Alvis Brazma
Senior Team Leader and Senior Scientist
brazma [at] ebi.ac.uk
ORCID: 0000-0001-5988-7409
EditBrazma Group
Senior Team Leader and Senior Scientist
brazma [at] ebi.ac.uk
ORCID: 0000-0001-5988-7409
EditMy group has been involved in bioinformatics research since the early days of this discipline. We started with applications of ML to biological sequence and microarray data analysis, in particular developing and applying algorithms to find patterns in groups of genomics sequences. Over the years our interests have ranged from gene expression data analysis, to gene regulation network analysis, to broader functional genomics and cancer. Twelve EMBL PhD students are alumni of Brazma group, and we have published over 200 scientific papers on a wider range of subjects, from computer science to biology and linking the two, jointly cited over 50,000 times. See here for our Research Vision.
For the last few years, I have been working on a popular science book, Living Computers – Replicators, Information Processing, and the Evolution of Life. The book explores the fundamental connections between life and information and how they emerged inextricably linked, taking the reader on a journey through all the major evolutionary transitions. We do not know what the first carriers of information were when life had just emerged, but for the last few billions of years, the most important information storage medium on Earth has been DNA. Evolution processes the information recorded in the entire collection of DNA on Earth using the algorithm of Darwinian selection of the fittest. Once life had emerged and started evolving (phase 1), the information in DNA was accumulating, at least for a while. One can say that evolution was learning from interactions with the environment, recording the useful bits of information in its genomes. A few hundred thousand years ago, quite recently on the evolutionary timescale, human language emerged and a major transition began; for the first time, large amounts of information began accumulating outside DNA. Moreover, language triggered evolutionary mechanisms different from and faster than biological evolution, namely cultural evolution; the emergence of human language was a transition as remarkable as the emergence of life itself (phase 2). Nevertheless, at least at our current state of evolution, the information in DNA is indispensable; if the DNA existing on Earth were to become too corrupted, all cultural information and life itself would swiftly disappear. But must life be like this? Or can future civilizations, possibly in thousands or millions of years colonizing planets of distant galaxies, be based on entirely different principles? Can there be another major transition (to phase 3) in which DNA becomes less central? And where will life go after the Solar system ceases to exist?
Selected publications
Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive – Building a Home for Life-Sciences Microscopy Data. J Mol Biol. 2022 Jun 15;434(11):167505.
Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nat Methods. 2021 Dec;18(12):1418-1422.
Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A. From ArrayExpress to BioStudies. (2021) Nucleic Acids Research 49 (D1), D1502-D1506.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F; Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Transparency and reproducibility in artificial intelligence. Nature. 2020 Oct;586(7829):E14-E16.
Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Antonio Vizcaíno J, Choudhary JS, Brazma A, Viksna J. Using Deep Learning to Extrapolate Protein Expression Measurements. Proteomics. 2020 Nov;20(21-22):e2000009.
Miao, Z., Moreno, P.,Huang, N., Papatheodorou, I., Brazma, A., Teichmann, S. Putative cell type discovery from single cell gene expression data. (2020) Nature Methods, 2020 Jun;17(6):621-628.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A*, Brooks AN*, Göke J, Rätsch G*, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. Genomic basis for RNA alterations in cancer. (2020) Nature. 578(7793):129-136. (*- corresponding authors).
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. (2020) Nature. 578(7793):82-93.
Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A. Expression Atlas update: from tissues to single cells. (2020) Nucleic Acids Res. 48(D1):D77-D83.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. ArrayExpress update – from bulk to single-cell expression data. Nucleic Acids Res. 2018 Oct.
Scelo, G: … Brazma, A; Lathrop, G M. Variation in genomic landscape of clear cell renal cell carcinoma across Europe. (2014) Nature Communications, 5:5135.
Gonzàlez-Porta, Mar; Frankish, Adam; Rung, Johan; Harrow, Jennifer; Brazma, A (2013) Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol 14:R70
International Cancer Genome Consortium; Hudson, Thomas J et al, International network of cancer genome projects. (2010) Nature464:993-998
Lukk, M; Kapushesky, M; Nikkilä, J; Parkinson, H; Goncalves, A; Huber, W; Ukkonen, E; Brazma, A. (2010) A global map of human gene expression. Nature Biotechnology, 28:322-324
Schlitt, T; Brazma, A (2006) Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci 361:483-494
Rustici, G; Mata, J; Kivinen, K; Lió, P; Penkett, C J; Burns, G; Hayles, J; Brazma, A; Nurse, P; Bähler, J. (2004) Periodic gene expression program of the fission yeast cell cycle. Nature Genetics 36:809-817
Ball, C A; Sherlock, G., Brazma, A; Quackenbush, J; (2002) Standards for microarray data. Science, 298:539
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365-71.
Brazma, A; Robinson, A; Cameron, G; Ashburner, A; (2000) One stop shop for Microarray Data. Nature, 403, 699-700
A. Brazma, I. Jonassen, J.Vilo, E. Ukkonen. Predicting gene regulatory elements in Silico on a genomic scale. Genome Research, Vol. 8, Issue 11, 1202-1215, November 1998
Brazma, A; Jonassen, I; Vilo, J; and Ukkonen, E; (1998) Pattern discovery in biosequences. In Proceedings of Fourth International Colloquium on Grammatical Inference (ICGI-98), Honovar and Slutzki (Eds.), volume 1433 of Lecture Notes in Computer Science, 255–270.
Brazma, A; I. Jonassen, I; Ukkonen, E; Vilo J; (1996) Discovering patterns and subfamilies in biosequences. In Proc. of 4th International Conference Intelligent Systems for Molecular Biology ISMB’96, AAAI Press, p.34-43.
Barzdin, J; Brazma, A; Kinber, J. (1990) Models of inductive syntactical synthesis, in Machine Intelligence. Vol 12, Oxford University Press, 139-148