John V Carlis
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Explore the profile of John V Carlis including associated specialties, affiliations and a list of published articles.
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25
Citations
1618
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Recent Articles
1.
Van Riper S, Higgins L, Carlis J, Griffin T
Bioinformatics
. 2016 May;
32(13):2035-7.
PMID: 27153682
Unlabelled: RIPPER is a framework for mass-spectrometry-based label-free relative quantification for proteomics and metabolomics studies. RIPPER combines a series of previously described algorithms for pre-processing, analyte quantification, retention time alignment,...
2.
Zeng M, Smith A, Shang L, Wietgrefe S, Voss J, Carlis J, et al.
J Immunol
. 2016 Feb;
196(6):2809-18.
PMID: 26864031
Live attenuated vaccines such as SIV with a deleted nef gene have provided the most robust protection against subsequent vaginal challenge with wild-type (WT) SIV in the SIV-rhesus macaque model...
3.
Smith A, Wietgrefe S, Shang L, Reilly C, Southern P, Perkey K, et al.
J Immunol
. 2014 Aug;
193(6):3126-33.
PMID: 25143442
Principles to guide design of an effective vaccine against HIV are greatly needed, particularly to protect women in the pandemic's epicenter in Africa. We have been seeking these principles by...
4.
Li Q, Zeng M, Duan L, Voss J, Smith A, Pambuccian S, et al.
J Immunol
. 2014 Aug;
193(6):3113-25.
PMID: 25135832
We sought design principles for a vaccine to prevent HIV transmission to women by identifying correlates of protection conferred by a highly effective live attenuated SIV vaccine in the rhesus...
5.
Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN)
Van Riper S, De Jong E, Higgins L, Carlis J, Griffin T
J Proteome Res
. 2014 Feb;
13(3):1281-92.
PMID: 24571364
Researchers are increasingly turning to label-free MS1 intensity-based quantification strategies within HPLC-ESI-MS/MS workflows to reveal biological variation at the molecule level. Unfortunately, HPLC-ESI-MS/MS workflows using these strategies produce results with...
6.
Van Riper S, De Jong E, Carlis J, Griffin T
Adv Exp Med Biol
. 2013 Feb;
990:1-35.
PMID: 23378000
As the main catalytic and structural molecules within living systems, proteins are the most likely biomolecules to be affected by radiation exposure. Proteomics, the comprehensive characterization of proteins within complex...
7.
De Jong E, Van Riper S, Koopmeiners J, Carlis J, Griffin T
Clin Chim Acta
. 2011 Sep;
412(23-24):2284-8.
PMID: 21889499
Background: Proteomic studies in saliva have demonstrated its potential as a diagnostic biofluid, however the salivary peptidome is less studied. Here we study the effects of several sample collection and...
8.
Zeng M, Smith A, Wietgrefe S, Southern P, Schacker T, Reilly C, et al.
J Clin Invest
. 2011 Mar;
121(3):998-1008.
PMID: 21393864
The hallmark of HIV-1 and SIV infections is CD4(+) T cell depletion. Both direct cell killing and indirect mechanisms related to immune activation have been suggested to cause the depletion...
9.
Bandhakavi S, Van Riper S, Tawfik P, Stone M, Haddad T, Rhodus N, et al.
J Proteome Res
. 2010 Dec;
10(3):1052-61.
PMID: 21142092
Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC's potential in shotgun proteomics. First, does...
10.
Onsongo G, Stone M, Van Riper S, Chilton J, Wu B, Higgins L, et al.
Proteomics
. 2010 Sep;
10(19):3533-8.
PMID: 20821806
Pulsed Q dissociation enables combining LTQ ion trap instruments with isobaric peptide tagging. Unfortunately, this combination lacks a technique which accurately reports protein abundance ratios and is implemented in a...