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Hire Dr. Francesco V.

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Using data, machine learning, and genomics to understand how the human immune system works in disease and aging

Profile Summary

I am a systems immunologist with 20 years of experience as a biomedical researcher in the fields of systems biology, single-cell'omics, and human immunology. I am interested in applying systems approaches to reveal changes in the human immune system in disease and and direct it to achieve better clinical outcomes. My research merges techniques from machine learning and statistical modeling with human immunology and high-throughput multi'omics profiling.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Molecular Biology
• ☆ Omics
• ☆ Basic Immunology
• ☆ Data Analysis
• ☆ Machine Learning
• ☆ Artificial Intelligence
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Python
• ☆ R
• ☆ Drug Development
• ☆ In vitro Diagnostics
• ☆ In vitro Diagnostic Design
• ☆ Biomarker Analysis
• ☆ Clinical Immunology
• ☆ Human Biology
• ☆ Immunotherapy
• ☆ Inflammation
• ☆ Cancer Research

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Data Mining, Data Insights

Work Experience

Group Leader (Manager/Staff Scientist)

Freenome (United States)

February 2019 - May 2023

Postdoctoral Fellow

Stanford University

March 2014 - February 2019

Education

PhD (Computational and Systems Biology)

Washington University in Saint Louis

August 2007 - December 2013

Certifications

• Certification details not provided.

Publications

OTHER

Zhao, X., Yan, X., Contrepois, K., Vallania, F., Ellenberger, M., Kashiwagi, C.M., Gagnon, S.D., Siebrand, C.J., Cabruja, M., Traber, G.M., et al.(2022). Lipidomic profiling reveals age-dependent changes in complex plasma membrane lipids that regulate neural stem cell aging . bioRxiv.

Vallania, F., Zisman, L., Macaubas, C., Hung, S.-C., Rajasekaran, N., Mason, S., Graf, J., Nakamura, M., Mellins, E.D., Khatri, P.(2020). Multicohort Analysis of Publicly-available Monocyte Expression Data Identifies Gene Signatures to Accurately Monitor Subset-specific Changes in Human Diseases . bioRxiv.

Vallania, F., Tam, A., Lofgren, S., Schaffert, S., Azad, T.D., Bongen, E., Alsup, M., Alonso, M., Davis, M., Engleman, E., et al.(2017). Leveraging heterogeneity across multiple data sets increases accuracy of cell-mixture deconvolution and reduces biological and technical biases . bioRxiv.

Haynes, W.A., Vashisht, R., Vallania, F., Liu, C., Gaskin, G.L., Bongen, E., Lofgren, S., Sweeney, T.E., Utz, P.J., Shah, N.H., et al.(2017). Integrated molecular, clinical, and ontological analysis identifies overlooked disease relationships . bioRxiv.

Tomczak, A., Mortensen, J.M., Winnenburg, R., Liu, C., Alessi, D.T., Swamy, V., Vallania, F., Lofgren, S., Haynes, W., Shah, N.H., et al.(2017). Interpretation of biological experiments changes with evolution of Gene Ontology and its annotations . bioRxiv.

JOURNAL ARTICLE

Lopez Angel, C.J., Pham, E.A., Du, H., Vallania, F., Fram, B.J., Perez, K., Nguyen, T., Rosenberg-Hasson, Y., Ahmed, A., Dekker, C.L., et al.(2021). Signatures of immune dysfunction in HIV and HCV infection share features with chronic inflammation in aging and persist after viral reduction or elimination . Proceedings of the National Academy of Sciences of the United States of America. 118. (14).

Vallania, F., Zisman, L., Macaubas, C., Hung, S.-C., Rajasekaran, N., Mason, S., Graf, J., Nakamura, M., Mellins, E.D., Khatri, P.(2021). Multicohort Analysis Identifies Monocyte Gene Signatures to Accurately Monitor Subset-Specific Changes in Human Diseases . Frontiers in Immunology. 12.

Francesco Vallania, Diederik E. van der Feen, Guido P. L. Bossers, Quint A. J. Hagdorn, Jan-Renier Moonen, Kondababu Kurakula, Robert Szulcek, James Chappell, Michele Donato, Klaas Kok, et al. (2020). Cellular senescence impairs the reversibility of pulmonary arterial hypertension . Science Translational Medicine.

Van Der Feen, D.E., Bossers, G.P.L., Hagdorn, Q.A.J., Moonen, J.-R., Kurakula, K., Szulcek, R., Chappell, J., Vallania, F., Donato, M., Kok, K., et al.(2020). Cellular senescence impairs the reversibility of pulmonary arterial hypertension . Science Translational Medicine. 12. (554).

Robinson, M., Sweeney, T.E., Barouch-Bentov, R., Sahoo, M.K., Kalesinskas, L., Vallania, F., Sanz, A.M., Ortiz-Lasso, E., Albornoz, L.L., Rosso, F., et al.(2019). A 20-Gene Set Predictive of Progression to Severe Dengue . Cell Reports. 26. (5). p. 1104-1111.e4.

Gaujoux, R., Starosvetsky, E., Maimon, N., Vallania, F., Bar-Yoseph, H., Pressman, S., Weisshof, R., Goren, I., Rabinowitz, K., Waterman, M., et al.(2019). Cell-centred meta-Analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD . Gut. 68. (4). p. 604-614.

Scott, M.K.D., Quinn, K., Li, Q., Carroll, R., Warsinske, H., Vallania, F., Chen, S., Carns, M.A., Aren, K., Sun, J., et al.(2019). Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study . The Lancet Respiratory Medicine. 7. (6). p. 497-508.

Francesco Vallania, Andrew Tam, Shane Lofgren, Steven Schaffert, Tej D. Azad, Erika Bongen, Winston Haynes, Meia Alsup, Michael Alonso, Mark Davis, et al. (2018). Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases . Nature Communications.

Francesco Vallania, Peggie Cheung, Mai Dvorak, Sarah E. Chang, Steven Schaffert, Michele Donato, Aditya M. Rao, Rong Mao, Paul J. Utz, Purvesh Khatri, et al. (2018). Single-cell epigenetics – Chromatin modification atlas unveiled by mass cytometry . Clinical Immunology.

Francesco Vallania, Aurelie Tomczak, Jonathan M. Mortensen, Rainer Winnenburg, Charles Liu, Dominique T. Alessi, Varsha Swamy, Shane Lofgren, Winston Haynes, Nigam H. Shah, et al. (2018). Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations . Scientific Reports.

Tomczak, A., Mortensen, J.M., Winnenburg, R., Liu, C., Alessi, D.T., Swamy, V., Vallania, F., Lofgren, S., Haynes, W., Shah, N.H., et al.(2018). Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations . Scientific Reports. 8. (1).

Bongen, E., Vallania, F., Utz, P.J., Khatri, P.(2018). KLRD1-expressing natural killer cells predict influenza susceptibility . Genome Medicine. 10. (1).

Cheung, P., Vallania, F., Warsinske, H.C., Donato, M., Schaffert, S., Chang, S.E., Dvorak, M., Dekker, C.L., Davis, M.M., Utz, P.J., et al.(2018). Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging . Cell. 173. (6). p. 1385-1397.e14.

Cheung, P., Vallania, F., Dvorak, M., Chang, S.E., Schaffert, S., Donato, M., Rao, A.M., Mao, R., Utz, P.J., Khatri, P., et al.(2018). Single-cell epigenetics – Chromatin modification atlas unveiled by mass cytometry . Clinical Immunology. 196. p. 40-48.

Vallania, F., Tam, A., Lofgren, S., Schaffert, S., Azad, T.D., Bongen, E., Haynes, W., Alsup, M., Alonso, M., Davis, M., et al.(2018). Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases . Nature Communications. 9. (1).

Roy Chowdhury, R., Vallania, F., Yang, Q., Lopez Angel, C.J., Darboe, F., Penn-Nicholson, A., Rozot, V., Nemes, E., Malherbe, S.T., Ronacher, K., et al.(2018). Erratum to: A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes (Nature, (2018), 560, 7720, (644-648), 10.1038/s41586-018-0439-x) . Nature. 564. (7734). p. E5.

Roy Chowdhury, R., Vallania, F., Yang, Q., Lopez Angel, C.J., Darboe, F., Penn-Nicholson, A., Rozot, V., Nemes, E., Malherbe, S.T., Ronacher, K., et al.(2018). A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes . Nature. 560. (7720). p. 644-648.

Sweeney, T.E., Haynes, W.A., Vallania, F., Ioannidis, J.P., Khatri, P.(2017). Methods to increase reproducibility in differential gene expression via meta-analysis . Nucleic Acids Research. 45. (1).

Avey, S., Cheung, F., Fermin, D., Frelinger, J., Gaujoux, R., Gottardo, R., Khatri, P., Kleinstein, S.H., Kotliarov, Y., Meng, H., et al.(2017). Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses . Science Immunology. 2. (14).

Jain, S., Noordam, M.J., Hoshi, M., Vallania, F.L., Conrad, D.F.(2014). Validating single-cell genomics for the study of renal development . Kidney International. 86. (5). p. 1049-1055.

Spencer, D.H., Tyagi, M., Vallania, F., Bredemeyer, A.J., Pfeifer, J.D., Mitra, R.D., Duncavage, E.J.(2014). Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data . Journal of Molecular Diagnostics. 16. (1). p. 75-88.

Vallania, F.L.M., Sherman, M., Goodwin, Z., Mogno, I., Cohen, B.A., Mitra, R.D.(2014). Origin and consequences of the relationship between protein mean and variance . PLoS ONE. 9. (7).

Cruchaga, C., Chakraverty, S., Mayo, K., Vallania, F.L.M., Mitra, R.D., Faber, K., Williamson, J., Bird, T., Diaz-Arrastia, R., Foroud, T.M., et al.(2012). Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families . PLoS ONE. 7. (2).

Vallania, F., Ramos, E., Cresci, S., Mitra, R.D., Druley, T.E.(2012). Detection of rare genomic variants from pooled sequencing using SPLINTER . Journal of Visualized Experiments. (64). p. 1-9.

Ramos, E., Levinson, B.T., Chasnoff, S., Hughes, A., Young, A.L., Thornton, K., Li, A., Vallania, F.L.M., Province, M., Druley, T.E.(2012). Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing . BMC Genomics. 13. (1).

Haller, G., Druley, T., Vallania, F.L., Mitra, R.D., Li, P., Akk, G., Steinbach, J.H., Breslau, N., Johnson, E., Hatsukami, D., et al.(2012). Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence . Human Molecular Genetics. 21. (3). p. 647-655.

Matkovich, S.J., Van Booven, D.J., Hindes, A., Kang, M.Y., Druley, T.E., Vallania, F.L.M., Mitra, R.D., Reilly, M.P., Cappola, T.P., Dorn II, G.W.(2010). Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease . Journal of Clinical Investigation. 120. (1). p. 280-289.

Vallania, F.L.M., Druley, T.E., Ramos, E., Wang, J., Borecki, I., Province, M., Mitra, R.D.(2010). High-throughput discovery of rare insertions and deletions in large cohorts . Genome Research. 20. (12). p. 1711-1718.

Mogno, I., Vallania, F., Mitra, R.D., Cohen, B.A.(2010). TATA is a modular component of synthetic promoters . Genome Research. 20. (10). p. 1391-1397.

Schiavone, D., Dewilde, S., Vallania, F., Turkson, J., Di Cunto, F., Poli, V.(2009). The RhoU/Wrch1 Rho GTPase gene is a common transcriptional target of both the gp130/STAT3 and Wnt-1 pathways . Biochemical Journal. 421. (2). p. 283-292.

Vallania, F., Schiavone, D., Dewilde, S., Pupo, E., Garbay, S., Calogero, R., Pontoglio, M., Provero, P., Poli, V.(2009). Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3 . Proceedings of the National Academy of Sciences of the United States of America. 106. (13). p. 5117-5122.

Druley, T.E., Vallania, F.L.M., Wegner, D.J., Varley, K.E., Knowles, O.L., Bonds, J.A., Robison, S.W., Doniger, S.W., Hamvas, A., Cole, F.S., et al.(2009). Quantification of rare allelic variants from pooled genomic DNA . Nature Methods. 6. (4). p. 263-265.

PREPRINT

Francesco Vallania, Liron Zisman, Claudia Macaubas, Shu-Chen Hung, Narendiran Rajasekaran, Sonia Mason, Jonathan Graf, Mary Nakamura, Elizabeth D Mellins, Purvesh Khatri (2020). Multicohort Analysis of Publicly-available Monocyte Expression Data Identifies Gene Signatures to Accurately Monitor Subset-specific Changes in Human Diseases .

CONFERENCE PAPER

Scott, M., Vallania, F., Khatri, P.(2017). Meta-analysis of continuous phenotypes identifies a gene signature that correlates with COPD disease status . Pacific Symposium on Biocomputing. 0. (212679). p. 266-275.

Haynes, W.A., Vallania, F., Liu, C., Bongen, E., Tomczak, A., Andres-Terrè, M., Lofgren, S., Tam, A., Deisseroth, C.A., Li, M.D., et al.(2017). Empowering multi-cohort gene expression analysis to increase reproducibility . Pacific Symposium on Biocomputing. 0. (212679). p. 144-153.

Haynes, W.A., Vallania, F., Khatri, P.(2017). Complementing single-cell RNA-seq using bulk transcriptional profiles . Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. 2017-January. p. 1446-1450.