Our group publishes papers presenting new methodologies, describing the results of studies that use our software, and reviewing current topics in the field of Bioinformatics. Scroll down or click here for a complete list of papers produced by our lab. Since 2013, we write blog posts summarizing new research papers and review articles:


Mouse Genetics

Population Structure

Review Articles


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Mangul, Serghei; Loohuis, Loes Olde M; Ori, Anil; Jospin, Guillaume; Koslicki, David; Yang, Harry Taegyun; Wu, Timothy; Boks, Marco P; Lomen-Hoerth, Catherine; Wiedau-Pazos, Martina; Cantor, Rita; de Vos, Willem M; Kahn, Rene S; Eskin, Eleazar; Ophoff, Roel A

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects. Journal Article

BioRxiv, (057570), 2016.

Abstract | Links | BibTeX | Tags: blood microbiome, RNA sequencing, schizophrenia, unmapped reads

Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Daley, Timothy; Christenson, Stephanie; Andersen, Agata Wesolowska; Spreafico, Roberto; Rios, Cydney; Eng, Celeste; Smith, Andrew D; Hernandez, Ryan D; Ophoff, Roel A; Santana, Jose Rodriguez; Woodruff, Prescott G; Burchard, Esteban; Seibold, Max A; Shifman, Sagiv; Eskin, Eleazar; Zaitlen, Noah

Dumpster diving in RNA-sequencing to find the source of every last read. Journal Article

BioRxiv, 2016.

Links | BibTeX | Tags: read origin protocol, RNA sequencing, unmapped reads


Org, Elin; Parks, Brian W W; Joo, Jong Wha J; Emert, Benjamin; Schwartzman, William; Kang, Eun Yong; Mehrabian, Margarete; Pan, Calvin; Knight, Rob; Gunsalus, Robert; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

Genetic and environmental control of host-gut microbiota interactions. Journal Article

Genome Res, 2015, ISSN: 1549-5469.

Abstract | Links | BibTeX | Tags: Mouse Genetics. HDMAP, RNA sequencing

Patananan, Alexander Nikolich; Budenholzer, Lauren Michelle; Eskin, Ascia; Torres, Eric Rommel; Clarke, Steven Gerard

Ethanol-induced differential gene expression and acetyl-CoA metabolism in a longevity model of the nematode Caenorhabditis elegans. Journal Article

Exp Gerontol, 61 , pp. 20-30, 2015, ISSN: 1873-6815.

Abstract | Links | BibTeX | Tags: Caenorhabditis, ethanol, RNA sequencing