Differences

This shows you the differences between two versions of the page.

--- research:publications [2022/11/18 12:28] – mikael
+++ research:publications [2024/04/12 09:30] (current) – mikael
@@ Line 1: / Line 1: @@
 ==== 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]]
+  - 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 ====
-  - Bayaraa T, et al. 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]]
+  - 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]]
-  - 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, Bodén M. 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]]
+  - 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]]
-  - 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, Boden M, Rao Z, Fleishman SJ, Schenk G, 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]]
+  - 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]]
-  - 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]]
+  - 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]]
   - Mora A, Rakar J, Monedero-Cobeta I, Yaghmaeian-Salmani B, Starkenberg A, Thor S, Bodén M. (2022) Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2. //Nucleic Acids Research//. 50(3):1280–1296. DOI [[https://doi.org/10.1093/nar/gkac006|10.1093/nar/gkac006]] [[https://doi.org/10.1101/2021.06.22.449386|Pre-print in bioRxiv]]
   - Yaghmaeian-Salmani B, Balderson B, Bauer S, Ekman H, Starkenberg A, Perlmann T, Piper M, Bodén M, Thor S. (2022) Selective Requirement for Polycomb Repressor Complex 2 in the Generation of Specific Hypothalamic Neuronal Sub-types. //Development//. 149(5):dev200076. DOI [[https://doi.org/10.1242/dev.200076|10.1242/dev.200076]] [[https://www.biorxiv.org/content/10.1101/2021.07.28.454060v1|Pre-print in bioRxiv]]
-  - Ross CM, Foley G, Bodén M, Gillam EMJ. (2021) Using the Evolutionary History of Proteins to Engineer Insertion-Deletion Mutants from Robust, Ancestral Templates Using Graphical Representation of Ancestral Sequence Predictions (GRASP). //Methods Molecular Biology//. 2397:85-110. DOI [[https://doi.org/10.1007/978-1-0716-1826-4_6|10.1007/978-1-0716-1826-4_6]].
+  - Ross CM, Foley G, Bodén M, Gillam EMJ. (2022) Using the Evolutionary History of Proteins to Engineer Insertion-Deletion Mutants from Robust, Ancestral Templates Using Graphical Representation of Ancestral Sequence Predictions (GRASP). //Methods Molecular Biology//. 2397:85-110. DOI [[https://doi.org/10.1007/978-1-0716-1826-4_6|10.1007/978-1-0716-1826-4_6]].
   - Wilson L et al. (2021) Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active Site Glutamic Acid. //Antimicrobial Agents and Chemotherapy//. 65(10):e0093621. DOI [[https://doi.org/10.1128/AAC.00936-21|10.1128/AAC.00936-21]].
   - Kojic M et al. (2021) Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. // Nature Communications//. 12:2678. DOI [[https://doi.org/10.1038/s41467-021-22888-5|10.1038/s41467-021-22888-5]]
@@ Line 36: / Line 42: @@
   - Williams SJ, Yin L, Foley G, Casey LW, Outram MA, Ericsson DJ, Lu J, Bodén M, Dry I and Kobe B (2016) Structure and function of the TIR domain from the grape NLR protein RPV1. //Frontiers in Plant Science//. DOI: [[http://dx.doi.org/10.3389/fpls.2016.01850|10.3389/fpls.2016.01850]]
   - Fraser J, Essebier A, Gronostajski RM, Bodén M, Wainwright BJ, Harvey TJ and Piper M (2016) Cell type-specific expression of NFIX in the developing and adult cerebellum. //Brain Structure and Function//. 222:5, pp 2251–2270. DOI: [[http://dx.doi.org/10.1007/s00429-016-1340-8|10.1007/s00429-016-1340-8]]
-  - Harris L, Zalucki O, Gobius I, Osinski J, Harvey T, Essebier A, Vidovic D, GladwynNg I, McDonald H, Burne T, Heng J, Richards L, Gronostajski R and Piper M (2016) Transcriptional regulation of intermediate progenitor cell generation during hippocampal development. //Development//. 143: 4620-4630; DOI: [[http://dx.doi.org/10.1242/dev.140681|10.1242/dev.140681]]
   - Patrick R, Horin C, Kobe B, Le Cao KA and Bodén M (2016) Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence. BBA - //Proteins and Proteomics//. 1864(11):1599-608. DOI:[[http://dx.doi.org/10.1016/j.bbapap.2016.08.001|10.1016/j.bbapap.2016.08.001]].
   - Essebier A, Vera Wolf P, Cao MD, Carroll BJ, Balasubramanian S and Bodén M (2016) Statistical enrichment of epigenetic states around triplet repeats that undergo expansions. //Frontiers in Neuroscience//. 10:92. DOI: [[http://dx.doi.org/10.3389/fnins.2016.00092|10.3389/fnins.2016.00092]] (Open access)