Wenan, Connelly, Jon, Pruett-Miller, Shondra, Chen, Xiang, Easton, John, Gawad, Charles
Published in Proceedings of the National Academy of Sciences - PNAS (15.06.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (15.06.2021)
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Single-cell analysis reveals the Comma-1D cell line as a unique model for mammary gland development and breast cancer
Werner, Rachel L, Nekritz, Erin A, Yan, Koon-Kiu, Ju, Bensheng, Shaner, Bridget, Easton, John, Yu, Jiyang, Silva, Jose
Published in Journal of cell science (15.05.2022)
Published in Journal of cell science (15.05.2022)
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Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas
Newman, Scott, Fan, Liying, Pribnow, Allison, Silkov, Antonina, Rice, Stephen V, Lee, Seungjae, Shao, Ying, Shaner, Bridget, Mulder, Heather, Nakitandwe, Joy, Shurtleff, Sheila, Azzato, Elizabeth M, Wu, Gang, Zhou, Xin, Barnhill, Raymond, Easton, John, Nichols, Kim E, Ellison, David W, Downing, James R, Pappo, Alberto, Potter, Philip M, Zhang, Jinghui, Bahrami, Armita
Published in Nature medicine (01.04.2019)
Published in Nature medicine (01.04.2019)
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The miR-424(322)/503 gene cluster regulates pro- versus anti-inflammatory skin DC subset differentiation by modulating TGF-β signaling
Zyulina, Victoria, Yan, Koon-Kiu, Ju, Bensheng, Schwarzenberger, Elke, Passegger, Christina, Tam-Amersdorfer, Carmen, Pan, Qingfei, Sconocchia, Tommaso, Pollack, Christian, Shaner, Bridget, Zebisch, Armin, Easton, John, Yu, Jiyang, Silva, Jose M., Strobl, Herbert
Published in Cell reports (Cambridge) (27.04.2021)
Published in Cell reports (Cambridge) (27.04.2021)
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Abstract 3652: USP7 heterozygous loss-of-function affects T-cell differentiation in pediatric T-ALL
Shaw, Timothy I., Dong, Li, High, Anthony, Liu, Yu, Ju, Bensheng, Kavdia, Kanisha, Pagala, Vishwajeeth, Shaner, Bridget, Easton, John, Qian, Chenxi, Yu, Jiyang, Janke, Janke, Choi, John Kim, Peng, Junmin, Gu, Wei, Downing, James R., Zhang, Jinghui
Published in Cancer research (Chicago, Ill.) (01.07.2019)
Published in Cancer research (Chicago, Ill.) (01.07.2019)
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Abstract 731: Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas
Newman, Scott, Fan, Liying, Pribnow, Allison, Silkov, Antonina, Rice, Stephen V., Lee, Seungjae, Shao, Ying, Shaner, Bridget, Mulder, Heather, Nakitandwe, Joy, Shurtleff, Sheila, Azzato, Elizabeth, Wu, Gang, Zhou, Xin, Barnhill, Raymond, Easton, John, Nichols, Kim E., Ellison, David W., James, Downing R., Pappo, Alberto, Potter, Philip M., Zhang, Jinghui, Bahrami, Armita
Published in Cancer research (Chicago, Ill.) (01.07.2019)
Published in Cancer research (Chicago, Ill.) (01.07.2019)
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Integrome signatures of lentiviral gene therapy for SCID-X1 patients
Yan, Koon-Kiu, Condori, Jose, Ma, Zhijun, Metais, Jean-Yves, Ju, Bensheng, Ding, Liang, Dhungana, Yogesh, Palmer, Lance E, Langfitt, Deanna M, Ferrara, Francesca, Throm, Robert, Shi, Hao, Risch, Isabel, Bhatara, Sheetal, Shaner, Bridget, Lockey, Timothy D, Talleur, Aimee C, Easton, John, Meagher, Michael M, Puck, Jennifer M, Cowan, Morton J, Zhou, Sheng, Mamcarz, Ewelina, Gottschalk, Stephen, Yu, Jiyang
Published in Science advances (06.10.2023)
Published in Science advances (06.10.2023)
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Accurate Genomic Variant Detection in Single Cells with Primary Template-Directed Amplification
Gonzalez, Veronica, Sivaraman Natarajan, Xia, Yuntao, Klein, David, Carter, Robert, Pang, Yakun, Shaner, Bridget, Kavya Annu, Putnam, Daniel, Chen, Wenan, Connelly, Jon, Pruett-Miller, Shondra, Chen, Xiang, Easton, John, Gawad, Charles
Published in bioRxiv (23.11.2020)
Published in bioRxiv (23.11.2020)
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miR-424(322) is a molecular switch controlling pro-inflammatory vs anti-inflammatory skin DC subset differentiation by modulating TGF-β signaling
Zyulina, Victoria, Koon-Kiu Yan, Ju, Bensheng, Passegger, Christina, Tam-Amersdorfer, Carmen, Pan, Qingfei, Sconocchia, Tommaso, Pollack, Christian, Shaner, Bridget, Zebisch, Armin, Easton, John, Yu, Jiyang, Silva, Jose M, Strobl, Herbert
Published in bioRxiv (08.09.2020)
Published in bioRxiv (08.09.2020)
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Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation
Koon-Kiu Yan, Nekritz, Erin, Ju, Bensheng, Dong, Xinran, Werner, Rachel, Alsina-Beauchamp, Dayanira, Rosencrance, Celeste, Mukhopadhyay, Partha, Pan, Qingfei, Gorbatenko, Andrej, Ding, Liang, Wang, Yanyan, Qian, Chenxi, Shi, Hao, Shaner, Bridget, Sivaraman Natarajan, Chi, Hongbo, Easton, John, Silva, Jose, Yu, Jiyang
Published in bioRxiv (17.08.2020)
Published in bioRxiv (17.08.2020)
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