2016 Publications

Whole genomic copy number alterations in circulating tumor cells from men with abiraterone or enzalutamide resistant metastatic castration-resistant prostate cancer.
Gupta S, Li J, Kemeny G, Bitting RL, Beaver J, Somarelli J, Ware KE, Gregory S, Armstrong AJ.
Clin Cancer Res. 2016 Sep 6. pii: clincanres.1211.2016. [Epub ahead of print]

[NGS] EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.
Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA.
BMC Bioinformatics. 2016 Jan 22;17:48. doi: 10.1186/s12859-016-0883-2.

Transdifferentiation of human endothelial progenitors into smooth muscle cells.
Ji H, Atchison L, Chen Z, Chakraborty S, Jung Y, Truskey GA, Christoforou N, Leong KW.
Biomaterials. 2016 Feb 3;85:180-194. doi: 10.1016/j.biomaterials.2016.01.066. [Epub ahead of print]

[NGS] Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs.
Larsen PA, Hayes CE, Williams CV, Junge RE, Razafindramanana J, Mass V, Rakotondrainibe H, Yoder AD.
Biol Lett. 2016 Jan;12(1):20150829. doi: 10.1098/rsbl.2015.0829.

[NGS] Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly.
Mao H, McMahon JJ, Tsai YH, Wang Z, Silver DL.
PLoS Genet. 2016 Sep;12(9):e1006282. doi: 10.1371/journal.pgen.1006282.

Disrupted iron homeostasis causes dopaminergic neurodegeneration in mice.
Matak P, Matak A, Moustafa S, Aryal DK, Benner EJ, Wetsel W, Andrews NC.
Proc Natl Acad Sci U S A. 2016 Feb 29. doi:pii: 201519473. [Epub ahead of print]

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.
Piccolo SR, Hoffman LM, Conner T, Shrestha G, Cohen AL, Marks JR, Neumayer LA, Agarwal CA, Beckerle MC, Andrulis IL, Spira AE, Moos PJ, Buys SS, Johnson WE, Bild AH.
Mol Syst Biol. 2016 Mar 10;12(3):860. doi: 10.15252/msb.20156506.

[RT-PCR] C-C Motif Chemokine 5 Attenuates Angiotensin II-Dependent Kidney Injury by Limiting Renal Macrophage Infiltration.
Rudemiller NP, Patel MB, Zhang JD, Jeffs AD, Karlovich NS, Griffiths R, Kan MJ, Buckley AF, Gunn MD, Crowley SD.
Am J Pathol. 2016 Sep 15. doi:pii: S0002-9440(16)30295-4. 10.1016/j.ajpath.2016.07.015. [Epub ahead of print]

Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins.
Tang NC, Chilkoti A.
Nat Mater. 2016 Jan 4. doi: 10.1038/nmat4521. [Epub ahead of print]

Cystine Deprivation Triggers Programmed Necrosis in VHL-Deficient Renal Cell Carcinomas.
Tang X, Wu J, Ding CK, Lu M, Keenan MM, Lin CC, Lin CA, Wang CC, George D, Hsu DS, Chi JT.
Cancer Res. 2016 Feb 1. [Epub ahead of print]

[microRNA] Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice.
Tkatchenko AV, Luo X, Tkatchenko TV, Vaz C, Tanavde VM, Maurer-Stroh S, Zauscher S, Gonzalez P, Young TL.
PLoS One. 2016;11(9):e0162541. doi: 10.1371/journal.pone.0162541.

MiR-148a functions to suppress metastasis and serves as a prognostic indicator in triple-negative breast cancer.
Xu X, Zhang Y, Jasper J, Lykken E, Alexander PB, Markowitz GJ, McDonnell DP, Li QJ, Wang XF.
Oncotarget. 2016 Mar 7. doi: 10.18632/oncotarget.7953. [Epub ahead of print]

2015 Publications

In vivo Modeling Implicates APOL1 in Nephropathy: Evidence for Dominant Negative Effects and Epistasis under Anemic Stress.
Anderson BR, Howell DN, Soldano K, Garrett ME, Katsanis N, Telen MJ, Davis EE, Ashley-Koch AE.
PLoS Genet. 2015 Jul;11(7):e1005349. doi: 10.1371/journal.pgen.1005349. Erratum in: PLoS Genet. 2015 Sep;11(9):e1005459.

A paclitaxel-loaded recombinant polypeptide nanoparticle outperforms Abraxane in multiple murine cancer models.
Bhattacharyya J, Bellucci JJ, Weitzhandler I, McDaniel JR, Spasojevic I, Li X, Lin CC, Chi JT, Chilkoti A.
Nat Commun. 2015 Aug 4;6:7939. doi: 10.1038/ncomms8939.

[NGS] Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.
Blair C, Campbell CR, Yoder AD.
Mol Ecol Resour. 2015 Sep;15(5):1079-90. doi: 10.1111/1755-0998.12376. Epub 2015 Feb 8.

Single epicardial cell transcriptome sequencing identifies Caveolin-1 as an essential factor in zebrafish heart regeneration.
Cao J, Navis A, Cox BD, Dickson AL, Gemberling M, Karra R, Bagnat M, Poss KD.
Development. 2015 Dec 10. doi:pii: dev.130534. [Epub ahead of print]

Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development.
Cederholm HM, Benfey PN.
New Phytol. 2015 Apr 9. doi: 10.1111/nph.13405. [Epub ahead of print]

[NGS] Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing.
Chen Y, Frazzitta AE, Litvintseva AP, Fang C, Mitchell TG, Springer DJ, Ding Y, Yuan G, Perfect JR.
Fungal Genet Biol. 2015 Feb;75:64-71. doi: 10.1016/j.fgb.2015.01.005. Epub 2015 Jan 24.

Noncanonical role of transferrin receptor 1 is essential for intestinal homeostasis.
Chen AC, Donovan A, Ned-Sykes R, Andrews NC.
Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11714-9. doi: 10.1073/pnas.1511701112. Epub 2015 Aug 31.

[NGS] Aryl hydrocarbon receptor knock-out exacerbates choroidal neovascularization via multiple pathogenic pathways.
Choudhary M, Kazmin D, Hu P, Thomas RS, McDonnell DP, Malek G.
J Pathol. 2015 Jan;235(1):101-12. doi: 10.1002/path.4433. Epub 2014 Oct 10.

[NGS] Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex.
Ferris KG, Rushton T, Greenlee AB, Toll K, Blackman BK, Willis JH.
Ann Bot. 2015 Aug;116(2):213-23. doi: 10.1093/aob/mcv080. Epub 2015 Jun 12.

[NGS] SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing.
Guo X, Lehner K, O'Connell K, Zhang J, Dave SS, Jinks-Robertson S.
G3 (Bethesda). 2015 Oct 23;5(12):2801-8. doi: 10.1534/g3.115.023317.

Preoperative Single-Fraction Partial Breast Radiation Therapy: A Novel Phase 1, Dose-Escalation Protocol With Radiation Response Biomarkers.
Horton JK, Blitzblau RC, Yoo S, Geradts J, Chang Z, Baker JA, Georgiade GS, Chen W, Siamakpour-Reihani S, Wang C, Broadwater G, Groth J, Palta M, Dewhirst M, Barry WT, Duffy EA, Chi JT, Hwang ES.
Int J Radiat Oncol Biol Phys. 2015 Jul 15;92(4):846-55. doi: 10.1016/j.ijrobp.2015.03.007. Epub 2015 Mar 14.

FAS Death Receptor: A Breast Cancer Subtype-Specific Radiation Response Biomarker and Potential Therapeutic Target.
Horton JK, Siamakpour-Reihani S, Lee CT, Zhou Y, Chen W, Geradts J, Fels DR, Hoang P, Ashcraft KA, Groth J, Kung HN, Dewhirst MW, Chi JT.
Radiat Res. 2015 Nov;184(5):456-69. doi: 10.1667/RR14089.1. Epub 2015 Oct 21.

Plasticity of Hopx(+) type I alveolar cells to regenerate type II cells in the lung.
Jain R, Barkauskas CE, Takeda N, Bowie EJ, Aghajanian H, Wang Q, Padmanabhan A, Manderfield LJ, Gupta M, Li D, Li L, Trivedi CM, Hogan BL, Epstein JA.
Nat Commun. 2015 Apr 13;6:6727. doi: 10.1038/ncomms7727.

E2F1-Mediated Induction of NFYB Attenuates Apoptosis via Joint Regulation of a Pro-Survival Transcriptional Program.
Jiang X, Nevins JR, Shats I, Chi JT.
PLoS One. 2015;10(6):e0127951. doi: 10.1371/journal.pone.0127951.

Arginine deprivation and immune suppression in a mouse model of Alzheimer's disease.
Kan MJ, Lee JE, Wilson JG, Everhart AL, Brown CM, Hoofnagle AN, Jansen M, Vitek MP, Gunn MD, Colton CA.
J Neurosci. 2015 Apr 15;35(15):5969-82. doi: 10.1523/JNEUROSCI.4668-14.2015.

ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate.
Keenan MM, Liu B, Tang X, Wu J, Cyr D, Stevens RD, Ilkayeva O, Huang Z, Tollini LA, Murphy SK, Lucas J, Muoio DM, Kim SY, Chi JT.
PLoS Genet. 2015 Oct;11(10):e1005599. doi: 10.1371/journal.pgen.1005599.

[NGS] Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia.
Kokes M, Dunn JD, Granek JA, Nguyen BD, Barker JR, Valdivia RH, Bastidas RJ.
Cell Host Microbe. 2015 May 13;17(5):716-25. doi: 10.1016/j.chom.2015.03.014. Epub 2015 Apr 23.

Pregnancy and SMTNL1 Deletion Promote the Switching of Skeletal Muscle to a Glycolytic Phenotype in Human and Mice.
Lontay B, Bodoor K, Sipos A, Weitzel DH, Loiselle D, Safi R, Zheng D, Devente J, Hickner RC, McDonnell DP, Ribar T, Haystead TA.
J Biol Chem. 2015 Jun 5. doi:pii: jbc.M115.658120. [Epub ahead of print]

MicroRNAs in endometrial cancers from black and white patients.
Maxwell GL, Shoji Y, Darcy K, Litzi T, Berchuck A, Hamilton CA, Conrads TP, Risinger JI.
Am J Obstet Gynecol. 2015 Feb;212(2):191.e1-10. doi: 10.1016/j.ajog.2014.08.028. Epub 2014 Aug 28.

Modulation of PICALM Levels Perturbs Cellular Cholesterol Homeostasis.
Mercer JL, Argus JP, Crabtree DM, Keenan MM, Wilks MQ, Chi JT, Bensinger SJ, Lavau CP, Wechsler DS.
PLoS One. 2015;10(6):e0129776. doi: 10.1371/journal.pone.0129776.

Syngeneic Murine Ovarian Cancer Model Reveals That Ascites Enriches for Ovarian Cancer Stem-Like Cells Expressing Membrane GRP78.
Mo L, Bachelder RE, Kennedy M, Chen PH, Chi JT, Berchuck A, Cianciolo G, Pizzo SV.
Mol Cancer Ther. 2015 Mar;14(3):747-56. doi: 10.1158/1535-7163.MCT-14-0579. Epub 2015 Jan 14.

Transcriptional control of tissue formation throughout root development.
Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN.
Science. 2015 Oct 23;350(6259):426-30. doi: 10.1126/science.aad1171.

HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
Qiu Y, Li M, Pasoreck EK, Long L, Shi Y, Galvão RM, Chou CL, Wang H, Sun AY, Zhang YC, Jiang A, Chen M.
Plant Cell. 2015 May;27(5):1409-27. doi: 10.1105/tpc.114.136093. Epub 2015 May 5.

Posttranslational Modifications of the Master Transcriptional Regulator NPR1 Enable Dynamic but Tight Control of Plant Immune Responses.
Saleh A, Withers J, Mohan R, Marqu??s J, Gu Y, Yan S, Zavaliev R, Nomoto M, Tada Y, Dong X.
Cell Host Microbe. 2015 Aug 12;18(2):169-82. doi: 10.1016/j.chom.2015.07.005. Erratum in: Cell Host Microbe. 2016 Jan 13;19(1):127-30.

Genomic profiling in locally advanced and inflammatory breast cancer and its link to DCE-MRI and overall survival.
Siamakpour-Reihani S, Owzar K, Jiang C, Scarbrough PM, Craciunescu OI, Horton JK, Dressman HK, Blackwell KL, Dewhirst MW.
Int J Hyperthermia. 2015 Mar 26:1-10. [Epub ahead of print]

Prognostic significance of differential expression of angiogenic genes in women with high-grade serous ovarian carcinoma.
Siamakpour-Reihani S, Owzar K, Jiang C, Turner T, Deng Y, Bean SM, Horton JK, Berchuck A, Marks JR, Dewhirst MW, Alvarez Secord A.
Gynecol Oncol. 2015 Aug 7. doi:pii: S0090-8258(15)30095-0. 10.1016/j.ygyno.2015.08.001. [Epub ahead of print]

Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.
Tang X, Keenan MM, Wu J, Lin CA, Dubois L, Thompson JW, Freedland SJ, Murphy SK, Chi JT.
PLoS Genet. 2015 Apr;11(4):e1005158. doi: 10.1371/journal.pgen.1005158.

Regulation of T cell function by microRNA-720.
Wang Y, Zhang Z, Ji D, Chen GF, Feng X, Gong LL, Guo J, Li ZW, Chen CF, Zhao BB, Li ZG, Li QJ, Yan HP, Sempowski G, Wang FS, He YW.
Sci Rep. 2015 Jul 22;5:12159. doi: 10.1038/srep12159.

Age-related changes in the cellular composition and epithelial organization of the mouse trachea.
Wansleeben C, Bowie E, Hotten DF, Yu YR, Hogan BL.
PLoS One. 2014;9(3):e93496. doi: 10.1371/journal.pone.0093496.

[NGS] RNA-Seq and ChIP-Seq reveal SQSTM1/p62 as a key mediator of JunB suppression of NF-??B-dependent inflammation.
Zhang X, Jin JY, Wu J, Qin X, Streilein R, Hall RP, Zhang JY.
J Invest Dermatol. 2015 Apr;135(4):1016-24. doi: 10.1038/jid.2014.519. Epub 2014 Dec 16.

Earlier Publications