Published Papers
2025
SMAGS-LASSO: A Novel Feature Selection Method for Sensitivity Maximization in Early Cancer Detection
Khoshfekr Rudsari H, Khorami-Sarvestani S, Fahrmann JF, Long JP, Hanash S, Do KA, Irajizad E. SMAGS-LASSO: A Novel Feature Selection Method for Sensitivity Maximization in Early Cancer Detection. Cancer Epidemiol Biomarkers Prev. 2025 Dec 1;34(12)...
Long-chain sulfatide enrichment is an actionable metabolic vulnerability in intraductal papillary mucinous neoplasm (IPMN)-associated pancreatic cancers
Chen Y, Ballarò R, Sans M, Thege FI, Zuo M, Dou R, Min J, Yip-Schneider M, Zhang J, Wu R, Irajizad E, Makino Y, Rajapakshe KI, Rudsari HK, Hurd MW, León-Letelier RA, Katayama H, Ostrin E, Vykoukal J, Dennison JB, Do KA, Hanash SM, Wolff RA, Guerre...
AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes
Zhu H, Asiaee A, Azinfar L, Li J, Liang H, Irajizad E, Do KA, Long JP. AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes. Brief Bioinform. 2025 Aug 31;26(5):bbaf426. doi:...
CAT: a conditional association test for microbiome data using a permutation approach
Shi Y, Zhang L, Do KA, Jenq RR, Peterson CB. CAT: a conditional association test for microbiome data using a permutation approach. Brief Bioinform. 2025 Jul 2;26(4):bbaf326. doi: 10.1093/bib/bbaf326. PMID: 40641046; PMCID: PMC12362256.
Grape-Pi: Graph-Based Neural Networks for Enhanced Protein Identification in Proteomics Pipelines
Chunhui Gu, Seyyed Mahmood Ghasemi, Yining Cai, Johannes F Fahrmann, James P Long, Hiroyuki Katayama, Chong Wu, Jody Vykoukal, Jennifer B Dennison, Samir Hanash, Kim-Anh Do, Ehsan Irajizad, Grape-Pi: Graph-Based Neural Networks for Enhanced Protei...
Integrated metabolomics and spatial transcriptomics of cystic pancreatic cancer precursors reveals dysregulated polyamine metabolism as a biomarker of progression
Ricardo A. León-Letelier, Yihui Chen, Rongzhang Dou, Ehsan Irajizad, Michele T. Yip-Schneider, Ranran Wu, Rahmah Ejaz, Hamid K. Rudsari, Yaxi Li, Rachelle Spencer, Riccardo Ballarò, Jody Vykoukal, Mark Hurd, Jennifer B. Dennison, Kim-Anh Do, Anirb...
A Novel Sensitivity Maximization at a Given Specificity Method for Binary Classifications
Ghasemi SM, Gu C, Fahrmann JF, Hanash S, Do KA, Long JP, Irajizad E. A Novel Sensitivity Maximization at a Given Specificity Method for Binary Classifications. Cancer Prev Res (Phila). 2025 Mar 3;18(3):117-123. doi: 10.1158/1940-6207.CAPR-24-0236....
Lead time trajectory of blood-based protein biomarkers for detection of pancreatic cancer based on repeat testing
Fahrmann JF, Yip-Schneider M, Vykoukal J, Spencer R, Dennison JB, Do KA, Long JP, Maitra A, Zhang J, Schmidt CM, Hanash S, Irajizad E. Lead time trajectory of blood-based protein biomarkers for detection of pancreatic cancer based on repeat testin...
Elevated levels of circulating microbial-associated uremic toxins are associated with metastatic duodenopancreatic neuroendocrine tumors in patients with Multiple Endocrine Neoplasia Type 1
Ballarò R, Wasylishen AR, Pieterman CRC, Olsen C, Irajizad E, Wu R, et al. Elevated levels of circulating microbial-associated uremic toxins are associated with metastatic duodenopancreatic neuroendocrine tumors in patients with Multiple Endocrine...
Causal models and prediction in cell line perturbation experiments
Long JP, Yang Y, Shimizu S, Pham T, Do KA. Causal models and prediction in cell line perturbation experiments. BMC Bioinformatics. 2025 Jan 7;26(1):4. doi: 10.1186/s12859-024-06027-7. PMID: 39773352; PMCID: PMC11707890.
2024
Cyst Fluid Proteins Stratify Malignant Risk of Intraductal Papillary Mucinous Neoplasm of the Pancreas
León-Letelier R, Chen Y, Dou R, Irajizad E, Yip-Schneider M, Wu R, et al. Cyst Fluid Proteins Stratify Malignant Risk of Intraductal Papillary Mucinous Neoplasm of the Pancreas. Submitted to Biomark Res. 2024 Dec 22.
Integrated metabolomics and spatial transcriptomics of cystic pancreatic cancer precursors reveals dysregulated polyamine metabolism as a biomarker of progression
León-Letelier R, Chen Y, Dou R, Irajizad E, Yip-Schneider M, Wu R, et al. Integrated metabolomics and spatial transcriptomics of cystic pancreatic cancer precursors reveals dysregulated polyamine metabolism as a biomarker of progression. Submitted...
Bayesian compositional regression with flexible microbiome feature aggregation and selection
Saha S, Zhang L, Do K-A, Peterson CB. Bayesian compositional regression with flexible microbiome feature aggregation and selection. arXiv. 2024 Nov 15;2406.01557v2. Available from: https://arxiv.org/abs/2406.01557v2
MicroRNAs are enriched at COVID-19 genomic risk regions, and their blood levels correlate with the COVID-19 prognosis of cancer patients infected by SARS-CoV-2
Anfossi S, Darbaniyan F, Quinlan J, Calin S, Shimizu M, Chen M, Rausseo P, Winters M, Bogatenkova E, Do KA, Martinez I, Li Z, Antal L, Olariu TR, Wistuba I, Calin GA. MicroRNAs are enriched at COVID-19 genomic risk regions, and their blood levels ...
A Blood-based Metabolite Signature for Personalized Risk Assessment of Pancreatic Cancer
León-Letelier RA, Yihui C, Ballaro R, Irajizad E, Do KA, Maitra A, et al. A Blood-based Metabolite Signature for Personalized Risk Assessment of Pancreatic Cancer. J Cancer Immunol. 2024;6(4):148-153.
Biomarker trajectory for earlier detection of lung cancer
Irajizad, Ehsan, Johannes F. Fahrmann, Iakovos Toumazis, Jody Vykoukal, Jennifer B. Dennison, Yu Shen, Kim-Anh Do, Edwin J. Ostrin, Ziding Feng, and Samir Hanash. Biomarker trajectory for earlier detection of lung cancer. EBioMedicine 108 (2024).
A metabolite-based liquid biopsy for detection of ovarian cancer
Fahrmann, J.F., Ghasemi, S.M., Han, C.Y. et al. A metabolite-based liquid biopsy for detection of ovarian cancer. Biomark Res 12, 91 (2024). https://doi.org/10.1186/s40364-024-00629-2
Validation of a Blood-Based Protein Biomarker Panel for a Risk Assessment of Lethal Lung Cancer in the Physicians’ Health Study
Song L, Irajizad E, Rundle A, Sesso HD, Gaziano JM, Vykoukal JV, Do K-A, Dennison JB, Ostrin EJ, Fahrmann JF, et al. Validation of a Blood-Based Protein Biomarker Panel for a Risk Assessment of Lethal Lung Cancer in the Physicians’ Health Study. C...
A novel method to guide biomarker combinations to optimize the sensitivity
Ghasem SM, Fahrmann JF, Hanash S, Do KA, Long JP, Irajizad E. A novel method to guide biomarker combinations to optimize the sensitivity. bioRxiv [Preprint]. 2024 Apr 15:2024.04.12.589302. doi: 10.1101/2024.04.12.589302. PMID: 38659773; PMCID: PMC...
Analysis of Microbiome Data
Peterson CB, Saha S, Do KA. Analysis of Microbiome Data. Annu Rev Stat Appl. 2024 Apr;11(1):483-504. doi: 10.1146/annurev-statistics-040522-120734. Epub 2023 Oct 13. PMID: 38962089; PMCID: PMC11218911.
Contributions of the Microbiome-Derived Metabolome for Risk Assessment and Prognostication of Pancreatic Cancer
León-Letelier RA, Dou R, Vykoukal J, Yip-Schneider MT, Maitra A, Irajizad E, Wu R, Dennison JB, Do KA, Zhang J, Schmidt CM, Hanash S, Fahrmann JF. Contributions of the Microbiome-Derived Metabolome for Risk Assessment and Prognostication of Pancre...
2023
Attempts to Understand Oral Mucositis in Head and Neck Cancer Patients through Omics Studies: A Narrative Review
San Valentin EMD, Do KA, Yeung SJ, Reyes-Gibby CC. Int J Mol Sci. 2023 Nov 30;24(23):16995
Mortality Benefit of a Blood-Based Biomarker Panel for Lung Cancer on the Basis of the Prostate, Lung, Colorectal, and Ovarian Cohort
Ehsan Irajizad, Johannes F. Fahrmann, Tracey Marsh, Jody Vykoukal, Jennifer B. Dennison, James P. Long, Kim-Anh Do, Ziding Feng, Samir Hanash, and Edwin J. Ostrin Journal of Clinical Oncology 2023 41:27, 4360-4368
A Blood-based Metabolomic Signature Predictive of Risk for Pancreatic Cancer
Irajizad E, Kenney A, Tang T, Vykoukal J, Wu R, Murage E, Dennison JB, Sans M, Long JP, Loftus M, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger JM, Maitra A, Do KA, Yu B, Wolpin BM, Han...
CAT: a conditional association test for microbiome data using a leave-out approach
Shi, Y., Zhang, L., Do, K.A., Jenq, R.R. and Peterson, C.B., 2023. CAT: a conditional association test for microbiome data using a leave-out approach. arXiv preprint arXiv:2309.08109.
Influence of oral microbiome on longitudinal patterns of oral mucositis severity in patients with squamous cell carcinoma of the head and neck
Irajizad E, Kenney A, Tang T, Vykoukal J, Wu R, Murage E, Dennison JB, Sans M, Long JP, Loftus M, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger JM, Maitra A, Do KA, Yu B, Wolpin BM, Han...
Estimating Causal Effects with Hidden Confounding using Instrumental Variables and Environments
Irajizad E, Kenney A, Tang T, Vykoukal J, Wu R, Murage E, Dennison JB, Sans M, Long JP, Loftus M, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger JM, Maitra A, Do KA, Yu B, Wolpin BM, Han...
Performance determinants of unsupervised clustering methods for microbiome data
Shi Y, Zhang L, Peterson CB, Do KA, Jenq RR. Performance determinants of unsupervised clustering methods for microbiome data. Microbiome. 2022 Feb 5;10(1):25. doi: 10.1186/s40168-021-01199-3. PMID: 35120564; PMCID: PMC8817542.
2022
A Blood-Based Metabolite Panel for Distinguishing Ovarian Cancer from Benign Pelvic Masses
Irajizad E, Han CY, Celestino J, Wu R, Murage E, Spencer R, Dennison JB, Vykoukal J, Long JP, Do KA, Drescher C, Lu K, Lu Z, Bast RC, Hanash S, Fahrmann JF. A Blood-Based Metabolite Panel for Distinguishing Ovarian Cancer from Benign Pelvic Masses...
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data
Li Z, Wang Y, Ganan-Gomez I, Colla S, Do KA. A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. Bioinformatics. 2022 Oct 31;38(21):4885-4892. doi: 10.1093/bioinformatics/btac617. PMID:...
Bayesian hierarchical quantile regression with application to characterizing the immune architecture of lung cancer
Das P, Peterson CB, Ni Y, Reuben A, Zhang J, Zhang J, Do KA, Baladandayuthapani V. Bayesian hierarchical quantile regression with application to characterizing the immune architecture of lung cancer. Biometrics. 2023 Sep;79(3):2474-2488. doi: 10.1...
Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemiar
Darbaniyan F, Zheng H, Kanagal-Shamanna R, Lockyer P, Montalban-Bravo G, Estecio M, Lu Y, Soltysiak KA, Chien KS, Yang H, Sasaki K, Class C, Ganan-Gomez I, Do KA, Garcia-Manero G, Wei Y. Transcriptomic Signatures of Hypomethylating Agent Failure i...
MDM2 antagonist improves therapeutic activity of azacitidine in myelodysplastic syndromes and chronic myelomonocytic leukemia
Yue Wei, Hong Zheng, Pamela Pennington Lockyer, Faezeh Darbaniyan, Ziyi Li, Rashmi Kanagal-Shamanna, Kelly A. Soltysiak, Hui Yang, Irene Ganan-Gomez, Guillermo Montalban-Bravo, Kelly S. Chien, Kim-Anh Do, Naval Daver & Guillermo Garcia-Manero ...
Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
Irajizad E, Wu R, Vykoukal J, Murage E, Spencer R, Dennison JB, Moulder S, Ravenberg E, Lim B, Litton J, Tripathym D, Valero V, Damodaran S, Rauch GM, Adrada B, Candelaria R, White JB, Brewster A, Arun B, Long JP, Do KA, Hanash S and Fahrmann JF (...
A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Response
Irajizad, E.; Fahrmann, J.F.; Long, J.P.; Vykoukal, J.; Kobayashi, M.; Capello, M.; Yu, C.-Y.; Cai, Y.; Hsiao, F.C.; Patel, N.; et al. A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Re...
A semi-mechanistic dose-finding design in oncology using pharmacokinetic/pharmacodynamic modeling
Su X, Li Y, Müller P, Hsu CW, Pan H, Do KA. A semi-mechanistic dose-finding design in oncology using pharmacokinetic/pharmacodynamic modeling. Pharm Stat. 2022 Nov;21(6):1149-1166. doi: 10.1002/pst.2249. Epub 2022 Jun 24. PMID: 35748220.
Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia
Wei Y, Kanagal-Shamanna R, Zheng H, Bao N, Lockyer PP, Class CA, Darbaniyan F, Lu Y, Lin K, Yang H, Montalban-Bravo G, Ganan-Gomez I, Soltysiak KA, Do KA, Colla S, Garcia-Manero G. Cooperation between KDM6B overexpression and TET2 deficiency in th...
CNGPLD: case–control copy-number analysis using Gaussian process latent difference
Shih DJH, Ruoxing L, Müller P, Zheng WJ, Do KA, Lin SY, Carter SL. CNGPLD: Case-control copy-number analysis using Gaussian process latent difference. Bioinformatics. 2022 Feb 17;38(8):2096–101. doi: 10.1093/bioinformatics/btac096. Epub ahead o...
Blood-based biomarker panel for personalized lung cancer risk assessment
Fahrmann, Johannes F., Tracey Marsh, Ehsan Irajizad, Nikul Patel, Eunice Murage, Jody Vykoukal, Jennifer B. Dennison et al. ‘Blood-based biomarker panel for personalized lung cancer risk assessment.’ Journal of Clinical Oncology 40, no. 8 (2022): ...
SRGN-Triggered Aggressive and Immunosuppressive Phenotype in a Subset of TTF-1–Negative Lung Adenocarcinomas
Tanaka I, Dayde D, Tai MC, Mori H, Solis LM, Tripathi SC, Fahrmann JF, Unver N, Parhy G, Jain R, Parra ER, Murakami Y, Aguilar-Bonavides C, Mino B, Celiktas M, Dhillon D, Casabar JP, Nakatochi M, Stingo F, Baladandayuthapani V, Wang H, Katayama...
Exploiting induced vulnerability to overcome PARPi resistance and clonal heterogeneity in BRCA mutant triple-negative inflammatory breast cancer
Shih DJH, Chen MK, Yin J, McGrail DJ, Dai H, Wei R, Zhang J, Zheng WJ, Do KA, Yang L, Hung MC, Lin SY. Exploiting induced vulnerability to overcome PARPi resistance and clonal heterogeneity in BRCA mutant triple-negative inflammatory breast cancer...
2021
CES2 sustains HNF4α expression to promote pancreatic adenocarcinoma progression through an epoxide hydrolase-dependent regulatory loop
Chen Y, Capello M, Rios Perez MV, Vykoukal JV, Roife D, Kang Y, Prakash LR, Katayama H, Irajizad E, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Do KA, Fiehn O, Maitra A, Wang H, Chiao PJ, Katz MHG, Fleming JB, Hanash SM, Fahrmann JF. CES2 ...
A Blood-based Polyamine Signature Associated With MEN1 Duodenopancreatic Neuroendocrine Tumor Progression
Fahrmann JF, Wasylishen AR, Pieterman CRC, Irajizad E, Vykoukal J, Murage E, Wu R, Dennison JB, Krishna H, Peterson CB, Lozano G, Zhao H, Do KA, Halperin DM, Agarwal SK, Blau JE, Del Rivero J, Nilubol N, Walter MF, Welch JM, Weinstein LS, Vriens M...
Myelodysplastic/myeloproliferative neoplasms-unclassifiable with isolated isochromosome 17q represents a distinct clinico-biologic subset: a multi-institutional collaborative study from the Bone Marrow Pathology Group
Kanagal-Shamanna R, Orazi A, Hasserjian RP, Arber DA, Reichard K, Hsi ED, Bagg A, Rogers HJ, Geyer J, Darbaniyan F, Do KA, Devins KM, Pozdnyakova O, George TI, Cin PD, Greipp PT, Routbort MJ, Patel K, Garcia-Manero G, Verstovsek S, Medeiros LJ, Wa...
PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma
Giuliani V, Miller MA, Liu CY, Hartono SR, Class CA, Bristow CA, Suzuki E, Sanz LA, Gao G, Gay JP, Feng N, Rose JL, Tomihara H, Daniele JR, Peoples MD, Bardenhagen JP, Geck Do MK, Chang QE, Vangamudi B, Vellano C, Ying H, Deem AK, Do KA, Genovese ...
2020
Bayesian Compositional Regression with Structured Priors for Microbiome Feature Selection
Zhang L, Shi Y, Jenq RR, Do KA, Peterson CB. Bayesian compositional regression with structured priors for microbiome feature selection. Biometrics. 2021 Sep;77(3):824-838. doi: 10.1111/biom.13335. Epub 2020 Jul 31. PMID: 32686846; PMCID: PMC8216648.
2018
Personalized Integrated Network Modeling of the Cancer Proteome Atlas
Ha MJ, Banerjee S, Akbani R, Liang H, Mills GB, Do KA, Baladandayuthapani V. Personalized Integrated Network Modeling of the Cancer Proteome Atlas. Sci Rep. 2018 Oct 8;8(1):14924. doi: 10.1038/s41598-018-32682-x. PMID: 30297783; PMCID: PMC6175854.
2017
iDINGO—integrative differential network analysis in genomics with Shiny application
Class CA, Ha MJ, Baladandayuthapani V, Do KA. iDINGO-integrative differential network analysis in genomics with Shiny application. Bioinformatics. 2018 Apr 1;34(7):1243-1245. doi: 10.1093/bioinformatics/btx750. PMID: 29194470; PMCID: PMC6030922.
2016
A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study
Chekouo T, Stingo FC, Doecke JD, Do KA. A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study. Biometrics. 2017 Jun;73(2):615-624. doi: 10.1111/biom.12587. Epub 2016 Sep 26. PMID: 27669160.
2015
DINGO: differential network analysis in genomics
Ha MJ, Baladandayuthapani V, Do KA. DINGO: differential network analysis in genomics. Bioinformatics. 2015 Nov 1;31(21):3413-20. doi: 10.1093/bioinformatics/btv406. Epub 2015 Jul 6. PMID: 26148744; PMCID: PMC4751246.