Gagnon_Tahiri : New updates

papers/Gagnon_Kebe_Tahiri/mybib.bib

@@ -1,4 +1,4 @@
- @article{cheviron_genomic_2012,
+@article{cheviron_genomic_2012,
 	title = {Genomic insights into adaptation to high-altitude environments},
 	volume = {108},
 	issn = {1365-2540},
@@ -10,18 +10,6 @@ @article{cheviron_genomic_2012
 	note = {Publisher: Nature Publishing Group},
 	pages = {354--361},
 }
-@article{manel_perspectives_2010,
-	title = {Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field},
-	volume = {19},
-	issn = {0962-1083},
-	number = {17},
-	journal = {Molecular Ecology},
-	author = {Manel, Stéphanie and Joost, Stéphane and Epperson, Bryan K and Holderegger, Rolf and Storfer, Andrew and Rosenberg, Michael S and Scribner, Kim T and Bonin, Aurélie and FORTIN, MARIE‐JOSÉE},
-	year = {2010},
-	doi = {10.1111/j.1365-294X.2010.04717.x},
-	note = {Publisher: Wiley Online Library},
-	pages = {3760--3772},
-}
 @article{balkenhol_landscape_2019,
 	title = {Landscape genomics: understanding relationships between environmental heterogeneity and genomic characteristics of populations},
 	issn = {3030045870},
@@ -175,12 +163,13 @@ @article{uhlir_adding_2021
 	note = {Publisher: PeerJ Inc.},
 	pages = {e12379},
 }
-@book{koshkarov_phylogeography_2022,
-	title = {Phylogeography: {Analysis} of genetic and climatic data of {SARS}-{CoV}-2},
-	shorttitle = {Phylogeography},
-	author = {Koshkarov, Aleksandr and Li, Wanlin and Luu, My-Linh and Tahiri, Nadia},
-	year = {2022},
-	doi = {10.25080/majora-212e5952-018},
+@inproceedings{koshkarov2022phylogeography,
+  title={Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2},
+  author={Koshkarov, Aleksandr and Li, Wanlin and Luu, My-Linh and Tahiri, Nadia},
+  booktitle={SciPy},
+  pages={159--166},
+  year={2022},
+  doi={10.25080/majora-212e5952-030}
 }
 @article{meisner_benthic_2014,
 	title = {Benthic habitats around {Iceland} investigated during the {IceAGE} expeditions},
@@ -220,15 +209,6 @@ @article{balkenhol_identifying_2009
 	pages = {455--463},
 	doi = {10.1007/s10980-009-9334-z},
 }
-@article{rogers2007corals,
-	title={Corals on seamounts},
-	author={Rogers, Alex D and Baco, Amy and Griffiths, Huw and Hart, Thomas and Hall-Spencer, Jason M},
-	journal={Seamounts: ecology, fisheries \& conservation},
-	pages={141--169},
-	year={2007},
-	publisher={Wiley Online Library},
-	doi = {10.1002/9780470691953.ch8},
-}
 @article{colosimo_widespread_2005,
 	title = {Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles},
 	volume = {307},
@@ -241,15 +221,6 @@ @article{colosimo_widespread_2005
 	pages = {1928--1933},
 	doi = {10.1126/science.1107239},
 }
-@article{wilson_speciation_1987,
-	author = {Wilson, George and Hessler, Robert},
-	year = {1987},
-	pages = {185-207},
-	title = {Speciation in the Deep Sea},
-	volume = {18},
-	journal = {Annual Review of Ecology and Systematics},
-	doi = {10.1146/annurev.es.18.110187.001153},
-}
 @article{levin2009ecological,
   title={Ecological theory and continental margins: where shallow meets deep},
   author={Levin, Lisa A and Dayton, Paul K},
@@ -281,7 +252,7 @@ @article{hugenholtz1998impact
   pages={4765--4774},
   year={1998},
   publisher={Am Soc Microbiol},
-  doi={10.1128/jb.180.18.4765-4774.1998}, 
+  doi={10.1128/jb.180.18.4765-4774.1998},
 }
 @article{rehm2009cumacea,
   title={Cumacea (Crustacea; Peracarida) of the Antarctic shelf-diversity, biogeography, and phylogeny= Cumacea (Crustacea; Peracarida) des antarktischen Schelfs-Diversit{\"a}t, Biogeographie und Phylogenie},
@@ -494,13 +465,54 @@ @article{tahiri2018new
   publisher={Springer},
   doi={10.1186/s12862-018-1163-8},
 }
-@article{choi2009comparison,
-  title={Comparison of phylogenetic trees through alignment of embedded evolutionary distances},
-  author={Choi, Kwangbom and Gomez, Shawn M},
-  journal={BMC bioinformatics},
-  volume={10},
-  pages={1--15},
-  year={2009},
-  publisher={Springer},
-  doi={10.1186/1471-2105-10-423},
+@article{li2024host,
+  title={Host--Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts},
+  author={Li, Wanlin and Tahiri, Nadia},
+  journal={Viruses},
+  volume={16},
+  number={7},
+  pages={1133},
+  year={2024},
+  publisher={MDPI},
+  doi={10.3390/v16071133},
+}
+@article{li2023aphylogeo,
+  title={aPhyloGeo-Covid: A web interface for reproducible phylogeographic analysis of SARS-CoV-2 variation using Neo4j and Snakemake},
+  author={Li, Wanlin and Tahiri, Nadia},
+  journal={NOUVEL ALGORITHME POUR {\'E}VALUER L’INFLUENCE ENVIRONNEMENTALE DU CORONAVIRUS PAR LE BIAIS D’UNE ANALYSE PHYLOG{\'E}OGRAPHIQUE},
+  pages={44},
+  year={2023},
+  doi={10.25080/gerudo-f2bc6f59-00f}
+}
+@article{li2024comparison,
+  title={Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review},
+  author={Li, Wanlin and Koshkarov, Aleksandr and Tahiri, Nadia},
+  journal={Ecology and Evolution},
+  volume={14},
+  number={8},
+  pages={e70054},
+  year={2024},
+  publisher={Wiley Online Library},
+  doi={10.1002/ece3.70054},
+}
+@article{rogers2007corals,
+	title={Corals on seamounts},
+	author={Rogers, Alex D and Baco, Amy and Griffiths, Huw and Hart, Thomas and Hall-Spencer, Jason M},
+	journal={Seamounts: ecology, fisheries \& conservation},
+	pages={141--169},
+	year={2007},
+	publisher={Wiley Online Library},
+	doi = {10.1002/9780470691953.ch8},
+}
+@article{manel_perspectives_2010,
+	title = {Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field},
+	volume = {19},
+	issn = {0962-1083},
+	number = {17},
+	journal = {Molecular Ecology},
+	author = {Manel, Stéphanie and Joost, Stéphane and Epperson, Bryan K and Holderegger, Rolf and Storfer, Andrew and Rosenberg, Michael S and Scribner, Kim T and Bonin, Aurélie and FORTIN, MARIE‐JOSÉE},
+	year = {2010},
+	doi = {10.1111/j.1365-294X.2010.04717.x},
+	note = {Publisher: Wiley Online Library},
+	pages = {3760--3772},
 }

papers/Gagnon_Kebe_Tahiri/myst.yml

@@ -1,39 +1,40 @@
 version: 1
-extends: ../proceedings.yml
 project:
-  doi: 10.25080/NVYF1037
   # Update this to match `scipy-2024-<folder>` the folder should be `<firstname_surname>`
   id: scipy-2024-gagnon_kebe_tahiri
-  title: Ecological and Geographic Influences on Cumacea Genetics in the Northern North Atlantic
+  title: Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic
   subtitle: by aPhyloGeo software
-  description: Cumacea are vital indicators of benthic health in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and geographic (i.e., spatial or regional) attributes on their genetic variability in the Northern North Atlantic, focusing on Icelandic waters.
+  description: The peracarid taxon Cumacea is an essential indicator of benthic quality in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and spatial (i.e., geographic or regional) variables on their genetic variability and adaptability in the Northern North Atlantic, focusing on Icelandic waters.
   # Authors should have affiliations, emails and ORCIDs if available
   authors:
     - name: Justin Gagnon
       email: [email protected]
       affiliations:
-        - Department of Computer Science, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada
+        - Department of Biology, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada
     - name: Nadia Tahiri
       email: [email protected]
       orcid: 0000-0002-1818-208X
       affiliations:
         - Department of Computer Science, University of Sherbrooke, 2500, boul. de l'Université, Sherbrooke, Quebec, J1K 2R1 Canada
       corresponding: true
   keywords:
+    - Adaptation
     - Atlantic
-    - Arctic
     - Bioinformatics
     - Biology
     - Cumacea
     - Iceland
-    - Phylogeny
     - Phylogeography
   # Add the abbreviations that you use in your paper here
   abbreviations:
     DD: decimal degrees
+    PSU: practical salinity units
     PCR: Polymerase Chain Reaction
     rRNA: Ribosomal ribonucleic acid
     GIN: Greenland, Iceland, and Norwegian
+    RF: Robinson-Foulds
+    nRF: normalized Robinson-Foulds
+    bp: base pairs
   # It is possible to explicitly ignore the `doi-exists` check for certain citation keys
   error_rules:
     - rule: doi-exists