Publications

Selected KClab trainee-led original publications

Jiang X,  Rudqvist N,  Jiang B,  Ye S, He S,  Liang Q,  Dou J,  Williams M,  Dunn JD,  Johnson JM,  Akagi K,  Xiao W,  Liang S,  Elayavalli S,  Sun B,  Cuentas ERP,  Ferrarotto R,  Garden A,  Fuller C,  Reddy J,  Gross N,  Lango M,  Leung CH,  Liu S,  Liu D,  Lee JJ,  Curran MA,  Phan J, Chen K*, Gillison ML*. Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade. Cancer Discovery, 04/2025. PMID: 40249124

Wang Y, Dede M, Mohanty V, Dou J, Li Z, Chen K. A statistical approach for systematic identification of transition cells from scRNA-seq data. Cell Reports Method, 2024, PMID: 39644902.

He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V*, Chen K*. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. iScience, 2024.

Tan Y*, Dede M*, Mohanty V, Dou J, Hill H, Bernstam E, Chen K. Forecasting acute kidney injury and resource utilization in ICU patients using longitudinal, multimodal models. Journal of Biomedical Informatics, 2024.

Liang S, Dou J, Iqbal R, Chen K. Label-Aware Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data. Commun Biol 7(1):326, 3/2024. e-Pub 3/2024. PMCID: PMC10940680.  A Human Cell Atlas (HCA bundle) publication.

Mohanty V. Inferring cancer metabolism from gene-expression data. Nature Review Cancer. 2024.

Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity. Nature Communications 14(8416), 2023.

Huang Y, Mohanty V, Dede M, Tsai K, Daher M, Li L, Rezvani K, Chen K. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux. Nature Communications 14(4883), 2023. PMID: 37573313.

Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K.  Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nature Biotechnology. e-Pub 8/2023. PMID: 37592035.

Hill HA, Jain P, Ok CY, Sasaki K, Chen H, Wang ML, Chen K. Integrative Prognostic Machine-Learning Models in Mantle Cell Lymphoma. Cancer Research Communications 3(8):1435-1446, 2023. PMID: 37538987.

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 9(30):eadd6997, 2023. PMID: 37494448.

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, 2022. e-Pub 12/2022. PMID: 36518525.

Dou J#, Liang S#, Mohanty V, Miao Q, Huang Y, Liang Q, Cheng X, Kim S, Choi J, Li Y, Li L, Daher M, Basar R, Rezvani K, Chen R, Chen K. Bi-order multimodal integration of single-cell data, Genome Biology 23(1):112, 2022. 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 18(6):2072-2079, 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, 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 1(5):374-384, 2021. PMCID: PMC10035340.

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 22(70), 2021. PMID: 33622385.

Miao Q, Wang F, Dou J, Iqbal R, Basar R, Muftuoglu M, Li L, Rezvani K, Chen K. Ab initio Spillover Compensation in CyTOF Data. Cytometry Part A 99(9):899-909, 2020. 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, 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, 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. PMID: 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, 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, 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 27(5): 793–800, 2017. e-Pub 1/2017. doi: 10.1101/gr.214767.116. 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, 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.