Publications & Talks

 

Journal Articles

 

  • C Ronda, SP Chen, V Cabral, SJ Yaung, HH Wang. Metagenomic engineering of the mammalian gut microbiome in situ. Nature Methods (2019).

  • JL Braff*, SJ Yaung*, KM Esvelt, GM Church. Characterization of Cas9-gRNA Orthologs. Cold Spring Harbor Lab Protocols (2016).

  • JL Braff*, SJ Yaung*, KM Esvelt, GM Church. Characterizing Cas9 Protospacer-Adjacent Motifs with High-Throughput Sequencing of Library Depletion Experiments. Cold Spring Harbor Lab Protocols (2016).

  • SJ Yaung, L Deng, N Li, JL Braff, GM Church, L Bry, HH Wang, GK Gerber. Improving microbial fitness in the mammalian gut using in vivo temporal functional metagenomics. Molecular Systems Biology 11:788 (2015).

  • SJ Yaung, KM Esvelt, GM Church. Complete Genome Sequences of T4-like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68. Genome Announcements 3:e01122-14 (2015).

  • SJ Yaung*, KM Esvelt*, GM Church. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4. PLOS ONE 9:e98811 (2014).

  • SJ Yaung, GM Church, HH Wang. Recent Progress in Engineering Human-associated Microbiomes, Methods in Molecular Biology 1151:3-25 (2014).

  • KM Esvelt, P Mali, JL Braff, M Moosburner, SJ Yaung, GM Church. Orthogonal Cas9 Proteins for RNA-guided Gene Regulation and Editing. Nature Methods 10:1116-1121 (2013).

  • G Zhou, A Moment, S Yaung, A Cote, T Hu. Evolution and Application of an Automated Platform for the Development of Crystallization Processes. Organic Process Research & Development 17:1320-1329 (2013).

  • PB Matthews, C Jhun, S Yaung, AN Azadani, JM Guccione, L Ge, EE Tseng. Finite Element Modeling of the Pulmonary Autograft at Systemic Pressure before Remodeling. Journal of Heart Valve Disease 20:45-52 (2011).

Please see Google Scholar for links to articles.

 

Invited Talks

 

  • "Enabling precision medicine and clinical cancer research with next-generation sequencing" at Silicon Valley Women in Engineering, San Jose, California. March 16, 2019.

  • "Making an Impact in Precision Medicine and Genomics" Mentoring Circles session at Grace Hopper Celebration of Women in Computing, Houston, Texas. September 26, 2018.

  • "Enabling Precision Medicine through Next-Generation Sequencing" at Women in Silicon Valley, San Francisco, California. March 22, 2018.

  • "Quantamerix and understanding public health challenges in rural China" at Global Health & Engineering Meetup at Boston University, Boston, Massachusetts. October 10, 2014.

  • "DNA Modifications Do Not Impede Cas9 Activity" at 114th General Meeting of the American Society for Microbiology, Boston, Massachusetts. May 20, 2014. Selected Young Investigator Oral Presenter to speak in symposium on "Genome Engineering and Control of Bacterial Physiology Mediated by Small RNAs".
     

Patents

 

  • U-P Rohr, A Lovejoy, S Yaung, J Lee, J Palma, L Yao. "Non-invasive test to predict response to therapy in colorectal cancer patients." PCT International Application WO 2018/146034, PCT/EP2018/052751, US Patent Application 62/455,994. Filed February 5, 2018.

  • A Lovejoy, S Yaung, A Balasubramanyam, J Palma. "NOVEL MUTATIONS IN ANAPLASTIC LYMPHOMA KINASE PREDICTING RESPONSE TO ALK INHIBITOR THERAPY IN LUNG CANCER PATIENTS." PCT International Application WO 2017/207696, PCT/EP2017/063318, US Patent Application 15/611612. Filed June 1, 2017.

  • KM Esvelt, S Yaung. "Precise microbiota engineering at the cellular level." US Patent Application 61/900002, PCT International Application WO 2015/069682, PCT/US2014/063994. Filed November 5, 2014.

  • GJ Xu, SJ Yaung. "Reader-less quantitative lateral flow assay." US Provisional Patent Application 61/609936. Filed March 12, 2012.
     

Conference Abstracts & Posters

 

  • M Ma, S Yaung, L Xi, C Ju, J Palma, M Schmid. "Assessment of a highly-curated somatic oncology mutation database to facilitate identification of clinically important variants in NGS results." Poster presented at European Human Genetics Conference, Gothenburg, Sweden. June 15-18, 2019.

  • SJ Yaung, F Fuhlbrück, J Wu, F Casey, M Peterson, W Zou, JF Palma, NS Patil, Y Jiang. "Evaluation of clonal hematopoiesis in late stage NSCLC using a next-generation sequencing panel targeting cancer genes." Journal of Clinical Oncology  37:9050, 2019. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. May 31 - June 4, 2019.

  • Y Jiang, NS Patil, J Wu, W Zou, S Yaung, A Balasubramanyam, S Flynn, M Peterson, E Peters, PS Hegde, S Mocci, M Kowanetz, J Palma. "Circulating tumor DNA assessment in plasma samples collected in Atezolizumab versus docetaxel in subjects with previously treated non-small-cell lung cancer (OAK) study." Poster presented at Annual Meeting of Society for Immunotherapy of Cancer, Washington, D.C., November 9-11, 2018. 

  • XM Ma, C Ju, A Balasubramanyam, L Xi, S Yaung, D Klass, M Thomas, F Lasitschka, M Meister, M Schneider, F Herth, T Muley, B Wehnl, JF Palma. "Optimization of ctDNA Quantification Methods for Longitudinal Disease Monitoring in Lung Adenocarcinoma." Poster presented at Association for Molecular Pathology Annual Meeting, San Antonio, Texas. November 1-3, 2018. 

  • S Yaung, L Xi, C Woestmann, S McNamara, B Hinzmann, S Froehler, N Tikoo, C Ju, A Balasubramanyam, H-P Adams, M Thomas, F Lasitschka, M Meister, M Schneider, FJF Herth, T Muley, B Wehnl, J Palma, XM Ma. "170P Ecological diversity indices as measurements of tumor heterogeneity correlates with clinical outcomes in late stage small cell lung cancer (SCLC)." Annals of Oncology 29:suppl_8, 2018. Poster presented at European Society for Medical Oncology 2018 Congress, Munich, Germany. October 19-23, 2018.

  • P Vitazka, N Tikoo, A Balasubramanyam, L Xi, S Yaung, E Kwok, A Lovejoy, D Klass, M Heibeck, K Probst, A Rehfeldt, E Meldgaard, A Madsen, M Clement, J Palma, B Sorensen, P Meldgaard. "1373P Identification of subjects with locally advanced lung cancer who are likely to respond to standard-of-care chemoradiotherapy by a longitudinal monitoring of circulating tumor DNA (ctDNA) using a comprehensive ultra-sensitive NGS assay." Annals of Oncology 29:suppl_8, 2018. Poster presented at European Society for Medical Oncology 2018 Congress, Munich, Germany. October 19-23, 2018.

  • J Palma, P Vitazka, N Tikoo, A Balasubramanyam, L Xi, S Yaung, E Kwok, A Lovejoy, D Klass, M Heibeck, K Probst, A Rehfeldt, E Meldgaard, A Madsen, M Clement, B Sorensen, P Meldgaard. "1426P Longitudinal plasma monitoring of subjects treated with EGFR-TKIs allows better understanding of evolution of acquired resistance and can inform optimal treatment strategies." Annals of Oncology 29:suppl_8, 2018. Poster presented at European Society for Medical Oncology 2018 Congress, Munich, Germany. October 19-23, 2018.

  • S Yaung, N Tikoo, A Nicholas, N Sommer, JC Bendell, H Hurwitz, R Price, JF Palma, JJ Lee, F Casey. "Correlation of measurements of tumor heterogeneity based on next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) with clinical outcomes in STEAM, a prospective, randomized, multicenter study in metastatic colorectal cancer (mCRC)." Journal of Clinical Oncology 36:3545, 2018. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 1-5, 2018.

  • S Yaung, L Xi, C Woestmann, S McNamara, B Hinzmann, S Fröhler, N Tikoo, C Ju, A Balasubramanyam, P Vitazka, A Pati, AF Lovejoy,  DM Klass, H Adams, M Thomas, F Herth, T Muley, B Wehnl, JF Palma, XM Ma. "Mutation count, a potential surrogate for tumor mutation load, of circulating tumor DNA (ctDNA) using targeted panel sequencing correlates with clinical outcomes in late stage lung adenocarcinoma and small cell lung cancer." Journal of Clinical Oncology 36:12045, 2018. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 1-5, 2018.

  • JF Palma, C Woestmann, S McNamara, B Hinzmann, S Fröhler, H Adams, M Feldkamp, S Siemann, M Lange, A Blüher, S Yaung, L Xi, N Tikoo, A Balasubramanyam, C Ju, A Pati, B Wehnl, T Muley, XM Ma, F Herth. "Early assessment of therapy response in small cell lung cancer via longitudinal ctDNA analysis." Journal of Clinical Oncology 36:8577, 2018. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 1-5, 2018.

  • XM Ma, L Xi, S Yaung, N Tikoo, A Balasubramanyam, C Ju, D Klass, AF Lovejoy, A Pati, O Solberg, Y Jiang, H Adams, B Wehnl, M Thomas, F Lasitschka, M Meister, M Schneider, F Herth, JF Palma, T Muley. "Early assessment of treatment effect in advanced lung adenocarcinoma via longitudinal ctDNA analysis." Journal of Clinical Oncology 36:12088, 2018. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 1-5, 2018.

  • XM Ma, N Tikoo, C Ju, A Balasubramanyam, L Xi, S Yaung, D Klass, AF Lovejoy, A Pati, O Solberg, Y Jiang, H Adams, M Thomas, F Lasitschka, M Meister, M Schneider, F Herth, T Muley, B Wehnl, JF Palma. "Longitudinal ctDNA analysis to enable early assessment of prognosis in lung adenocarcinoma in the absence of matched tissue biopsy." Journal of Clinical Oncology 36:12077, 2018. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 1-5, 2018.

  • P Lal, J Lee, H Adams, L Yao, F Fuhlbrück, S Yaung, S McNamara, C Wöstmann, S Fröhler, L Fang, R Kube, F Marusch, M Heise, T Steinmüller, M Pross, R Mantke, J Palma, André Rosenthal. "Concordance of genomic single-nucleotide variations (SNV) by next-generation sequencing (NGS) in paired tumor tissue and plasma in colorectal cancer (CRC)." Oral presentation at American Association for Clinical Research, Chicago, Illinois. April 14-18, 2018.

  • I Garcia-Murillas, P Proszek, C Fribbens, L Yuan, H Bye, M Hubank, J Jiang, S Yaung, J Palma, S Johnston, A Ring, N Turner. "Circulating tumor DNA analysis with ultra-high sensitivity sequencing in metastatic breast cancer." Poster presented at San Antonio Breast Cancer Symposium, San Antonio, Texas. December 5-9, 2017.

  • Y Jiang, H Adams, L Yao, S Yaung, F Fuhlbrueck, S Froehler, L Fang, P Lai, J Achenbach, O Oster, O Schega, R Kruegel, J Palma, A Rosenthal. "Concordance of Genomic Alterations by Next Generation Sequencing (NGS) in Tumor Tissue versus Cell-Free DNA in Stage I-IV NSCLC." Poster presented at Association for Molecular Pathology Annual Meeting, Salt Lake City, Utah. November 16-18, 2017.

  • AF Lovejoy, A Pati, A Munoz, S Yaung, J Jin, D Klass. "In-depth Assessment Reveals Powerful Performance and Flexibility of AVENIO ctDNA Analysis Kits." Poster presented at Association for Molecular Pathology Annual Meeting, Salt Lake City, Utah. November 16-18, 2017.

  • J Jiang, H Adams, M Lange, S Siemann, M Feldkamp, S Schulze, S Froehler, S Yaung, L Yao, A Balasubramanyam, N Tikoo, HJ Achenbach, R Krügel, J Palma, A Rosenthal. "Longitudinal Mutation Monitoring in Plasma by Deep Sequencing as a Potential Predictor of Disease Progression in NSCLC." Oral presentation at World Conference on Lung Cancer, Yokohama, Japan. October 15-18, 2017.

  • JJ Lee, JF Palma, L Yao, AF Lovejoy, S Yaung, D Zhang, N Wingate-Pearse, M Yau, C Williams, M Pimentel, A Munoz, K Mayol, C Mancao, A Nicholas, N Sommer, JC Bendell, H Hurwitz, U Rohr. "Evaluation of clinical outcomes by analysis of mutations in tumor tissue and circulating plasma DNA using next-generation sequencing (NGS) from STEAM, a prospective, randomized, multicenter study in metastatic colorectal cancer (mCRC)." Journal of Clinical Oncology 35:11510, 2017. Poster presented and discussed at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 2-6, 2017.

  • M Diehn, AA Alizadeh, H Adams, JJ Lee, S Klassen, JF Palma, B Hinzman, AF Lovejoy, AM Newman, L Yao, S Yaung, A Balasubramanyam, U Rohr, A Rosenthal, R Kube, T Steinmuller, F Marusch, R Mantke, M Heise, M. "Early prediction of clinical outcomes in resected II and III colorectal cancer (CRC) through deep sequencing of circulating tumor DNA (ctDNA)." Journal of Clinical Oncology 35:3591, 2017. Poster presented at American Society for Clinical Oncology Annual Meeting, Chicago, Illinois. June 2-6, 2017.

  • S Yaung, A Lovejoy, D Klass, F Casey, A Arcot, M Loyzer, W Chiu, N Azhar, S Beckert, M Lange, S Siemann, S Froehler, S Gunn, JF Palma. "Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA." Poster presented at American Association for Cancer Research Annual Meeting, Washington, D.C. April 1-5, 2017.

  • SJ Yaung, L Deng, N Li, JL Braff, GM Church, L Bry, HH Wang, GK Gerber. "Temporal functional metagenomics sequencing to improve microbial fitness in the mammalian gut." HST Forum, Boston, Massachusetts. April 16, 2015.

  • SJ Yaung, HH Wang, KM Esvelt, GM Church. "Engineering Gene Transfer Networks in the Human Microbiome." Wyss Institute Annual Retreat, Boston, Massachusetts. November 19, 2012.

  • PB Matthews, S Yaung, AN Azadani, N Jaussaud, C Jhun, JM Guccione, TS Guy, EE Tseng. "Pulmonary Autograft Wall Stress Calculation With Finite Element Modeling." Biennial Meeting of the Society for Heart Valve Disease, Berlin, Germany. June 27-30, 2009.

  • P Dhawan*, S Yaung*, H Uppal*, D Puppala, M Sweeney, J Murray, P Hajek, E Oquendo, C Wilson, N Priedigkeit, D Goldstein, D Misner, S Platz, R Capaldi, K Kolaja. "The Role of Mitochondrial Toxicity in the Cardiotoxicity of Small Molecule Kinase Inhibitors." Annual Meeting of the Society of Toxicology, Baltimore, Maryland. March 15-19, 2009.