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--- research:publications [2023/01/06 10:47] – mikael
+++ research:publications [2024/04/12 09:30] (current) – mikael
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 ==== Pre-prints of note ====
-  - Balderson B, Piper M, Thor S and Bodén M. Cytocipher detects significantly different populations of cells in single cell RNA-seq data. [[https://www.biorxiv.org/content/10.1101/2022.08.12.503759v2|https://www.biorxiv.org/content/10.1101/2022.08.12.503759v2]]
   - Mora A, Schmidt C, Balderson B, Frezza C and Bodén M. SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer. [[https://www.biorxiv.org/content/10.1101/2022.07.02.498058v1|https://www.biorxiv.org/content/10.1101/2022.07.02.498058v1]]
-  - Sun Y, Shim W, Shen S, Sinniah E, Pham D, Su Z, Mizikovsky D, White MD, Ho JWK, Nguyen, Bodén M, Palpant NJ. Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. [[https://doi.org/10.1101/2022.10.12.512003|https://doi.org/10.1101/2022.10.12.512003]]
   - Shen S et al. An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution. [[https://doi.org/10.1101/2022.10.12.511862|https://doi.org/10.1101/2022.10.12.511862]]
 ==== Journal papers ====
-  - Afonso J et al. (2023) Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. //Biochemistry and Biophysics Reports//. [[https://doi.org/10.1016/j.bbrep.2023.101420|10.1016/j.bbrep.2023.101420]]
+  - Tule S, Foley G, Zhao C, Forbes M and Bodén M. (Accepted) Optimal Phylogenetic Reconstruction of Insertion and Deletion Events. //Bioinformatics/ISMB 2024 Proceedings//. DOI [[https://doi.org/10.1093/bioinformatics/btae254|10.1093/bioinformatics/btae254]] [[https://doi.org/10.1101/2024.01.24.577130|Pre-print]]
-  - Bayaraa T et al. (2022) Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus. //Chemistry - A European Journal//. [[https://doi.org/10.1002/chem.202203140|10.1002/chem.202203140]]
+  - Balderson B, Fane M, Harvey TJ, Piper M, Smith A and Bodén M. (2024) Systematic analysis of the Transcriptional Landscape of Melanoma Reveals Drug-target Expression Plasticity. //Briefings in Functional Genomics//. DOI [[https://doi.org/10.1093/bfgp/elad055|10.1093/bfgp/elad055]]
-  - Foley G, Mora A, Ross CM, Bottoms S, Sützl L, Lamprecht ML, Zaugg J, Essebier A, Balderson B, Newell R, Thomson RES, Kobe B, Barnard RT, Guddat L, Schenk G, Carsten J, Gumulya Y, Rost B, Haltrich D, Sieber V, Gillam EMJ and Bodén M. (2022) Identifying and engineering ancient variants of enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). //PLoS Comput Biol//. 18(10): e1010633. DOI [[https://doi.org/10.1371/journal.pcbi.1010633|10.1371/journal.pcbi.1010633]][[https://biorxiv.org/cgi/content/short/2019.12.30.891457v2|Pre-print]]
+  - Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G and Sieber V (2023) Development of a Highly Selective NAD+-Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. //ChemSusChem// DOI [[https://doi.org/10.1002/cssc.202301132|10.1002/cssc.202301132]]
+  - Balderson B, Piper M, Thor S and Bodén M. (2023) Cytocipher detects significantly different populations of cells in single cell RNA-seq data. //Bioinformatics//. 39(7):btad435. DOI [[https://doi.org/10.1093/bioinformatics/btad435|10.1093/bioinformatics/btad435]][[https://www.biorxiv.org/content/10.1101/2022.08.12.503759v2|biorxiv]]
+  - Sun Y, Shim W, Shen S, Sinniah E, Pham D, Su Z, Mizikovsky D, White MD, Ho JWK, Nguyen Q, Bodén M, Palpant NJ. (2023) Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. //Nucleic Acids Research//. DOI [[https://doi.org/10.1093/nar/gkad307|10.1093/nar/gkad307]]
+  - Afonso J et al. (2023) Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. //Biochemistry and Biophysics Reports//. DOI [[https://doi.org/10.1016/j.bbrep.2023.101420|10.1016/j.bbrep.2023.101420]]
+  - Bayaraa T et al. (2022) Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus. //Chemistry - A European Journal//. DOI [[https://doi.org/10.1002/chem.202203140|10.1002/chem.202203140]]
+  - Foley G, Mora A, Ross CM, Bottoms S, Sützl L, Lamprecht ML, Zaugg J, Essebier A, Balderson B, Newell R, Thomson RES, Kobe B, Barnard RT, Guddat L, Schenk G, Carsten J, Gumulya Y, Rost B, Haltrich D, Sieber V, Gillam EMJ and Bodén M. (2022) Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). //PLoS Comput Biol//. 18(10): e1010633. DOI [[https://doi.org/10.1371/journal.pcbi.1010633|10.1371/journal.pcbi.1010633]][[https://biorxiv.org/cgi/content/short/2019.12.30.891457v2|Pre-print]]
   - Lv Y, Zheng S, Goldenzweig A, Liu F, Gao Y, Yang X, Kandale A, McGeary RP, Williams S, Kobe B, Schembri MA, Landsberg MJ, Wu B, Brück TB, Sieber V, Bodén M, Rao Z, Fleishman SJ, Schenk G and Guddat LW. (2022) Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals. //Applied Biosciences//. 1(2):163-178. DOI [[https://doi.org/10.3390/applbiosci1020011|10.3390/applbiosci1020011]]
   - Harris KL, Thomson RES et al. (2022) Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defence reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. //Molecular Biology and Evolution//. DOI [[https://doi.org/10.1093/molbev/msac116|10.1093/molbev/msac116]]