Our group is celebrating the end of a productive calendar year—and the conclusion of our first semester at USC School of Pharmacy! We are proud to share the preprints and papers we produced with our incredible collaborators at ZarLab in the Department of Computational Medicine at UCLA, members of our own group now in the Titus Department of Clinical Pharmacy at USC, and the Genotype-Tissue Expression (GTEx) Consortium.

Earlier this week, we celebrated our lab’s accomplishments in Fall 2019 with a festive dinner of exotic meat and plant-based sausages at Wurstküche in the Arts District in downtown Los Angeles! Our group enjoyed having a chance to socialize outside the lab and, for our graduate students, relax after taking final exams.

Mangul Lab enjoying a lab dinner at Wurstküche in DTLA!

On a related note, the Mangul Lab started a new tradition to celebrate the release of our preprints and papers! Each time a member of our group submits a preprint, we celebrate with a social lab gathering. The member who contributed most substantially to the preprint has the honors of pinning a copy of the paper on the left side of a wall in our lab. We then toast to the paper with refreshments! When a preprint is accepted and published by a journal, we celebrate again, and the contributing author moves the paper over the right side of the wall. This particular evening, we pinned and toasted to the four preprints our lab produced in 2019!

 

Please see below for a complete list of preprints and publications released by our group during 2019.

 

USC lab preprints released in 2019:

Keith Mitchell, Jaqueline J Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Jared Littman, Brian L Hill, Nicholas C Wu, Harry Taegyun Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Shabanets, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul: Benchmarking of computational error-correction methods for next-generation sequencing data. In: Genome Biology, 21 (71), 2020.

Jaqueline J Brito, Thiago Mosqueiro, Jeremy Rotman, Victor Xue, Douglas J Chapski, Juan De la Hoz, Paulo Matias, Lana S Martin, Alex Zelikovsky, Matteo Pellegrini, Serghei Mangul: Telescope: an interactive tool for managing large scale analysis from mobile devices. In: GigaScience, 9 (1), pp. giz163, 2020.

Caitlin Loeffler, Aaron Karlsberg, Lana S Martin, Eleazar Eskin, David Koslicki, Serghei Mangul: Improving the usability and comprehensiveness of microbial databases. In: BMC Biology, Forthcoming.

Caitlin Loeffler, Keylie M Gibson, Lana S Martin, Yutong Chang, Jeremy Rotman, Ian V Toma, Christopher E Mason, Eleazar Eskin, Joseph P Zackular, Keith A Crandall, David Koslicki, Serghei Mangul: Unlocking the diagnostic and therapeutic potential of metagenomics. In: arXiv, 2019.


UCLA lab published in 2019:

Suraj P Bhat, Rajendra K Gangalum, Dongjae Kim, Serghei Mangul, Raj K Kashyap, Xinkai Zhou, David Elashoff: Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity. In: Journal of Biological Chemistry, 294 , pp. 13530-13544, 2019.

Serghei Mangul: Interpreting and integrating big data in the life sciences. In: Emerging Topics in Life Sciences, 3 (4), pp. 335-341, 2019.

Serghei Mangul, Thiago Mosqueiro, Richard J Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian L Hill, Jaqueline J Brito, Russell Jared Littman, Benjamin Statz: Challenges and recommendations to improve the installability and archival stability of omics computational tools. In: PLoS Biology, 17 (6), pp. e3000333, 2019.

Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C Wu, David Koslicki, Eleazar Eskin: MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. In: BMC Genomics, 20 (5), pp. 423, 2019.

Serghei Mangul, Lana S Martin, Brian L Hill, Angela Ka-Mei Lam, Margaret G Distler, Alex Zelikovsky, Eleazar Eskin, Jonathan Flint: Systematic benchmarking of omics computational tools. In: Nature Communications, 10 (1393), pp. 1-11, 2019.

Serghei Mangul, Lana S Martin, Ben Langmead, Javier E Sanchez-Galan, Ian V Toma, Fereydoun Hormozdiari, Pavel Pevzner, Eleazar Eskin: How bioinformatics and open data can boost basic science in countries and universities with limited resources. In: Nature Biotechnology, 37 (3), pp. 324, 2019.

Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen: Hidden Treasures in Contemporary RNA Sequencing. In: Hidden Treasures in Contemporary RNA Sequencing. SpringerBriefs in Computer Science, pp. 1–93, Springer, 2019.

Serghei Mangul, Lana S Martin, Eleazar Eskin, Ran Blekhman: Improving the usability and archival stability of bioinformatics software. In: Genome Biology, 20 (47), pp. 1-3, 2019.

Suraj P Bhat, Rajendra K Gangalum, Dongjae Kim, Serghei Mangul, Raj K Kashyap, Xinkai Zhou, David Elashoff: Absence of Single Cell Transcriptional Heterogeneity in the transgenic paradigm of the inherited Lamellar cataract. In: Investigative Ophthalmology & Visual Science, 60 (9), pp. 1381-1381, 2019.


GTEx Consortium preprint released in 2019:

Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Munoz-Aguirre, Valentin Wucher, Silva Kasela, Stephane E Castel, Andrew R Hamel, Ana Vinuela, Amy L Roberts: Cell type specific genetic regulation of gene expression across human tissues. In: bioRxiv, pp. 806117, 2019.