Lorenzo Concia

Research Associate
Life Sciences Computing

Email: lconcia@tacc.utexas.edu

Lorenzo is a computational biologist with a background in experimental molecular biology. He uses multi-OMICS data to tackle the study of plant genomes under multiple aspects, including genomics, epigenomics, gene expression, and chromosome conformation. He has a specific interest in crops and in large and complex genomes, such as corn (Zea mays) and wheat (Triticum aestivum).

After earning a PhD in Genetics and Molecular Biology at the University of Pavia in Italy he worked at North Carolina State University, Université Paris-Saclay, and École Normale Supérieure in France. He joined TACC in 2023 as a Research Associate to work at the interface between genomics, epigenomics, and computational biology.

Current Projects

Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S, Probst AV, Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M. Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. Genome Res. 2021 Jun 3;31(7):1230–44. doi: 10.1101/gr.273771.120. Epub ahead of print. PMID: 34083408; PMCID: PMC8256866.

Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M, Ntoukakis V. Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog. 2021 May 20;17(5):e1009572. doi: 10.1371/journal.ppat.1009572. PMID: 34015058; PMCID: PMC8171942.

Juery C, Concia L, De Oliveira R, Papon N, Ramírez-González R, Benhamed M, Uauy C, Choulet F, Paux E. New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome. 2021 Mar;14(1):e20069. doi: 10.1002/tpg2.20069. Epub 2020 Nov 5. PMID: 33155760.

Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res. 2020 Jun 19;48(11):5953-5966. doi: 10.1093/nar/gkaa369. PMID: 32396165; PMCID: PMC7293002.

Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D, Benhamed M. Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol. 2020 Apr 29;21(1):104. doi: 10.1186/s13059-020-01998-1. PMID: 32349780; PMCID: PMC7189446.

Wheeler E, Brooks AM, Concia L, Vera DL, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass HW, Martienssen RA, Thompson WF, Hanley-Bowdoin L. Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. Plant Physiol. 2020 May;183(1):206-220. doi: 10.1104/pp.19.01520. Epub 2020 Mar 23. PMID: 32205451; PMCID: PMC7210620.

Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol. 2019 May 21;20(1):100. doi: 10.1186/s13059-019-1705-4. PMID: 31113491; PMCID: PMC6528313.

International Wheat Genome Sequencing Consortium (IWGSC). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018 Aug 17;361(6403):eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16. PMID: 30115783.

Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A; International Wheat Genome Sequencing Consortium; Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C. The transcriptional landscape of polyploid wheat. Science. 2018 Aug 17;361(6403):eaar6089. doi: 10.1126/science.aar6089. PMID: 30115782.

Concia L, Brooks AM, Wheeler E, Zynda GJ, Wear EE, LeBlanc C, Song J, Lee TJ, Pascuzzi PE, Martienssen RA, Vaughn MW, Thompson WF, Hanley-Bowdoin L. Genome-Wide Analysis of the Arabidopsis Replication Timing Program. Plant Physiol. 2018 Mar;176(3):2166-2185. doi: 10.1104/pp.17.01537. Epub 2018 Jan 4. PMID: 29301956; PMCID: PMC5841712.

Wear EE, Song J, Zynda GJ, LeBlanc C, Lee TJ, Mickelson-Young L, Concia L, Mulvaney P, Szymanski ES, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips. Plant Cell. 2017 Sep;29(9):2126-2149. doi: 10.1105/tpc.17.00037. Epub 2017 Aug 25. PMID: 28842533; PMCID: PMC5635974.

Zynda GJ, Song J, Concia L, Wear EE, Hanley-Bowdoin L, Thompson WF, Vaughn MW. Repliscan: a tool for classifying replication timing regions. BMC Bioinformatics. 2017 Aug 7;18(1):362. doi: 10.1186/s12859-017-1774-x. PMID: 28784090; PMCID: PMC5547489.

Wear EE, Concia L, Brooks AM, Markham EA, Lee TJ, Allen GC, Thompson WF, Hanley-Bowdoin L. Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry. Methods Mol Biol. 2016;1370:69-86. doi: 10.1007/978-1-4939-3142-2_6. PMID: 26659955.

Longoni P, Rodolfi M, Pantaleoni L, Doria E, Concia L, Picco AM, Cella R. Functional analysis of the degradation of cellulosic substrates by a Chaetomium globosum endophytic isolate. Appl Environ Microbiol. 2012 May;78(10):3693-705. doi: 10.1128/AEM.00124-12. Epub 2012 Mar 2. PMID: 22389369; PMCID: PMC3346360.

Cueva A, Concia L, Cella R. Molecular characterization of a Cyrtochilum loxense Somatic Embryogenesis Receptor-like Kinase (SERK) gene expressed during somatic embryogenesis. Plant Cell Rep. 2012 Jun;31(6):1129-39. doi: 10.1007/s00299-012-1236-x. Epub 2012 Feb 21. PMID: 22350407.

Amoroso A, Concia L, Maggio C, Raynaud C, Bergounioux C, Crespan E, Cella R, Maga G. Oxidative DNA damage bypass in Arabidopsis thaliana requires DNA polymerase λ and proliferating cell nuclear antigen 2. Plant Cell. 2011 Feb;23(2):806-22. doi: 10.1105/tpc.110.081455. Epub 2011 Feb 15. PMID: 21325140; PMCID: PMC3077771.

Areas of Research

  • Computation Biology
  • Analysis of multi-OMICS data