Diaz Lab MSB cover art

Publications

In recent years, the Diaz Lab has published research in a variety of academic journals, including Cancer Discovery, Genome Biology, and Cell. Below includes a selection of recent publications.

 

The phenotypes of proliferating glioblastoma cells reside on a single axis of variation

Wang L, Babikir H, Muller S, Yagnik G, Shamardani K, Catalan F, Kohanbash G, Alvarado B, Di Lullo E, Kriegstein A, Shah S, Wadhwa H, Chang SM, Philips JJ, Aghi MK, Diaz AA

Cancer Discov. 2019 Sep 25; pii: CD-19-0329. doi: 10.1158/2159-8290.CD-19-0329. [Epub ahead of print].
PubMed Link >

Peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas

Müller S, Agnihotri S, Shoger KE, Myers MI, Smith N, Chaparala S, Villanueva CR, Chattopadhyay A, Lee AV, Butterfield LH, Diaz A*, Okada H*, Pollack IF*, Kohanbash G*

JCI Insight. 2018 Apr 5; 3 (7): 98791. doi: 10.1172/jci.insight.98791. eCollection 2018 Apr 5.
PubMed Link >

The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output

Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M

Cell Stem Cell. 2018 Mar 1; 22 (3): 369-383.e8. doi: 10.1016/j.stem.2018.02.004.
PubMed Link >

CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones

Müller S, Cho A, Liu SJ, Lim DA, Diaz A

Bioinformatics. 2018 Sep 15; 34 (18): 3217-3219. doi: 10.1093/bioinformatics/bty316.
PubMed Link >

Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment.

Müller S, Kohanbash G, Liu SJ, Alvarado B, Carrera D, Bhaduri A, Watchmaker PB, Yagnik G, Di Lullo E, Malatesta M, Amankulor NM, Kriegstein AR, Lim DA, Aghi M, Okada H, Diaz A

Genome Biol. 2017 Dec 20; 18 (1): 234. doi: 10.1186/s13059-017-1362-4.
PubMed Link >

Single-cell Co-expression Subnetwork Analysis

Bartlett TE, Müller S, Diaz A

Sci Rep. 2017 Nov 8; 7 (1): 15066. doi: 10.1038/s41598-017-15525-z.
PubMed Link >

Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint

Müller S, Diaz A

Front Genet. 2017 May 31; 8: 73. doi: 10.3389/fgene.2017.00073. eCollection 2017. Review.
PubMed Link >

Single-cell sequencing maps gene expression to mutational phylogenies in PDGF and EGF driven gliomas

Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen A, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein A, Lim DA, Diaz A

Mol Syst Biol. 2016 Nov 25; 12 (11): 889. doi: 10.15252/msb.20166969.
PubMed Link >

SCell: integrated analysis of single-cell RNA-seq data

Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A

Bioinformatics. 2016 Jul 15; 32 (14): 2219-20. doi: 10.1093/bioinformatics/btw201. Epub 2016 Apr 19.
PubMed Link >

Single cell analysis of long non-coding RNAs in the developing human neocortex

Liu S, Nowakowski T, Pollen A, Lui J, Horlbeck M, Attenello F, He D, Weissman J, Kriegstein A, Diaz A*, Lim DA*

Genome Biol. 2016 Apr 14; 17: 67. doi: 10.1186/s13059-016-0932-1.
PubMed Link >

A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver

Suzawa M, Miranda DA, Ramos KA, Ang KK, Faivre EJ, Wilson CG, Caboni L, Arkin MR, Kim YS, Fletterick RJ, Diaz A, Schneekloth JS, Ingraham HA

Elife. 2015 Dec 11; 4: e09003. doi: 10.7554/eLife.09003.
PubMed Link >

Molecular identity of human outer radial glia during cortical development

Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR

Cell. 2015 Sep 24; 163 (1): 55-67. doi: 10.1016/j.cell.2015.09.004.
PubMed Link >

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis

Diaz AA, Qin H, Ramalho-Santos M, Song JS

Nucleic Acids Res. 2015 Feb 18; 43 (3): e16. doi: 10.1093/nar/gku1197. Epub 2014 Nov 26.
PubMed Link >

Systematic identification of barriers to human iPSC generation

Qin H*, Diaz A*, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M.

Cell. 2014 Jul 17; 158 (2): 449-461. doi: 10.1016/j.cell.2014.05.040.
PubMed Link >

Recurrent epimutations activate gene body promoters in primary glioblastoma

Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF

Genome Res. 2014; 24 (5): 761-74. doi: 10.1101/gr.164707.113. Epub 2014 Apr 7.
PubMed Link >