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Items: 35


Prediction of Human Immunodeficiency Virus Type 1 Subtype-Specific Off-Target Effects Arising from CRISPR-Cas9 Gene Editing Therapy.

Link RW, Nonnemacher MR, Wigdahl B, Dampier W.

CRISPR J. 2018 Aug;1:294-302. doi: 10.1089/crispr.2018.0020.


Cyclin D1 integrates G9a-mediated histone methylation.

Li Z, Jiao X, Di Sante G, Ertel A, Casimiro MC, Wang M, Katiyar S, Ju X, Klopfenstein DV, Tozeren A, Dampier W, Chepelev I, Jeltsch A, Pestell RG.

Oncogene. 2019 May;38(22):4232-4249. doi: 10.1038/s41388-019-0723-8. Epub 2019 Feb 4.


Gene Editing of HIV-1 Co-receptors to Prevent and/or Cure Virus Infection.

Allen AG, Chung CH, Atkins A, Dampier W, Khalili K, Nonnemacher MR, Wigdahl B.

Front Microbiol. 2018 Dec 17;9:2940. doi: 10.3389/fmicb.2018.02940. eCollection 2018. Review.


GOATOOLS: A Python library for Gene Ontology analyses.

Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H.

Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z.


Broad-Spectrum and Personalized Guide RNAs for CRISPR/Cas9 HIV-1 Therapeutics.

Dampier W, Sullivan NT, Mell JC, Pirrone V, Ehrlich GD, Chung CH, Allen AG, DeSimone M, Zhong W, Kercher K, Passic S, Williams JW, Szep Z, Khalili K, Jacobson JM, Nonnemacher MR, Wigdahl B.

AIDS Res Hum Retroviruses. 2018 Nov;34(11):950-960. doi: 10.1089/AID.2017.0274. Epub 2018 Aug 27.


Immunomodulatory Effects of Human Cryopreserved Viable Amniotic Membrane in a Pro-Inflammatory Environment In Vitro.

Witherel CE, Yu T, Concannon M, Dampier W, Spiller KL.

Cell Mol Bioeng. 2017 Oct;10(5):451-462. doi: 10.1007/s12195-017-0494-7. Epub 2017 Aug 4.


Designing broad-spectrum anti-HIV-1 gRNAs to target patient-derived variants.

Dampier W, Sullivan NT, Chung CH, Mell JC, Nonnemacher MR, Wigdahl B.

Sci Rep. 2017 Oct 31;7(1):14413. doi: 10.1038/s41598-017-12612-z.


Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences.

Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Pirrone V, Zhong W, Kercher K, Passic S, Williams J, Liu Y, James T, Jacobson JM, Szep Z, Wigdahl B, Krebs FC.

Int J Genomics. 2017;2017:4081585. doi: 10.1155/2017/4081585. Epub 2017 May 17.


Transcriptome analysis of IL-10-stimulated (M2c) macrophages by next-generation sequencing.

Lurier EB, Dalton D, Dampier W, Raman P, Nassiri S, Ferraro NM, Rajagopalan R, Sarmady M, Spiller KL.

Immunobiology. 2017 Jul;222(7):847-856. doi: 10.1016/j.imbio.2017.02.006. Epub 2017 Feb 20.


Deconvolution of heterogeneous wound tissue samples into relative macrophage phenotype composition via models based on gene expression.

Ferraro NM, Dampier W, Weingarten MS, Spiller KL.

Integr Biol (Camb). 2017 Apr 18;9(4):328-338. doi: 10.1039/c7ib00018a.


Mitochondrial Haplogroup Influences Motor Function in Long-Term HIV-1-Infected Individuals.

Azar A, Devlin K, Mell JC, Giovannetti T, Pirrone V, Nonnemacher MR, Passic S, Kercher K, Williams JW, Jacobson JM, Wigdahl B, Dampier W, Libon DJ, Sell C.

PLoS One. 2016 Oct 6;11(10):e0163772. doi: 10.1371/journal.pone.0163772. eCollection 2016.


Specific amino acids in HIV-1 Vpr are significantly associated with differences in patient neurocognitive status.

Dampier W, Antell GC, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, James T, Devlin KN, Giovannetti T, Libon DJ, Szep Z, Ehrlich GD, Wigdahl B, Krebs FC.

J Neurovirol. 2017 Feb;23(1):113-124. doi: 10.1007/s13365-016-0462-3. Epub 2016 Jul 11.


Prolonged Morphine Exposure Induces Increased Firm Adhesion in an in Vitro Model of the Blood-Brain Barrier.

Strazza M, Pirrone V, Wigdahl B, Dampier W, Lin W, Feng R, Maubert ME, Weksler B, Romero IA, Couraud PO, Nonnemacher MR.

Int J Mol Sci. 2016 Jun 9;17(6). pii: E916. doi: 10.3390/ijms17060916.


HIV-1 Genetic Variation Resulting in the Development of New Quasispecies Continues to Be Encountered in the Peripheral Blood of Well-Suppressed Patients.

Dampier W, Nonnemacher MR, Mell J, Earl J, Ehrlich GD, Pirrone V, Aiamkitsumrit B, Zhong W, Kercher K, Passic S, Williams JW, Jacobson JM, Wigdahl B.

PLoS One. 2016 May 19;11(5):e0155382. doi: 10.1371/journal.pone.0155382. eCollection 2016.


Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures.

Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, Schwartz G, Hershberg U, Krebs FC, Wigdahl B.

Retrovirology. 2016 May 3;13(1):32. doi: 10.1186/s12977-016-0266-9.


HIV-1 Promoter Single Nucleotide Polymorphisms Are Associated with Clinical Disease Severity.

Nonnemacher MR, Pirrone V, Feng R, Moldover B, Passic S, Aiamkitsumrit B, Dampier W, Wojno A, Kilareski E, Blakey B, Ku TS, Shah S, Sullivan NT, Jacobson JM, Wigdahl B.

PLoS One. 2016 Apr 21;11(4):e0150835. doi: 10.1371/journal.pone.0150835. eCollection 2016.


HIV-1 Latency and Eradication: Past, Present and Future.

Datta PK, Kaminski R, Hu W, Pirrone V, Sullivan NT, Nonnemacher MR, Dampier W, Wigdahl B, Khalili K.

Curr HIV Res. 2016;14(5):431-441. Review.


Kinase-independent role of cyclin D1 in chromosomal instability and mammary tumorigenesis.

Casimiro MC, Di Sante G, Crosariol M, Loro E, Dampier W, Ertel A, Yu Z, Saria EA, Papanikolaou A, Li Z, Wang C, Addya S, Lisanti MP, Fortina P, Cardiff RD, Tozeren A, Knudsen ES, Arnold A, Pestell RG.

Oncotarget. 2015 Apr 20;6(11):8525-38.


HIV Excision Utilizing CRISPR/Cas9 Technology: Attacking the Proviral Quasispecies in Reservoirs to Achieve a Cure.

Dampier W, Nonnemacher MR, Sullivan NT, Jacobson JM, Wigdahl B.

MOJ Immunol. 2014 Oct 17;1(4). pii: 00022.


Defining differential genetic signatures in CXCR4- and the CCR5-utilizing HIV-1 co-linear sequences.

Aiamkitsumrit B, Dampier W, Martin-Garcia J, Nonnemacher MR, Pirrone V, Ivanova T, Zhong W, Kilareski E, Aldigun H, Frantz B, Rimbey M, Wojno A, Passic S, Williams JW, Shah S, Blakey B, Parikh N, Jacobson JM, Moldover B, Wigdahl B.

PLoS One. 2014 Sep 29;9(9):e107389. doi: 10.1371/journal.pone.0107389. eCollection 2014.


Bioinformatic analysis of HIV-1 entry and pathogenesis.

Aiamkitsumrit B, Dampier W, Antell G, Rivera N, Martin-Garcia J, Pirrone V, Nonnemacher MR, Wigdahl B.

Curr HIV Res. 2014;12(2):132-61. Review.


Cocaine alters cytokine profiles in HIV-1-infected African American individuals in the DrexelMed HIV/AIDS genetic analysis cohort.

Parikh N, Dampier W, Feng R, Passic SR, Zhong W, Frantz B, Blakey B, Aiamkitsumrit B, Pirrone V, Nonnemacher MR, Jacobson JM, Wigdahl B.

J Acquir Immune Defic Syndr. 2014 Jul 1;66(3):256-64. doi: 10.1097/QAI.0000000000000163.


CCAAT enhancer binding protein and nuclear factor of activated T cells regulate HIV-1 LTR via a novel conserved downstream site in cells of the monocyte-macrophage lineage.

Dahiya S, Liu Y, Nonnemacher MR, Dampier W, Wigdahl B.

PLoS One. 2014 Feb 14;9(2):e88116. doi: 10.1371/journal.pone.0088116. eCollection 2014.


Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases.

Clark PM, Dawany N, Dampier W, Byers SW, Pestell RG, Tozeren A.

Inflamm Bowel Dis. 2012 Dec;18(12):2315-33. doi: 10.1002/ibd.22958. Epub 2012 Apr 5.


Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis.

Smith SB, Dampier W, Tozeren A, Brown JR, Magid-Slav M.

PLoS One. 2012;7(3):e33174. doi: 10.1371/journal.pone.0033174. Epub 2012 Mar 14.


ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice.

Casimiro MC, Crosariol M, Loro E, Ertel A, Yu Z, Dampier W, Saria EA, Papanikolaou A, Stanek TJ, Li Z, Wang C, Fortina P, Addya S, Tozeren A, Knudsen ES, Arnold A, Pestell RG.

J Clin Invest. 2012 Mar;122(3):833-43. doi: 10.1172/JCI60256. Epub 2012 Feb 6. Erratum in: J Clin Invest. 2013 May 1;123(5):2332.


HIV protein sequence hotspots for crosstalk with host hub proteins.

Sarmady M, Dampier W, Tozeren A.

PLoS One. 2011;6(8):e23293. doi: 10.1371/journal.pone.0023293. Epub 2011 Aug 15.


Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.

Sarmady M, Dampier W, Tozeren A.

PLoS One. 2011;6(6):e20735. doi: 10.1371/journal.pone.0020735. Epub 2011 Jun 28.


Large-scale integration of microarray data reveals genes and pathways common to multiple cancer types.

Dawany NB, Dampier WN, Tozeren A.

Int J Cancer. 2011 Jun 15;128(12):2881-91. doi: 10.1002/ijc.25854. Epub 2011 Apr 11.


Attenuation of Forkhead signaling by the retinal determination factor DACH1.

Zhou J, Wang C, Wang Z, Dampier W, Wu K, Casimiro MC, Chepelev I, Popov VM, Quong A, Tozeren A, Zhao K, Lisanti MP, Pestell RG.

Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6864-9. doi: 10.1073/pnas.1002746107. Epub 2010 Mar 29.


Host sequence motifs shared by HIV predict response to antiretroviral therapy.

Dampier W, Evans P, Ungar L, Tozeren A.

BMC Med Genomics. 2009 Jul 23;2:47. doi: 10.1186/1755-8794-2-47.


Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs.

Evans P, Dampier W, Ungar L, Tozeren A.

BMC Med Genomics. 2009 May 18;2:27. doi: 10.1186/1755-8794-2-27.


Collagen's triglycine repeat number and phylogeny suggest an interdomain transfer event from a Devonian or Silurian organism into Trichodesmium erythraeum.

Layton BE, D'Souza AJ, Dampier W, Zeiger A, Sabur A, Jean-Charles J.

J Mol Evol. 2008 Jun;66(6):539-54. doi: 10.1007/s00239-008-9111-7. Epub 2008 Jun 3.


Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets.

Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A.

BMC Bioinformatics. 2007 Oct 26;8:415.


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