ButterflyBase: a platform for lepidopteran genomics. - Alexie Papanicolaou; Steffi Gebauer-Jung; Mark L. Blaxter; W. Owen McMillan; Chris D. Jiggins (Nucleic Acids Res., 2008)

Next generation transcriptomes for next generation genomes using est2assembly. - Alexie Papanicolaou; Remo Stierli; Richard H. ffrench-Constant; David G. Heckel (BMC Bioinform., 2009)

The GMOD Drupal Bioinformatic Server Framework. - Alexie Papanicolaou; David G. Heckel (Bioinform., 2010)

Blue: correcting sequencing errors using consensus and context. - Paul Greenfield; Konsta Duesing; Alexie Papanicolaou; Denis C. Bauer (Bioinform., 2014)

OfftargetFinder: a web tool for species-specific RNAi design. - Robert T. Good; Temi Varghese; John Golz; Derek A. Russell; Alexie Papanicolaou; Owain Edwards; Charles Robin (Bioinform., 2016)