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Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in‐depth proteomic analysis.
Published in:
Journal of Extracellular Vesicles, 2022, v. 11, n. 2, p. 1, doi. 10.1002/jev2.12184
By:
- Correll, Vanessa L.;
- Otto, Joseph J.;
- Risi, Cristina M.;
- Main, Brian P.;
- Boutros, Paul C.;
- Kislinger, Thomas;
- Galkin, Vitold E.;
- Nyalwidhe, Julius O.;
- Semmes, O. John;
- Yang, Lifang
Publication type:
Article
Adult T cell leukemia: a tale of two T cells.
Published in:
2006
By:
- Semmes, O. John
Publication type:
journal article
Measurement reproducibility in the early stages of biomarker development.
Published in:
Disease Markers, 2004, v. 20, n. 6, p. 295, doi. 10.1155/2004/726517
By:
- Liggett, Walter S.;
- Barker, Peter E.;
- Semmes, O. John;
- Cazares, Lisa H.
Publication type:
Article
SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers.
Published in:
Disease Markers, 2003, v. 19, n. 4-5, p. 229
By:
- Laronga, Christine;
- Becker, Stephen;
- Watson, Patrice;
- Gregory, Betsy;
- Cazares, Lisa;
- Lynch, Henry;
- Perry, Roger R.;
- Wright Jr., George L.;
- Drake, Richard R.;
- Semmes, O. John
Publication type:
Article
Serum protein expression profiling for cancer detection: Validation of a SELDI-based approach for prostate cancer.
Published in:
Disease Markers, 2003, v. 19, n. 4-5, p. 185
By:
- Grizzle, William E.;
- Bao-Ling Adam;
- Bigbee, William L.;
- Conrads, Thomas P.;
- Carroll, Christopher;
- Ziding Feng;
- Izbicka, Elzbieta;
- Jendoubi, Moncef;
- Johnsey, Donald;
- Kagan, Jacob;
- Leach, Robin J.;
- McCarthy, Diane B.;
- Semmes, O. John;
- Srivastava, Shiv;
- Srivastava, Sudhir;
- Thompson, Ian M.;
- Thornquist, Mark D.;
- Verma, Mukesh;
- Zhen Zhang;
- Zhiqiang Zou
Publication type:
Article
The search for biomarkers of human embryo developmental potential in IVF: a comprehensive proteomic approach.
Published in:
Molecular Human Reproduction, 2013, v. 19, n. 4, p. 250, doi. 10.1093/molehr/gas063
By:
- Nyalwidhe, Julius;
- Burch, Tanya;
- Bocca, Silvina;
- Cazares, Lisa;
- Green-Mitchell, Shamina;
- Cooke, Marissa;
- Birdsall, Paige;
- Basu, Gaurav;
- Semmes, O. John;
- Oehninger, Sergio
Publication type:
Article
Differential capture of serum proteins for expression profiling and biomarker discovery in pre- and posttreatment head and neck cancer samples.
Published in:
2008
By:
- Freed GL;
- Cazares LH;
- Fichandler CE;
- Fuller TW;
- Sawyer CA;
- Stack BC Jr.;
- Schraff S;
- Semmes OJ;
- Wadsworth JT;
- Drake RR;
- Freed, Gary L;
- Cazares, Lisa H;
- Fichandler, Craig E;
- Fuller, Thomas W;
- Sawyer, Christopher A;
- Stack, Brendan C Jr;
- Schraff, Scott;
- Semmes, O John;
- Wadsworth, J Trad;
- Drake, Richard R
Publication type:
journal article
Differential Capture of Serum Proteins for Expression Profiling and Biomarker Discovery in Pre- and Posttreatment Head and Neck Cancer Samples.
Published in:
Laryngoscope, 2008, v. 118, n. 1, p. 61, doi. 10.1097/MLG.0b013e31814cf389
By:
- Freed, Gary L.;
- Cazares, Lisa H.;
- Fichandler, Craig E.;
- Fuller, Thomas W.;
- Sawyer, Christopher A.;
- Stack, Brendan C.;
- Schraff, Scott;
- Semmes, O John;
- Wadsworth, J Trad;
- Drake, Richard R.
Publication type:
Article
MALDI tissue imaging: from biomarker discovery to clinical applications.
Published in:
Analytical & Bioanalytical Chemistry, 2011, v. 401, n. 1, p. 17, doi. 10.1007/s00216-011-5003-6
By:
- Cazares, Lisa H.;
- Troyer, Dean A.;
- Binghe Wang;
- Drake, Richard R.;
- Semmes, O. John
Publication type:
Article
Enhancement in MALDI-TOF MS analysis of the low molecular weight human serum proteome.
Published in:
Journal of Mass Spectrometry, 2011, v. 46, n. 1, p. 85, doi. 10.1002/jms.1864
By:
- Gatlin, Christine L.;
- White, Krista Y.;
- Tracy, Maureen B.;
- Wilkins, Christopher E.;
- John Semmes, O.;
- Nyalwidhe, Julius O.;
- Drake, Richard R.;
- Malyarenko, Dariya I.
Publication type:
Article
Staphylococcus aureus Clumping Factor A Binds to Complement Regulator Factor I and Increases Factor I Cleavage of C3b.
Published in:
Journal of Infectious Diseases, 2008, v. 198, n. 1, p. 125, doi. 10.1086/588825
By:
- Hair, Pamela S.;
- Ward, Michael D.;
- Semmes, O. John;
- Foster, Timothy J.;
- Cunnion, Kenji M.
Publication type:
Article
In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
Published in:
Proteomics, 2013, v. 13, n. 10/11, p. 1667, doi. 10.1002/pmic.201200561
By:
- Principe, Simona;
- Jones, E. Ellen;
- Kim, Yunee;
- Sinha, Ankit;
- Nyalwidhe, Julius O.;
- Brooks, Jasmin;
- Semmes, O. John;
- Troyer, Dean A.;
- Lance, Raymond S.;
- Kislinger, Thomas;
- Drake, Richard R.
Publication type:
Article
Membrane Protein Structure Determination: Methods and Protocols Jean-Jacques Lacapère (Editor) Series: Methods in Molecular Biology, Vol. 654 Humana Press, Springer Protocols, 1st Edn., XII, 2010, pp. 459 ISBN: 978-1-60761-761-7.
Published in:
Proteomics, 2011, v. 11, n. 16, p. 3435, doi. 10.1002/pmic.201190080
By:
- Semmes, O. John
Publication type:
Article
Precision enhancement of MALDI-TOF MS using high resolution peak detection and label-free alignment.
Published in:
Proteomics, 2008, v. 8, n. 8, p. 1530, doi. 10.1002/pmic.200701146
By:
- Tracy, Maureen B.;
- Chen, Haijian;
- Weaver, Dennis M.;
- Malyarenko, Dariya I.;
- Sasinowski, Maciek;
- Cazares, Lisa H.;
- Drake, Richard R.;
- Semmes, O. John;
- Tracy, Eugene R.;
- Cooke, William E.
Publication type:
Article
Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status.
Published in:
Proteomics, 2004, v. 4, n. 3, p. 826, doi. 10.1002/pmic.200300625
By:
- Mary Ann Comunale;
- Taj S. Mattu;
- Melissa A. Lowman;
- Alison A. Evans;
- W. Thomas London;
- O. John Semmes;
- Michael Ward;
- Richard Drake;
- Patrick R. Romano;
- Laura F. Steel;
- Timothy M. Block;
- Anand Mehta
Publication type:
Article
Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer.
Published in:
Journal of Cellular Biochemistry, 2006, v. 98, n. 3, p. 496, doi. 10.1002/jcb.20855
By:
- O. John Semmes;
- Gunjan Malik;
- Mike Ward
Publication type:
Article
Interaction of retroviral Tax oncoproteins with tristetraprolin and regulation of tumor necrosis factor-alpha expression.
Published in:
2003
By:
- Twizere, Jean-Claude;
- Kruys, Véronique;
- Lefèbvre, Laurent;
- Vanderplasschen, Alain;
- Collete, Delphine;
- Debacq, Christophe;
- Lai, Wi S.;
- Jauniaux, Jean-Claude;
- Bernstein, Lori R.;
- Semmes, O. John;
- Burny, Arsène;
- Blackshear, Perry J.;
- Kettmann, Richard;
- Willems, Luc;
- Kruys, Véronique;
- Lefèbvre, Laurent;
- Burny, Arsène
Publication type:
journal article
Characterization of prostate macrophage heterogeneity, foam cell markers, and CXCL17 upregulation in a mouse model of steroid hormone imbalance.
Published in:
Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-71137-4
By:
- Silver, Samara V.;
- Tucker, Kayah J.;
- Vickman, Renee E.;
- Lanman, Nadia A.;
- Semmes, O. John;
- Alvarez, Nehemiah S.;
- Popovics, Petra
Publication type:
Article
Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants.
Published in:
Cancers, 2021, v. 13, n. 20, p. 5034, doi. 10.3390/cancers13205034
By:
- Prakash, Amol;
- Taylor, Lorne;
- Varkey, Manu;
- Hoxie, Nate;
- Mohammed, Yassene;
- Goo, Young Ah;
- Peterman, Scott;
- Moghekar, Abhay;
- Yuan, Yuting;
- Glaros, Trevor;
- Steele, Joel R.;
- Faridi, Pouya;
- Parihari, Shashwati;
- Srivastava, Sanjeeva;
- Otto, Joseph J.;
- Nyalwidhe, Julius O.;
- Semmes, O. John;
- Moran, Michael F.;
- Madugundu, Anil;
- Mun, Dong Gi
Publication type:
Article
Computational protein biomarker prediction: a case study for prostate cancer.
Published in:
BMC Bioinformatics, 2004, v. 5, p. 26, doi. 10.1186/1471-2105-5-26
By:
- Wagner, Michael;
- Naik, Dayanand N.;
- Pothen, Alex;
- Kasukurti, Srinivas;
- Ram Devineni, Raghu;
- Bao-Ling Adam;
- Semmes, O. John;
- Wright Jr., George L.
Publication type:
Article
Analysis of Potential Phosphorylation Sites in Human T Cell Leukemia Virus Type 1 Tax.
Published in:
Journal of Biomedical Science, 1999, v. 6, n. 3, p. 206, doi. 10.1159/000025388
By:
- Krause Boehm, Amber;
- Stawhecker, Judith A.;
- Semmes, O. John;
- Jankowski, Patrick E.;
- Lewis, Robert;
- Hinrichs, Steven H.
Publication type:
Article
Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.
Published in:
Cancer (0008543X), 2004, v. 100, n. 9, p. 1814, doi. 10.1002/cncr.20203
By:
- Lajos Pusztai;
- Betsy W. Gregory;
- Keith A. Baggerly;
- Bo Peng;
- John Koomen;
- Henry M. Kuerer;
- Francisco J. Esteva;
- W. Fraser Symmans;
- Peter Wagner;
- Gabriel N. Hortobagyi;
- Christine Laronga;
- O. John Semmes;
- George L. Wright;
- Richard R. Drake;
- Antonia Vlahou
Publication type:
Article
Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.
Published in:
2004
By:
- Pusztai, Lajos;
- Gregory, Betsy W;
- Baggerly, Keith A;
- Peng, Bo;
- Koomen, John;
- Kuerer, Henry M;
- Esteva, Francisco J;
- Symmans, W Fraser;
- Wagner, Peter;
- Hortobagyi, Gabriel N;
- Laronga, Christine;
- Semmes, O John;
- Wright, George L Jr;
- Drake, Richard R;
- Vlahou, Antonia
Publication type:
journal article
Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells.
Published in:
Cancer Cell International, 2006, v. 6, p. 13, doi. 10.1186/1475-2867-6-13
By:
- Belgnaoui, S. Mehdi;
- Gosden, Roger G.;
- Semmes, O. John;
- Haoudi, Abdelali
Publication type:
Article
Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer.
Published in:
Nature Communications, 2016, v. 7, n. 6, p. 11906, doi. 10.1038/ncomms11906
By:
- Kim, Yunee;
- Jeon, Jouhyun;
- Mejia, Salvador;
- Yao, Cindy Q;
- Ignatchenko, Vladimir;
- Nyalwidhe, Julius O;
- Gramolini, Anthony O;
- Lance, Raymond S;
- Troyer, Dean A;
- Drake, Richard R;
- Boutros, Paul C;
- Semmes, O. John;
- Kislinger, Thomas
Publication type:
Article
Resampling and deconvolution of linear time-of-flight records for enhanced protein profiling.
Published in:
Rapid Communications in Mass Spectrometry: RCM, 2006, v. 20, n. 11, p. 1670, doi. 10.1002/rcm.2496
By:
- Malyarenko, Dariya I.;
- Cooke, William E.;
- Tracy, Eugene R.;
- Drake, Richard R.;
- Shin, Susanna;
- Semmes, O. John;
- Sasinowski, Maciek;
- Manos, Dennis M.
Publication type:
Article
Deconvolution filters to enhance resolution of dense time-of-flight survey spectra in the time-lag optimization range.
Published in:
Rapid Communications in Mass Spectrometry: RCM, 2006, v. 20, n. 11, p. 1661, doi. 10.1002/rcm.2487
By:
- Malyarenko, Dariya I.;
- Cooke, William E.;
- Tracy, Eugene R.;
- Trosset, Michael W.;
- Semmes, O. John;
- Sasinowski, Maciek;
- Manos, Dennis M.
Publication type:
Article
The Tudor Domain Protein Spindlin1 Is Involved in Intrinsic Antiviral Defense against Incoming Hepatitis B Virus and Herpes Simplex Virus Type 1.
Published in:
PLoS Pathogens, 2014, v. 10, n. 9, p. 1, doi. 10.1371/journal.ppat.1004343
By:
- Ducroux, Aurélie;
- Benhenda, Shirine;
- Rivière, Lise;
- Semmes, O. John;
- Benkirane, Monsef;
- Neuveut, Christine
Publication type:
Article
SELDI protein profiling of dunning R-3327 derived cell lines: Identification of molecular markers of prostate cancer progression.
Published in:
Prostate, 2007, v. 67, n. 14, p. 1565, doi. 10.1002/pros.20646
By:
- Malik, Gunjan;
- Rojahn, Elizabeth;
- Ward, Michael D.;
- Gretzer, Mathew B.;
- Partin, Alan W.;
- Semmes, O. John;
- Veltri, Robert W.
Publication type:
Article
Functional and physical interaction between the mismatch repair and FA-BRCA pathways.
Published in:
Human Molecular Genetics, 2011, v. 20, n. 22, p. 4395, doi. 10.1093/hmg/ddr366
By:
- Williams, Stacy A.;
- Wilson, James B.;
- Clark, Allison P.;
- Mitson-Salazar, Alyssa;
- Tomashevski, Andrei;
- Ananth, Sahana;
- Glazer, Peter M.;
- Semmes, O. John;
- Bale, Allen E.;
- Jones, Nigel J.;
- Kupfer, Gary M.
Publication type:
Article
Changes in the Hippocampal Proteome Associated with Spatial Memory Impairment after Exposure to Low (20 cGy) Doses of 1 GeV/n <sup>56</sup>Fe Radiation.
Published in:
Radiation Research, 2017, v. 187, n. 3, p. 287, doi. 10.1667/RR14067.1
By:
- Britten, Richard A.;
- Jewell, Jessica S.;
- Davis, Leslie K.;
- Miller, Vania D.;
- Hadley, Melissa M.;
- Semmes, O. John;
- Lonart, György;
- Dutta, Sucharita M.
Publication type:
Article
A novel approach for clustering proteomics data using Bayesian fast Fourier transform.
Published in:
Bioinformatics, 2005, v. 21, n. 10, p. 2210, doi. 10.1093/bioinformatics/bti383
By:
- Halima Bensmail;
- Jennifer Golek;
- Michelle M. Moody;
- John O. Semmes;
- Abdelali Haoudi
Publication type:
Article
Serum protein expression profiling in pediatric Hodgkin lymphoma: A report from the Children's Oncology Group.
Published in:
Pediatric Blood & Cancer, 2008, v. 51, n. 2, p. 216, doi. 10.1002/pbc.21581
By:
- Qi, Lining;
- Cazares, Lisa;
- Johnson, Cris;
- de Alarcon, Pedro;
- Kupfer, Gary M.;
- Semmes, O. John
Publication type:
Article
promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling.
Published in:
Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad025
By:
- Ranathunge, Chathurani;
- Patel, Sagar S;
- Pinky, Lubna;
- Correll, Vanessa L;
- Chen, Shimin;
- Semmes, O John;
- Armstrong, Robert K;
- Combs, C Donald;
- Nyalwidhe, Julius O
Publication type:
Article
Prostate cancer reshapes the secreted and extracellular vesicle urinary proteomes.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49424-5
By:
- Khoo, Amanda;
- Govindarajan, Meinusha;
- Qiu, Zhuyu;
- Liu, Lydia Y.;
- Ignatchenko, Vladimir;
- Waas, Matthew;
- Macklin, Andrew;
- Keszei, Alexander;
- Neu, Sarah;
- Main, Brian P.;
- Yang, Lifang;
- Lance, Raymond S.;
- Downes, Michelle R.;
- Semmes, O. John;
- Vesprini, Danny;
- Liu, Stanley K.;
- Nyalwidhe, Julius O.;
- Boutros, Paul C.;
- Kislinger, Thomas
Publication type:
Article
Correction: The Tudor Domain Protein Spindlin1 Is Involved in Intrinsic Antiviral Defense against Incoming Hepatitis B Virus and Herpes Simplex Virus Type 1.
Published in:
2020
By:
- Ducroux, Aurélie;
- Benhenda, Shirine;
- Rivière, Lise;
- Semmes, O. John;
- Benkirane, Monsef;
- Neuveut, Christine
Publication type:
Correction Notice
Increased bisecting N-acetylglucosamine and decreased branched chain glycans of N-linked glycoproteins in expressed prostatic secretions associated with prostate cancer progression.
Published in:
Proteomics - Clinical Applications, 2013, v. 7, n. 9/10, p. 677, doi. 10.1002/prca.201200134
By:
- Nyalwidhe, Julius O.;
- Betesh, Lucy R.;
- Powers, Thomas W.;
- Jones, E. Ellen;
- White, Krista Y.;
- Burch, Tanya C.;
- Brooks, Jasmin;
- Watson, Megan T.;
- Lance, Raymond S.;
- Troyer, Dean A.;
- Semmes, O. John;
- Mehta, Anand;
- Drake, Richard R.
Publication type:
Article
Focus on Cancer Proteomics.
Published in:
Proteomics - Clinical Applications, 2013, v. 7, n. 5/6, p. 315, doi. 10.1002/prca.201370034
By:
- Semmes, O. John;
- Conrads, Thomas
Publication type:
Article
On-tissue identification of insulin: In situ reduction coupled with mass spectrometry imaging.
Published in:
Proteomics - Clinical Applications, 2011, v. 5, n. 7/8, p. 448, doi. 10.1002/prca.201000152
By:
- Green-Mitchell, Shamina M.;
- Cazares, Lisa H.;
- Semmes, O. John;
- Nadler, Jerry L.;
- Nyalwidhe, Julius O.
Publication type:
Article
Improved signal processing and normalization for biomarker protein detection in broad-mass-range TOF mass spectra from clinical samples.
Published in:
Proteomics - Clinical Applications, 2011, v. 5, n. 7/8, p. 440, doi. 10.1002/prca.201000095
By:
- Tracy, Maureen B.;
- Cooke, William E.;
- Gatlin, Christine L.;
- Cazares, Lisa H.;
- Weaver, Dennis M.;
- Semmes, O. John;
- Tracy, Eugene R.;
- Manos, Dennis M.;
- Malyarenko, Dariya I.
Publication type:
Article
Mining the low molecular weight proteome of blood.
Published in:
Proteomics - Clinical Applications, 2007, v. 1, n. 8, p. 758, doi. 10.1002/prca.200700175
By:
- Drake, Richard R.;
- Cazares, Lisa;
- Semmes, O. John
Publication type:
Article

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