Publications

Selected trainee-led original publications

Yuefan Huang, Vakul Mohanty, Merve Dede, Kyle Tsai, May Daher, Li Li, Katayoun Rezvani & Ken Chen*. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux. Nature Communications. Aug. 16. 2023.

Jinzhuang Dou, Yukun Tan, Kian Hong Kock, Jun Wang, Xuesen Cheng, Le Min Tan, Kyung Yeon Han, Chung Chau Hon, Woong Yang Park, Jay W Shin, Haijing Jin, Yujia Wang, Han Chen, Li Ding, Shyam Prabhakar, Nicholas Navin, Rui Chen, Ken Chen*. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nature Biotechnology. Aug. 17, 2023

Holly A. Hill, Preetesh Jain, Chi Young Ok, Koji Sasaki, Han Chen, Michael L. Wang, Ken Chen. Integrative Prognostic Machine-Learning Models in Mantle Cell Lymphoma. Cancer Research Communications. Aug. 02 2023.

Li L#, Mohanty V#, Dou J#, Huang Y#, Banerjee PP, Miao Q, Lohr JG, Vijaykumar T, Frede J, Knoechel B, Muniz-Feliciano L, Laskowski TJ, Liang S, Moyes JS, Nandivada V, Basar R, Kaplan M, Daher M, Liu E, Li Y, Acharya S, Lin P, Shanley M, Rafei H, Marin D, Mielke S, Champlin RE, Shpall EJ, Chen K*, Rezvani K*. Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering. Science Advance. 26 Jul 2023.

Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail DJ, Bernatchez C, Davies M, Li Y, Chen R, Yi SS, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer 4(4):zcac038, 12/2022. e-Pub 12/2022. PMCID: PMC9732527.

Jinzhuang Dou#, Shaoheng Liang #, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li, Li Li, May Daher, Rafet Basar, Katayoun Rezvani, Rui Chen, Ken Chen. Bi-order multimodal integration of single-cell data, Genome Biology, 2022 May 9;23(1):112. PMID: 35534898

Liang S, Liang Q, Chen R, Chen K. Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data. IEEE/ACM Trans Comput Biol Bioinform, 11/2021. PMID: 34232885

Mohanty V, Wang F, Mills G, CTD2 Consortium, Chen K. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers. Cell Reports Medicine, Volume 2, Issue 7, 100349, July 20, 2021. PMID: 34337565

Liang S, Mohanty V, Dou J, Miao Q, Huang Y, Müftüoğlu M, Ding L, Peng W, Chen K. Single-cell manifold-preserving feature selection for detecting rare cell populations, Nature Computational Science, 2021 May.

Wang F, Wang Q, Mohanty V, Liang S, Dou J, Han J, Minussi DC, Gao R, Ding L, Navin N, Chen K. MEDALT: Single-cell copy number lineage tracing enabling gene discovery, Genome Biology, 2021 Feb. PMID: 33622385.

Qi Miao, Fang Wang, Jinzhuang Dou, Ramiz Iqbal, Rafet Basar, Muharrem Muftuoglu, Li Li, Katy Rezvani, and Ken Chen. Ab initio Spillover Compensation in CyTOF Data. Cytometry Part A, 2020 Dec 20. PMID: 33342071.

Liang S, Wang F, Han J, Chen K. Latent periodic process inference from single-cell RNA-seq data. Nature Communications 11(1):1441, 3/2020. e-Pub 3/2020. PMID: 32188848.

Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: ab initio marker selection for single cell transcriptome profiling. PLoS Computational Biology 15(10):e1007445, 10/2019. e-Pub 10/2019. PMID: 31658262.

Wang F, Zhang S, Kim TB, Lin YY, Iqbal R, Wang Z, Mohanty V, Sircar K, Karam JA, Wendl MC, Meric-Bernstam F, Weinstein JN, Ding L, Mills GB, Chen K. Integrated Transcriptomic-Genomic tool Texomer profiles cancer tissues. Nature Methods. e-Pub 4/2019. PMID: 30988467.

Zafar H, Navin N, Chen K, Nakhleh L. SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Genome Research. e-Pub 2019. PMI: 31628257.

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Biology 18(1):178, 9/2017. e-Pub 9/2017. PMID: 28927434.

Wang Z, Kim TB, Peng B, Karam JA, Creighton CJ, Joon AY, Kawakami F, Trevisan P, Jonasch E, Chow CW, Rodriguez-Canales J, Tamboli P, Tannir NM, Wood CG, Monzon FA, Baggerly KA, Varella-Garcia M, Czerniak B, Wistuba II, Mills GB, Shaw K, Chen K, Sircar K. Sarcomatoid renal cell carcinoma has a distinct molecular pathogenesis, driver mutation profile and transcriptional landscape. Clinical Cancer Research. e-Pub 7/2017. PMID: 28710314.

Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K. novoBreak: local assembly for breakpoint detection in cancer genomes. Nature Methods 14(1):65-67, 1/2017. e-Pub 11/2016. PMCID: PMC5199621.

Fan X, Chaisson M, Nakhleh L, Chen K. HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies. Genome Research doi: 10.1101/gr.214767.116. e-Pub 1/2017. PMID: 28104618.

Chen T, Wang Z, Zhou W, Chong Z, Meric-Bernstam F, Mills GB, Chen K. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics 17 Suppl 2:394, 2016. e-Pub 6/2016. PMCID: PMC4928158.

Zafar H, Wang Y, Nakhleh L, Navin N, Chen K. Monovar: single nucleotide variant detection in single cells. Nature Methods 13(6):505-7, 6/2016. e-Pub 4/2016. PMCID: PMC4887298.
Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K. ClinSeK: a targeted variant characterization framework for clinical sequencing. Genome Medicine 7(1):34, 2015. e-Pub 3/2015. PMID: 25918555.

Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multi-level variant annotator for precision genomics. Nature Methods 12(11):1002-3, 10/2015. PMID: 26513549.

Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics. e-Pub 1/2014. PMID: 24389657.

Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K. CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features. PLoS One 8(10):e77945, 2013. e-Pub 10/2013. PMID: 24205039.