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--- bioinformatics_essay28 [2022/12/25 12:27] – 134.190.232.124
+++ bioinformatics_essay28 [2023/01/01 10:20] (current) – 134.190.232.124
@@ Line 18: / Line 18: @@
   - Troubleshooting – The authors should include some tips for users on what went wrong in their lab. What steps did they find tricky, and what were the solutions? Do the authors refer to the corresponding protocol step in the Troubleshooting section?
   - Alternates – Are there any reagents or pieces of equipment that cannot be substituted, OR are there reagents that have similar versions from other companies?
+**References:**
+  - Xi Zhang*, Yining Hu, David Roy Smith*. (2021). Protocol for HSDFinder to help identify, categorize and annotate duplicate genes in eukaryotic nuclear genomes. STAR Protocols. DOI: 10.1016/j.xpro.2021.100619
+  - Xi Zhang*, Yining Hu, David Roy Smith*. (2021). Protocol for using NoBadWordsCombiner to merge and minimize ‘bad words’ from BLAST hits against multiple eukaryotic gene annotation databases. DOI: 10.1016/j.xpro.2021.100888
+  - Xi Zhang*, Yining Hu, Laura Eme, Shinichiro Maruyama, Robert JM Eveleigh, Bruce A. Curtis, Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo, Klaas J. van Wijk, John M. Archibald*. (2022) TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.DOI: 10.1016/j.xpro.2022.101175
+  - Xi Zhang*, Yining Hu, Zhenyu Cheng, John M. Archibald*. (2022). HSDecipher: pipeline for comparative genomics analysis of highly similar duplicates data in eukaryotic genomes. Star Protocols.
 <Last updated by Xi Zhang on Dec 25th,2022>