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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. , 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. , 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. 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. , 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. 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. . 2024.

Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity.  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.  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. . 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.  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.  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. 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,  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.  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. , Volume 2, Issue 7, 100349, 2021. PMID: 34337565.

Liang S, Mohanty V, Dou J, Miao Q, Huang Y, M¨¹ft¨¹o?lu M, Ding L, Peng W, Chen K. Single-cell manifold-preserving feature selection for detecting rare cell populations,  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,  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.  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. 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. 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. . 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. . 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. 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. . 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. 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. 27(5): 793¨C800, 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. 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. 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. 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. 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. . 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. 8(10):e77945, 2013. e-Pub 10/2013. PMID: 24205039.