Add elm citation

docs/src/en/cite.md

@@ -3,18 +3,18 @@
 # Citation
 
 If you use `gget` in a publication, please cite:   
-Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
+Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btac836](https://doi.org/10.1093/bioinformatics/btac836)
 
 - If using `gget alphafold`, please also cite:  
-  - Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2
+  - Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). [https://doi.org/10.1038/s41586-021-03819-2](https://doi.org/10.1038/s41586-021-03819-2)
 
   And, if applicable:  
-  - Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. bioRxiv 2021.10.04.463034; https://doi.org/10.1101/2021.10.04.463034
+  - Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. bioRxiv 2021.10.04.463034; [https://doi.org/10.1101/2021.10.04.463034](https://doi.org/10.1101/2021.10.04.463034)
 
 - If using `gget archs4`, please also cite:   
   - Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications 9. Article number: 1366 (2018), doi:10.1038/s41467-018-03751-6
 
-  - Bray NL, Pimentel H, Melsted P and Pachter L, Near optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, p 525--527 (2016). https://doi.org/10.1038/nbt.3519
+  - Bray NL, Pimentel H, Melsted P and Pachter L, Near optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, p 525--527 (2016). [https://doi.org/10.1038/nbt.3519](https://doi.org/10.1038/nbt.3519)
 
 - If using `gget blast`, please also cite:  
   - Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2. PMID: 2231712.
@@ -23,13 +23,14 @@ Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference data
   - Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. doi: 10.1101/gr.229202. PMID: 11932250; PMCID: PMC187518.
 
 - If using `gget cellxgene`, please also cite:  
-  - Chanzuckerberg Initiative. (n.d.). CZ CELLxGENE Discover. Retrieved [insert date here], from https://cellxgene.cziscience.com/
+  - Chanzuckerberg Initiative. (n.d.). CZ CELLxGENE Discover. Retrieved [insert date here], from [https://cellxgene.cziscience.com/](https://cellxgene.cziscience.com/)
 
 - If using `gget diamond`, please also cite:  
-  - Buchfink, B., Xie, C. & Huson, D. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015). https://doi.org/10.1038/nmeth.3176
+  - Buchfink, B., Xie, C. & Huson, D. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015). [https://doi.org/10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176)
 
-- If using `gget elm`, please also cite:  
-  - Manjeet Kumar, Sushama Michael, Jesús Alvarado-Valverde, Bálint Mészáros, Hugo Sámano‐Sánchez, András Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Örd, Anurag Nagpal, Nazanin Farahi, Melanie Käser, Ramya Kraleti, Norman E Davey, Rita Pancsa, Lucía B Chemes, Toby J Gibson, The Eukaryotic Linear Motif resource: 2022 release, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D497–D508, https://doi.org/10.1093/nar/gkab975
+- If using `gget elm`, please also cite:
+  - Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter, Fast and scalable querying of eukaryotic linear motifs with gget elm, Bioinformatics, 2024, btae095, [https://doi.org/10.1093/bioinformatics/btae095](https://doi.org/10.1093/bioinformatics/btae095)
+  - Manjeet Kumar, Sushama Michael, Jesús Alvarado-Valverde, Bálint Mészáros, Hugo Sámano‐Sánchez, András Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Örd, Anurag Nagpal, Nazanin Farahi, Melanie Käser, Ramya Kraleti, Norman E Davey, Rita Pancsa, Lucía B Chemes, Toby J Gibson, The Eukaryotic Linear Motif resource: 2022 release, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D497–D508, [https://doi.org/10.1093/nar/gkab975](https://doi.org/10.1093/nar/gkab975)
 
 - If using `gget enrichr`, please also cite:     
   - Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A.
@@ -38,11 +39,10 @@ Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
   - Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A.
 Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377.  
 
-  - Xie Z, Bailey A, Kuleshov MV, Clarke DJB., Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, & Ma’ayan A.
-Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. 2021. doi: 10.1002/cpz1.90. 
+  - Xie Z, Bailey A, Kuleshov MV, Clarke DJB., Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, & Ma’ayan A. Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. 2021. doi: 10.1002/cpz1.90. 
 
 - If using `gget muscle`, please also cite:  
-  - Edgar RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169. https://doi.org/10.1101/2021.06.20.449169.
+  - Edgar RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169. [https://doi.org/10.1101/2021.06.20.449169](https://doi.org/10.1101/2021.06.20.449169)
 
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