Finalize biological principles introduction

assets/bibliography.bib

@@ -185,35 +185,6 @@
                   xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/pkubioinformatics/NanoReviser</ext-link>.}
 }
 
-
-
-@Article{Davis2021,
-  author          = {Davis, Eric M. and Sun, Yu and Liu, Yanling and Kolekar,
-                  Pandurang and Shao, Ying and Szlachta, Karol and Mulder,
-                  Heather L. and Ren, Dongren and Rice, Stephen V. and Wang,
-                  Zhaoming and Nakitandwe, Joy and Gout, Alexander M. and
-                  Shaner, Bridget and Hall, Salina and Robison, Leslie L. and
-                  Pounds, Stanley and Klco, Jeffery M. and Easton, John and Ma,
-                  Xiaotu},
-  title           = {SequencErr: measuring and suppressing sequencer errors in
-                  next-generation sequencing data},
-  journal         = {Genome Biology},
-  year            = 2021,
-  month           = {Jan},
-  day             = 25,
-  volume          = 22,
-  number          = 1,
-  pages           = 37,
-  abstract        = {There is currently no method to precisely measure the
-                  errors that occur in the sequencing instrument/sequencer,
-                  which is critical for next-generation sequencing applications
-                  aimed at discovering the genetic makeup of heterogeneous
-                  cellular populations.},
-  issn            = {1474-760X},
-  doi             = {10.1186/s13059-020-02254-2},
-  url             = {https://doi.org/10.1186/s13059-020-02254-2}
-}
-
 @article{HEATHER20161,
   title           = {The sequence of sequencers: The history of sequencing DNA},
   journal         = {Genomics},
@@ -507,3 +478,42 @@
   pages           = 8,
   year            = 1958
 }
+
+@article{10.1093/bioinformatics/btg109,
+  author          = {Lee, Christopher},
+  title           = "{Generating consensus sequences from partial order multiple
+                  sequence alignment graphs}",
+  journal         = {Bioinformatics},
+  volume          = 19,
+  number          = 8,
+  pages           = {999-1008},
+  year            = 2003,
+  month           = 05,
+  abstract        = "{Motivation: Consensus sequence generation is important in
+                  many kinds of sequence analysis ranging from sequence assembly
+                  to profile-based iterative search methods. However, how can a
+                  consensus be constructed when its inherent assumption—that the
+                  aligned sequences form a single linear consensus—is not
+                  true?Results: Partial Order Alignment (POA) enables
+                  construction and analysis of multiple sequence alignments as
+                  directed acyclic graphs containing complex branching
+                  structure. Here we present a dynamic programming algorithm
+                  (heaviest\_bundle) for generating multiple consensus sequences
+                  from such complex alignments. The number and relationships of
+                  these consensus sequences reveals the degree of structural
+                  complexity of the source alignment. This is a powerful and
+                  general approach for analyzing and visualizing complex
+                  alignment structures, and can be applied to any alignment. We
+                  illustrate its value for analyzing expressed sequence
+                  alignments to detect alternative splicing, reconstruct full
+                  length mRNA isoform sequences from EST fragments, and separate
+                  paralog mixtures that can cause incorrect SNP
+                  predictions.Availability: The heaviest\_bundle source code is
+                  available at http://www.bioinformatics.ucla.edu/poaContact:
+                  leec@mbi.ucla.edu*To whom correspondence should be
+                  addressed.}",
+  issn            = {1367-4803},
+  doi             = {10.1093/bioinformatics/btg109},
+  url             = {https://doi.org/10.1093/bioinformatics/btg109},
+  eprint          = {https://academic.oup.com/bioinformatics/article-pdf/19/8/999/642375/btg109.pdf},
+}