All Publications

  • Broadening Participation: 21st Century Opportunities for Amateurs in Biology Research. Integrative and comparative biology de Lange, O., Youngflesh, C., Ibarra, A., Perez, R., Kaplan, M. 2021


    The modern field of biology has its roots in the curiosity and skill of amateur researchers and has never been purely the domain of professionals. Today, professionals and amateurs contribute to biology research, working both together and independently. Well-targeted and holistic investment in amateur biology research could bring a range of benefits that, in addition to positive societal benefits, may help to address the considerable challenges facing our planet in the 21st century. We highlight how recent advances in amateur biology have been facilitated by innovations in digital infrastructure as well as the development of community biology laboratories, launched over the last decade, and we provide recommendations for how individuals can support the integration of amateurs into biology research. The benefits of investment in amateur biology research could be many-fold, however without a clear consideration of equity, efforts to promote amateur biology could exacerbate structural inequalities around access to and benefits from STEM. The future of the field of biology relies on integrating a diversity of perspectives and approaches-amateur biology researchers have an important role to play.

    View details for DOI 10.1093/icb/icab180

    View details for PubMedID 34427632

  • Growing a circular economy with fungal biotechnology: a white paper. Fungal biology and biotechnology Meyer, V., Basenko, E. Y., Benz, J. P., Braus, G. H., Caddick, M. X., Csukai, M., de Vries, R. P., Endy, D., Frisvad, J. C., Gunde-Cimerman, N., Haarmann, T., Hadar, Y., Hansen, K., Johnson, R. I., Keller, N. P., Krasevec, N., Mortensen, U. H., Perez, R., Ram, A. F., Record, E., Ross, P., Shapaval, V., Steiniger, C., van den Brink, H., van Munster, J., Yarden, O., Wosten, H. A. 2020; 7: 5


    Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation's sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.

    View details for DOI 10.1186/s40694-020-00095-z

    View details for PubMedID 32280481

  • Enabling community-based metrology for wood-degrading fungi. Fungal biology and biotechnology Perez, R., Luccioni, M., Kamakaka, R., Clamons, S., Gaut, N., Stirling, F., Adamala, K. P., Silver, P. A., Endy, D. 2020; 7: 2


    Background: Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings.Results: We show that a widely-available and globally-regularized consumer product (Pringles) can support the growth of wood-degrading fungi, and that growth on Pringles-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to~75%.Conclusions: Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi.

    View details for DOI 10.1186/s40694-020-00092-2

    View details for PubMedID 32206323

  • Profile-QSAR 2.0: Kinase Virtual Screening Accuracy Comparable to Four-Concentration IC(50)s for Realistically Novel Compounds JOURNAL OF CHEMICAL INFORMATION AND MODELING Martin, E. J., Polyakov, V. R., Tian, L., Perez, R. C. 2017; 57 (8): 2077–88


    While conventional random forest regression (RFR) virtual screening models appear to have excellent accuracy on random held-out test sets, they prove lacking in actual practice. Analysis of 18 historical virtual screens showed that random test sets are far more similar to their training sets than are the compounds project teams actually order. A new, cluster-based "realistic" training/test set split, which mirrors the chemical novelty of real-life virtual screens, recapitulates the poor predictive power of RFR models in real projects. The original Profile-QSAR (pQSAR) method greatly broadened the domain of applicability over conventional models by using as independent variables a profile of activity predictions from all historical assays in a large protein family. However, the accuracy still fell short of experiment on realistic test sets. The improved "pQSAR 2.0" method replaces probabilities of activity from naïve Bayes categorical models at several thresholds with predicted IC50s from RFR models. Unexpectedly, the high accuracy also requires removing the RFR model for the actual assay of interest from the independent variable profile. With these improvements, pQSAR 2.0 activity predictions are now statistically comparable to medium-throughput four-concentration IC50 measurements even on the realistic test set. Beyond the yes/no activity predictions from a typical high-throughput screen (HTS) or conventional virtual screen, these semiquantitative IC50 predictions allow for predicted potency, ligand efficiency, lipophilic efficiency, and selectivity against antitargets, greatly facilitating hitlist triaging and enabling virtual screening panels such as toxicity panels and overall promiscuity predictions.

    View details for DOI 10.1021/acs.jcim.7b00166

    View details for Web of Science ID 000408790100032

    View details for PubMedID 28651433

  • Metal-organic hybrid resonant terahertz absorbers with SU-8 photoresist dielectric layer JOURNAL OF MICRO-NANOLITHOGRAPHY MEMS AND MOEMS Grbovic, D., Alves, F., Kearney, B., Waxer, B., Perez, R., Omictin, G. 2013; 12 (4)