This would provide an epoch making discovery/resources in evolutionary neurogenomics!
Our new library is doing a great job!!!
Our first paper is out!!! which has utilized our RRBS (reduced representation of bisulfite sequencing) method we have developed in house!!! Congratulations, the team Bayoumy!!!
Sun YW, Chen KM, Imamura Kawasawa Y, Salzberg AC, Cooper TK, Caruso C, Aliaga C, Zhu J, Gowda K, Amin S, El-Bayoumy K. Hypomethylated Fgf3 is a potential biomarker for early detection of oral cancer in mice treated with the tobacco carcinogen dibenzo[def,p]chrysene. PLoS One. 2017 Oct 26;12(10):e0186873.
2 more just got accepted! Can’t wait to see them out too! Thank you!!!
- Clawson GA, Matters GL, Xin P, McGovern C, Wafula E, dePamphilis C, Meckley M, Wong J, Stewart L, D’Jamoos C, Altman N, Imamura Kawasawa Y, Du Z, Honaas L, Abraham T. “Stealth dissemination” of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma. PLoS One. 2017 Sep 28;12(9):e0184451. doi: 10.1371/journal.pone.0184451. eCollection 2017. PubMed PMID: 28957348.
- Zirong Gu, John Kalamboglas, Shin Yoshioka, Wenqi Han, Zhuo Li, Yuka Imamura Kawasawa, Sirisha Pochareddy, Zhen Li, Fuchen Liu, Xuming Xu, Sagara Wijeratne, Masaki Ueno, Emily Blatz, Joseph Salomone, Atsushi Kumanogoh, Mladen-Roko Rasin, Brian Gebelein, Matthew T. Weirauch, Nenad Sestan, John H. Martin, Yutaka Yoshida. Control of Species-dependent Cortico-motoneuronal Connections Underlying Manual Dexterity. Science, July 28 2017 : 400-40.
- Wilson RT, Masters LD, Barnholtz-Sloan JS, Salzberg AC, Hartman TJ. Ancestry-Adjusted Vitamin D Metabolite Concentrations in Association with Cytochrome 3A (CYP3A) Polymorphisms. Am J Epidemiol. 2017 Jun 30. doi: 10.1093/aje/kwx187. [Epub ahead of print] PubMed PMID: 28673024.
- Popova EY, Salzberg AC, Yang C, Zhang SS, Barnstable CJ. Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. PLoS One. 2017 Jun 22;12(6):e0179230. doi: 10.1371/journal.pone.0179230. eCollection 2017. PubMed PMID: 28640837.
- Lee SY, Zhu J, Salzberg AC, Zhang B, Liu DJ, Muscat JE, Langan ST, Connor JR. Analysis of single nucleotide variants of HFE gene and association to survival in The Cancer Genome Atlas GBM data. PLoS One. 2017 Mar 30;12(3):e0174778. doi: 10.1371/journal.pone.0174778. eCollection 2017. PubMed PMID: 28358914; PubMed Central PMCID: PMC5373638.
- Schieffer KM, Choi CS, Emrich S, Harris L, Deiling S, Karamchandani DM, Salzberg A, Kawasawa YI, Yochum GS, Koltun WA. RNA-seq implicates deregulation of the immune system in the pathogenesis of diverticulitis. Am J Physiol Gastrointest Liver Physiol. 2017 Jun 15:ajpgi.00136.2017. doi: 10.1152/ajpgi.00136.2017. [Epub ahead of print] PubMed PMID: 28619727.
My EIBDG project won a funding support from AFF (Association of Faculty and Friends at Milton S. Hershey Medical Center and Penn State College of Medicine)!!! Thank you very much, AFF, for your generous support!!!
#Working on scheduling new training classes in fall 2017! Details to be announced in below web site, twitter, and by a mass email to Hershey audience!
Ventral corticospinal tract projections exist postnatally in mice but disappear soon after birth.
Total of 7 sessions have been running this spring! This is part of my education project namely EIBDG (Education Initiative in Big Data Genomics). Since this was my 1st sessions, I invited only existing Core users, but in the future sessions (coming back in fall!) I will call any level of participants! Only that the space is limited so I will limit participants by first come first served basis.
|NAT1||3/3/17||useful unix commands|
|NAT2||3/24/17||FastQC, Fastq filtering, RNA-seq alignment, Cufflinks|
|NAT3||4/7/17||smRNA-seq, how to transfer files, RNA–seq; manipulating more on.bam; QC Picard, visualizing in IGV, UCSC track, subfractioning|
|NAT4||4/21/17||Reviewing NAT1-3… More analysis by R; PCA, heatmap, etc, differential gene expression (other than Cufflinks)|
|NAT5||5/10/17 (Wed) in HG318||Exome alignment, variant calling, variant annotation|
|NAT6||6/2/17 (Fri) in C2610||SRA, dbGap, TCGA, optional: GSEA|
|NAT7||6/9/17||ChIP-seq alignment, peak calling, differential binding analysis|
Including 2 first author papers (Yuka and Anna) and 1 Nature Communications!!!
- Imamura Kawasawa, Y., Shahid, M., Son, A.I., Morizono, H., Basha, A., Salzberg, A.C., Torii, M, Hashimoto-Torii, K. Genome-wide profiling of differentially spliced mRNAs in human fetal cortical tissue exposed to alcohol. Alcohol, Accepted.
- Ishii, S.*, Torii, M.*, Son, A.I., Rajendraprasad, M., Morozov, M.Y., Imamura Kawasawa Y., Salzberg, A.C., Fujimoto, M., Brennand K., Nakai, A., Mezger, V., Gage, F., Rakic, P. and Hashimoto-Torii, K. Variations in brain defects result from cellular mosaicism in the activation of heat shock signaling. Nature Comm,In Press. (*contributed equally)
- Salzberg AC, Harris-Becker A, Popova EY, Keasey N, Loughran TP, Claxton DF, Grigoryev SA. Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability. PLoS One. 2017 Mar 16;12(3):e0173723. doi: 10.1371/journal.pone.0173723. PubMed PMID: 28301528.
QuantSeq 3′ mRNA-seq has been becoming a popular gene expression NGS application in my core! I will show how our ‘real-world’ biomedical data was comparable between 3’ mRNA-seq and conventional mRNA-seq. I will also show how data stays consistent across varying sequencing depth and input RNA amount. 2 more weeks to finish up my analysis! 🙂
The Oncotarget paper from The Pu Lab just got published! GS core contributed to variant finding, RNA-seq, and bioinformatics/statistical analyses!
- Teye EK, Sido A, Xin P, Finnberg NK, Gokare P, Kawasawa YI, Salzberg AC, Shimko S, Bayerl M, Ehmann WC, Claxton DF, Rybka WB, Drabick JJ, Wang HG, Abraham T, El-Deiry WS, Brodsky RA, Hohl RJ, Pu JJ. PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features. Oncotarget. 2017 Feb 7. doi:10.18632/oncotarget.15136. [Epub ahead of print] PubMed PMID: 28187452.
Also, a conference abstract is accepted for The Futai Lab@UMass! GS core contributed to ChIP-seq and RNA-seq analyses!
- Mao W, Uchigashima M, Salzberg AC, Hasegawa Y, Hock H, Imamura Y, Watanabe M, Akbarian S, Futai K. Epigenetic Regulation of Homeostatic Synaptic Plasticity. The 39th Annual Meeting of Japanese Neuroscience Society (2017)