Dr Matteo Ferla

Postdoctoral Researcher

About Me

I am half English (Wessex) and half Italian (Sicily) and to make things more confusing I have lived in a few other places: New Hampshire, New Zealand (Dunedin, close to Rohan and Lothlórien) and Copenhagen. I collect hobbies of the nerdier kind: everything for me seems to turn into an intriguing experiment and in my free time, I sometimes code for fun, rewire the electrics in the house, 3D print something utterly useless and cursed or solder components for an equally useless and janky Raspberry-Pi–based sensor.

Research Interests

I am a computational biochemist working in drug design.

My loyalties lie with molecular thermodynamics, but I am starting to fall the allure of deep learning.

I am currently working on Fragmenstein, github.com/matteoferla/Fragmenstein, a tool that stitches molecules together and reanimates them in order to help assess follow up compounds in fragment-based drug discovery.

Previously, I have developed Michalenglo (michelanglo.sgc.ox.ac.uk/), a tool allowing the sharing of representations of 3D structures of protein with interactive annotations, and Venus (venus.cmd.ox.ac.uk/venus), a tool that combines different sources of information in order to determine what could be the effect of a missense variant beyond simple destabilisation.

For other projects of mine, visit my github: github.com/matteoferla

Additionally, I have a science blog (blog.matteoferla.com) ranging from technical tutorials to monographic discussions/rants.

Publications

Scala, M., Tomati, V., Ferla, M., Lena, M., Cohen, J., Fatemi, A., Brokamp, E., Bican, A., Phillips, J., Koziura, M., Nicouleau, M., Rio, M., Siquier, K., Boddaert, N., Musante, I., Tamburro, S., Baldassari, S., Iacomino, M., Scudieri, P., Undiagnosed Diseases Network, ., Rosenfeld, J., Bellus, G., Reed, S., Al Saif, H., Russo, R., Walsh, M., Cantagrel, V., Crunk, A., Gustincich, S., Ruggiero, S., Fitzgerald, M., Helbig, I., Striano, P., Severino, M., Salpietro, V., Pedemonte, N. and Zara, F. (2024) “De novo variants in DENND5B cause a neurodevelopmental disorder.”, American journal of human genetics, 111(3), pp. 529–543.

Ferla, M., Sánchez-García, R., Skyner, R., Gahbauer, S., Taylor, J., von Delft, F., Marsden, B. and Deane, C. (2024) “Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology”, ChemRxiv.

Maroofian, R., Kaiyrzhanov, R., Cali, E., Zamani, M., Zaki, M., Ferla, M., Tortora, D., Sadeghian, S., Saadi, S., Abdullah, U., Karimiani, E., Efthymiou, S., Yeşil, G., Alavi, S., Al Shamsi, A., Tajsharghi, H., Abdel-Hamid, M., Saadi, N., Al Mutairi, F., Alabdi, L., Beetz, C., Ali, Z., Toosi, M., Rudnik-Schöneborn, S., Babaei, M., Isohanni, P., Muhammad, J., Khan, S., Al Shalan, M., Hickey, S., Marom, D., Elhanan, E., Kurian, M., Marafi, D., Saberi, A., Hamid, M., Spaull, R., Meng, L., Lalani, S., Maqbool, S., Rahman, F., Seeger, J., Palculict, T., Lau, T., Murphy, D., Mencacci, N., Steindl, K., Begemann, A., Rauch, A., Akbas, S., Aslanger, A., Salpietro, V., Yousaf, H., Ben-Shachar, S., Ejeskär, K., Al Aqeel, A., High, F., Armstrong-Javors, A., Zahraei, S., Seifi, T., Zeighami, J., Shariati, G., Sedaghat, A., Asl, S., Shahrooei, M., Zifarelli, G., Burglen, L., Ravelli, C., Zschocke, J., Schatz, U., Ghavideldarestani, M., Kamel, W., Van Esch, H., Hackenberg, A., Taylor, J., Al-Gazali, L., Bauer, P., Gleeson, J., Alkuraya, F., Lupski, J., Galehdari, H., Azizimalamiri, R., Chung, W., Baig, S., Houlden, H. and Severino, M. (2023) “Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders.”, Brain : a journal of neurology, 146(12), pp. 5031–5043.

Boby, M., Fearon, D., Ferla, M., Filep, M., Koekemoer, L., Robinson, M., Chodera, J., Lee, A., London, N., von Delft, A., von Delft, F., Achdout, H., Aimon, A., Alonzi, D., Arbon, R., Aschenbrenner, J., Balcomb, B., Bar-David, E., Barr, H., Ben-Shmuel, A., Bennett, J., Bilenko, V., Borden, B. and Boulet, P. (2023) “Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors”, Science, 382(6671).

Pagnamenta, A., Camps, C., Giacopuzzi, E., Taylor, J., Hashim, M., Calpena, E., Kaisaki, P., Hashimoto, A., Yu, J., Sanders, E., Schwessinger, R., Hughes, J., Lunter, G., Dreau, H., Ferla, M., Lange, L., Kesim, Y., Ragoussis, V., Vavoulis, D., Allroggen, H., Ansorge, O., Babbs, C., Banka, S., Baños-Piñero, B. and Beeson, D. (2023) “Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases”, Genome Medicine, 15.

Pagnamenta, A., Belles, R., Salbert, B., Wentzensen, I., Guillen Sacoto, M., Santos, F., Caffo, A., Ferla, M., Banos-Pinero, B., Pawliczak, K., Makvand, M., Najmabadi, H., Genomics England Research Consortium, ., Maroofian, R., Lester, T., Yanez-Felix, A., Villarroel-Cortes, C., Xia, F., Al Fayez, K., Al Hashem, A., Shears, D., Irving, M., Offiah, A., Kariminejad, A. and Taylor, J. (2023) “The prevalence and phenotypic range associated with biallelic PKDCC variants.”, Clinical genetics, 104(1), pp. 121–126.

Gahbauer, S., Correy, G., Schuller, M., Ferla, M., Doruk, Y., Rachman, M., Wu, T., Diolaiti, M., Wang, S., Neitz, R., Fearon, D., Radchenko, D., Moroz, Y., Irwin, J., Renslo, A., Taylor, J., Gestwicki, J., von Delft, F., Ashworth, A., Ahel, I., Shoichet, B. and Fraser, J. (2023) “Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.”, Proceedings of the National Academy of Sciences of the United States of America, 120(2), p. e2212931120.

Cali, E., Suri, M., Scala, M., Ferla, M., Alavi, S., Faqeih, E., Bijlsma, E., Wigby, K., Baralle, D., Mehrjardi, M., Schwab, J., Platzer, K., Steindl, K., Hashem, M., Jones, M., Niyazov, D., Jacober, J., Littlejohn, R., Weis, D., Zadeh, N., Rodan, L., Goldenberg, A., Lecoquierre, F., Dutra-Clarke, M., Horvath, G., Young, D., Orenstein, N., Bawazeer, S., Vulto-van Silfhout, A., Herenger, Y., Dehghani, M., Seyedhassani, S., Bahreini, A., Nasab, M., Ercan-Sencicek, A., Firoozfar, Z., Movahedinia, M., Efthymiou, S., Striano, P., Karimiani, E., Salpietro, V., Taylor, J., Redman, M., Stegmann, A., Laner, A., Abdel-Salam, G., Li, M., Bengala, M., Müller, A., Digilio, M., Rauch, A., Gunel, M., Titheradge, H., Schweitzer, D., Kraus, A., Valenzuela, I., McLean, S., Phornphutkul, C., Salih, M., Begtrup, A., Schnur, R., Torti, E., Haack, T., Prada, C., Alkuraya, F., Houlden, H. and Maroofian, R. (2023) “Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature, obesity, and craniofacial and digital abnormalities.”, Genetics in medicine : official journal of the American College of Medical Genetics, 25(1), pp. 135–142.

Pagnamenta, A., Diaz-Gonzalez, F., Banos-Pinero, B., Ferla, M., Toosi, M., Calder, A., Karimiani, E., Doosti, M., Wainwright, A., Wordsworth, P., Bailey, K., Ejeskär, K., Lester, T., Maroofian, R., Heath, K., Tajsharghi, H., Shears, D., Taylor, J. and Genomics England Research Consortium, . (2022) “Variable skeletal phenotypes associated with biallelic variants in <i>PRKG2</i>.”, Journal of medical genetics, 59(10), pp. 947–950.

Gahbauer, S., Correy, G., Schuller, M., Ferla, M., Doruk, Y., Rachman, M., Wu, T., Diolaiti, M., Wang, S., Neitz, R., Fearon, D., Radchenko, D., Moroz, Y., Irwin, J., Renslo, A., Taylor, J., Gestwicki, J., von Delft, F., Ashworth, A., Ahel, I., Shoichet, B. and Fraser, J. (2022) “Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2.”, bioRxiv [Preprint].

Contact Details

Email: matteo.ferla@stats.ox.ac.uk

Office:

Research Groups

Oxford Protein Informatics Group