Discovering Biological Guilds through Topological Abstraction. - Gil Alterovitz; Marco Ramoni (AMIA, 2006)

Gene Lethality Detection and Characterization via Topological Analysis of Regulatory Networks. - Gil Alterovitz; Vinayak Muralidhar; Marco Ramoni (IEEE Trans. Circuits Syst. I Regul. Pap., 2006)

Linking Protein Mass with Function via Organismal Massome Networks. - Gil Alterovitz; Eugenia Lyashenko; Michael Xiang; Marco Ramoni (BIBE, 2007)

A Systematic Approach to Quantifying Evolutionary Functional Trends Across the Universal Tree of Life. - Gil Alterovitz; Taro Muso; Paresh Malalur; Marco Ramoni (BIBE, 2007)

GO PaD: the Gene Ontology Partition Database. - Gil Alterovitz; Michael Xiang; Mamta Mohan; Marco Ramoni (Nucleic Acids Res., 2007)

Bioinformatics and Proteomics: An Engineering Problem Solving-Based Approach. - Gil Alterovitz; Marco Ramoni (IEEE Trans. Educ., 2007)

Erratum to "Bioinformatics and Proteomics: An Engineering Problem Solving-Based Approach". - Gil Alterovitz; Marco Ramoni (IEEE Trans. Educ., 2007)

An information theoretic framework for genomic data analysis. - Aaron McKenna; Gil Alterovitz (BIBE, 2008)

System-Wide Peripheral Biomarker Discovery Using Information Theory. - Gil Alterovitz; Michael Xiang; Jonathan Liu; Amelia Chang; Marco Ramoni (Pacific Symposium on Biocomputing, 2008)

Automated programming for bioinformatics algorithm deployment. - Gil Alterovitz; Adnaan Jiwaji; Marco Ramoni (Bioinform., 2008)

Session Introduction. - Gil Alterovitz; Judith A. Blake; Jonathan M. Dreyfuss; Drew Endy; Marco Ramoni (Pacific Symposium on Biocomputing, 2009)

Session Introduction. - Gil Alterovitz; Silvio Cavalcanti; Taro Muso; Marco Ramoni; May Wang (Pacific Symposium on Biocomputing, 2010)

The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. - Gil Alterovitz; Taro Muso; Marco Ramoni (Briefings Bioinform., 2010)

Mapping transcription mechanisms from multimodal genomic data. - Hsun-Hsien Chang; Michael J. McGeachie; Gil Alterovitz; Marco Ramoni (BMC Bioinform., 2010)

Introduction to the special issue on information theory in molecular biology and neuroscience. - Olgica Milenkovic; Gil Alterovitz; Gerard Battail; Todd P. Coleman; Joachim Hagenauer; Sean P. Meyn; Nathan D. Price 001; Marco Ramoni; Ilya Shmulevich; Wojciech Szpankowski (IEEE Trans. Inf. Theory, 2010)

Is the reduction of dimensionality to a small number of features always necessary in constructing predictive models for analysis of complex diseases or behaviours? - Amin Zollanvari; Nancy L. Saccone; Laura J. Bierut; Marco Ramoni; Gil Alterovitz (EMBC, 2011)

Phenome-Based Analysis as a Means for Discovering Context-Dependent Clinical Reference Ranges. - Jeremy L. Warner; Gil Alterovitz (AMIA, 2012)

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. - Chang F. Quo; Chanchala Kaddi; John H. Phan; Amin Zollanvari; Mingqing Xu; May D. Wang; Gil Alterovitz (Briefings Bioinform., 2012)

Constructing a Novel Cancer Ontology. - Michael C. Gao; Jeremy L. Warner; Peter C. Yang; Gil Alterovitz (AMIA, 2013)

Sharing of Genomic Information: Perspectives from Stakeholders. - Jeremy L. Warner; Gil Alterovitz; Joshua C. Denny; Robert Fassett; Kevin S. Hughes (AMIA, 2013)

Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information. - Jeremy L. Warner; Quan Ding; David A. Kreda; Zi'ou Zheng; Keshav Gupta; Joshua C. Denny; Gil Alterovitz (AMIA, 2013)

Causal discovery based on healthcare information. - Jing Yang 008; Ning An 001; Gil Alterovitz; Lian Li 001; Aiguo Wang (BIBM, 2013)

Analytic Approaches to Phenotypic Complexity. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (MedInfo, 2013)

Automated Synthesis and Visualization of a Chemotherapy Treatment Regimen Network. - Jeremy L. Warner; Peter C. Yang; Gil Alterovitz (MedInfo, 2013)

Brief communication: External phenome analysis enables a rational federated query strategy to detect changing rates of treatment-related complications associated with multiple myeloma. - Jeremy L. Warner; Gil Alterovitz; Kelly Bodio; Robin M. Joyce (J. Am. Medical Informatics Assoc., 2013)

Accelerating incremental wrapper based gene selection with K-Nearest-Neighbor. - Aiguo Wang; Ning An 001; Guilin Chen; Lian Li 001; Gil Alterovitz (BIBM, 2014)

Incremental wrapper based gene selection with Markov blanket. - Aiguo Wang; Ning An 001; Guilin Chen; Jing Yang 008; Lian Li 001; Gil Alterovitz (BIBM, 2014)

Bayesian Prognostic Model for Genomic Discovery in Bipolar Disorder. - Swetha S. Bobba; Amin Zollanvari; Gil Alterovitz (BIOINFORMATICS, 2014)

Modified Anderson-Darling Test-Based Target Detector in Non-Homogenous Environments. - Yang Li; Yinsheng Wei; Bingfei Li; Gil Alterovitz (Sensors, 2014)

Improving PLS-RFE based gene selection for microarray data classification. - Aiguo Wang; Ning An 001; Guilin Chen; Lian Li 001; Gil Alterovitz (Comput. Biol. Medicine, 2015)

Predicting hypertension without measurement: A non-invasive, questionnaire-based approach. - Aiguo Wang; Ning An 001; Guilin Chen; Lian Li 001; Gil Alterovitz (Expert Syst. Appl., 2015)

SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. - Gil Alterovitz; Jeremy L. Warner; Peijin Zhang; Yishen Chen; Mollie Ullman-Cullere; David A. Kreda; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2015)

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2015)

Accelerating wrapper-based feature selection with K-nearest-neighbor. - Aiguo Wang; Ning An 001; Guilin Chen; Lian Li 001; Gil Alterovitz (Knowl. Based Syst., 2015)

Gene expression prediction using low-rank matrix completion. - Arnav Kapur; Kshitij Marwah; Gil Alterovitz (BMC Bioinform., 2016)

SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care. - Jeremy L. Warner; Matthew J. Rioth; Kenneth D. Mandl; Joshua C. Mandel; David A. Kreda; Isaac S. Kohane; Daniel Carbone; Ross Oreto; Lucy Wang; Shilin Zhu; Heming Yao; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2016)

Classification of hospital acquired complications using temporal clinical information from a large electronic health record. - Jeremy L. Warner; Peijin Zhang; Jenny Liu; Gil Alterovitz (J. Biomed. Informatics, 2016)

A Partial Correlation Statistic Structure Learning Algorithm Under Linear Structural Equation Models. - Jing Yang 008; Ning An 001; Gil Alterovitz (IEEE Trans. Knowl. Data Eng., 2016)

Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization. - Jiaoyun Yang; Haipeng Wang; Huitong Ding; Ning An 001; Gil Alterovitz (BMC Bioinform., 2017)

SNP by SNP by environment interaction network of alcoholism. - Amin Zollanvari; Gil Alterovitz (BMC Syst. Biol., 2017)

Wrapper-based gene selection with Markov blanket. - Aiguo Wang; Ning An 001; Jing Yang 008; Guilin Chen; Lian Li 001; Gil Alterovitz (Comput. Biol. Medicine, 2017)

Biobrick chain recommendations for genetic circuit design. - Jiaoyun Yang; Song Yu; Bowen Gong; Ning An 001; Gil Alterovitz (Comput. Biol. Medicine, 2017)

Subtype dependent biomarker identification and tumor classification from gene expression profiles. - Aiguo Wang; Ning An 001; Guilin Chen; Li Liu 001; Gil Alterovitz (Knowl. Based Syst., 2018)

Deep Probabilistic Matrix Factorization Framework for Online Collaborative Filtering. - Kangkang Li 001; Xiuze Zhou; Fan Lin; Wenhua Zeng; Gil Alterovitz (IEEE Access, 2019)

Predicting of Associations Between MicroRNA and Human Diseases Based on Multiple Similarities and Arbitrarily-Order Proximity Network Embedding. - Xiujin Wu; Wenhua Zeng; Yuxiu Xu; Beizhan Wang; Xiangrong Liu; Fan Lin; Gil Alterovitz (IEEE Access, 2019)

Extracting causal relations from the literature with word vector mapping. - Ning An 001; Yongbo Xiao; Jing Yuan; Jiaoyun Yang; Gil Alterovitz (Comput. Biol. Medicine, 2019)

Sparse online collaborative filtering with dynamic regularization. - Kangkang Li 001; Xiuze Zhou; Fan Lin; Wenhua Zeng; Beizhan Wang; Gil Alterovitz (Inf. Sci., 2019)

Personal Cognitive Health Library. - Lingling Zhang; Ning An 001; Huitong Ding; Ning Xie; Chi Zhang; Gil Alterovitz (AMIA, 2020)

Smoky Mountain Data Challenge 2020: An Open Call to Solve Data Problems in the Areas of Neutron Science, Material Science, Urban Modeling and Dynamics, Geophysics, and Biomedical Informatics. - Suzanne Parete-Koon; Peter F. Peterson; Garrett E. Granroth; Wenduo Zhou; Pravallika Devineni; Nouamane Laanait; Junqi Yin; Albina Y. Borisevich; Ketan Maheshwari; Melissa R. Allen-Dumas; Srinath Ravulaparthy; Kuldeep R. Kurte; et al. (SMC, 2020)

Digital personal health libraries: a systematic literature review. - Huitong Ding; Chi Zhang; Ning An 001; Lingling Zhang; Ning Xie; Gil Alterovitz (CoRR, 2020)

Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. - Nathan D. Seligson; Jeremy L. Warner; William S. Dalton; David Martin; Robert S. Miller; Debra Patt; Kenneth L. Kehl; Matvey B. Palchuk; Gil Alterovitz; Laura K. Wiley; Ming Huang 006; Feichen Shen; et al. (J. Am. Medical Informatics Assoc., 2020)

An efficient causal structure learning algorithm for linear arbitrarily distributed continuous data. - Jing Yang 008; Na Li; Ning An 001; Yu Chen 018; Gil Alterovitz (J. Supercomput., 2020)

AI for infectious disease modelling and therapeutics. - Gil Alterovitz; Wei-Lun Alterovitz; Gail H. Cassell; Lixin Zhang 006; A. Keith Dunker (PSB, 2021)

How Much Does the (Social) Environment Matter? Using Artificial Intelligence to Predict COVID-19 Outcomes with Socio-demographic Data. - Christos A. Makridis; Anish Mudide; Gil Alterovitz (PSB, 2021)

SARS-CoV-2 Drug Discovery based on Intrinsically Disordered Regions. - Anish Mudide; Gil Alterovitz (PSB, 2021)

netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. - Zhengyang Dong; Gil Alterovitz (Bioinform., 2021)

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. - Robert H. Dolin; Shaileshbhai R. Gothi; Aziz A. Boxwala; Bret S. E. Heale; Ammar Husami; James Jones; Himanshu Khangar; Shubham Londhe; Frank Naeymi-Rad; Soujanya Rao; Barbara Rapchak; James Shalaby; et al. (BMC Bioinform., 2021)

Leveraging machine learning to characterize the role of socio-economic determinants on physical health and well-being among veterans. - Christos A. Makridis; David Y. Zhao; Cosmin Adrian Bejan; Gil Alterovitz (Comput. Biol. Medicine, 2021)

Transfer Learning Based Multi-Objective Evolutionary Algorithm for Community Detection of Dynamic Complex Networks. - Jungang Zou; Fan Lin; Beizhan Wang; Siyu Gao; Gaoshan Deng; Wenhua Zeng; Gil Alterovitz (CoRR, 2021)

Interoperable genetic lab test reports: mapping key data elements to HL7 FHIR specifications and professional reporting guidelines. - Aly Khalifa; Clinton C. Mason; Jennifer H. Garvin; Marc S. Williams; Guilherme Del Fiol; Brian R. Jackson; Steven B. Bleyl; Gil Alterovitz; Stanley M. Huff (J. Am. Medical Informatics Assoc., 2021)

An explainable machine learning platform for pyrazinamide resistance prediction and genetic feature identification of Mycobacterium tuberculosis. - Andrew Zhang; Ling Teng; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2021)

A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. - Ken Wiley; Laura Findley; Madison Goldrich; Tejinder K. Rakhra-Burris; Ana Stevens; Pamela Williams; Carol J. Bult; Rex L. Chisholm; Patricia Deverka; Geoffrey S. Ginsburg; Eric D. Green; Gail P. Jarvik; et al. (J. Am. Medical Informatics Assoc., 2022)

Transfer Learning for Mortality Prediction in Non-Small Cell Lung Cancer with Low-Resolution Histopathology Slide Snapshots. - Matthew Clark; Christopher Meyer; Jaime Ramos-Cejudo; Danne C. Elbers; Karen E. Pierce-Murray; Rafael Fricks; Gil Alterovitz; Luigi Rao; Mary T. Brophy; Nhan V. Do; Robert L. Grossman; Nathanael R. Fillmore (MedInfo, 2023)

Informing the ethical review of human subjects research utilizing artificial intelligence. - Christos A. Makridis; Anthony Boese; Rafael Fricks; Don E. Workman; Molly Klote; Joshua Mueller; Isabel J. Hildebrandt; Michael Kim; Gil Alterovitz (Frontiers Comput. Sci., 2023)

Predicting ward transfer mortality with machine learning. - José Lezama; Gil Alterovitz; Colleen E. Jakey; Ana L. Kraus; Michael J. Kim; Andrew A. Borkowski (Frontiers Artif. Intell., 2023)

Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration. - Robert H. Dolin; Bret S. E. Heale; Gil Alterovitz; Rohan Gupta; Justin Aronson; Aziz A. Boxwala; Shaileshbhai R. Gothi; David Haines; Arthur Hermann; Tonya Hongsermeier; Ammar Husami; James Jones; et al. (J. Am. Medical Informatics Assoc., 2023)

A General-purpose AI Avatar in Healthcare. - Nicholas Yan; Gil Alterovitz (CoRR, 2024)