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Joseph A. Loo, Ph.D.

Laboratory Address:
Mol Sci Bldg 1424
Paul Boyer Hall 416

Work Address:
Paul Boyer Hall 402

Affiliations
Affiliations
Professor, Chemistry and Biochemistry, Biochemistry, Molecular Biology, Biological Chemistry
Member, Biochemistry, Biophysics & Structural Biology GPB Home Area, Molecular Biology Institute, UCLA-DOE Institute for Genomics & Proteomics
Researcher, Biochemistry, Chemical Biology, Proteomics and Bioinformatics
Research Interests
Our research focuses on the development of novel bioanalytical tools based on mass spectrometry approaches and their application for the structural characterization of proteins and their post-translational modifications, proteomics, and for biomedical research. Using electrospray ionization mass spectrometry (ESI-MS), we study large noncovalently-bound macromolecular complexes and their interactions with inhibitors and important ligands. ESI-MS is used to characterize the quaternary structure of important protein complexes and to identify biologically relevant protein-ligand complexes. MS-based methods are being developed for characterizing protein-protein interface interactions to be used as a predicative tool for the bonding characteristics of the interactions. Mass spectrometry sequencing methods can pinpoint ligand binding sites, for example, nucleotide binding sites to protein kinases. Novel methods for isolating and identifying important protein complexes, or machines, will depend on the high sensitivity of bioanalytical mass spectrometry. Proteome mapping of important organisms can form the framework for future studies aimed at elucidating biochemical pathways. Monitoring protein expression of causative infectious agents in the presence of potential drugs and their comparison with a reference profile can be used to determine mechanism of action and identify potential protein targets for drug discovery.
Biography

Dr. Joseph A. Loo is a Professor in the Department of Biological Chemistry, David Geffen School of Medicine, and in the Department of Chemistry & Biochemistry at the University of California, Los Angeles (UCLA), and he is the Faculty Director of the UCLA Mass Spectrometry and Proteomics Technology Center. He is also a member of UCLA/DOE Laboratory for Genomics and Proteomics, the UCLA Molecular Biology Institute, and the UCLA Jonsson Comprehensive Cancer Center. He is an expert in the mass spectrometry characterization of proteins and their post-translational modifications, and is the author of over 180 scientific publications. In 2000-2002, he served on the Board of Directors for the American Society for Mass Spectrometry. He has been on the Editorial Boards of the journals Bioconjugate Chemistry, Analytical Chemistry, Journal of the American Society for Mass Spectrometry (JASMS), and Chemical & Engineering News and currently he serves on the Editorial Advisory Board for Rapid Communications in Mass Spectrometry and as an Associate Editor for JASMS. His research interests include the development of bioanalytical methods for the structural characterization of proteins and their application for proteomics and disease biomarkers. He was one of the first researchers to apply electrospray ionization mass spectrometry (ESI-MS) to directly measure noncovalently-bound macromolecular assemblies and their interactions with other binding partners and ligands. The method can be applied to measure drug binding to their targeted proteins to even larger complexes in excess of 1 MDa. Currently, his laboratory is developing technologies to profile proteins in human salivary fluids for their application for human disease biomarker discovery. He co-authored a study with a consortium composed of groups from UCLA, UCSF, and Scripps that details the first catalog and preliminary analysis of ductal salivary proteins. In 2008, he received one of the first grants made under the new "Exceptional, Unconventional Research Enabling Knowledge Acceleration (EUREKA)" NIH program. The goal of this program is to "help investigators test novel, often unconventional hypotheses or tackle major methodological or technical challenges". The Loo award is to study the "Impact of Non-Canonical Decoding on the Proteome". Before he joined UCLA in 2001, he was Group Leader of the Biological Mass Spectrometry and Proteomics Teams at Warner-Lambert/Parke-Davis Pharmaceutical (currently Pfizer Global Research). He worked at Parke-Davis/Pfizer for nearly 10 years before moving to UCLA.

Publications

A selected list of publications:

Nguyen Thi H, Kim Sung-Hye, Decker Caitlin G, Wong Darice Y, Loo Joseph A, Maynard Heather D   A heparin-mimicking polymer conjugate stabilizes basic fibroblast growth factor Nature chemistry, 2013; 5(3): 221-7.
Spirig Thomas, Malmirchegini G Reza, Zhang Jiang, Robson Scott A, Sjodt Megan, Liu Mengyao, Krishna Kumar Kaavya, Dickson Claire F, Gell David A, Lei Benfang, Loo Joseph A, Clubb Robert T   Staphylococcus aureus uses a novel multidomain receptor to break apart human hemoglobin and steal its heme The Journal of biological chemistry, 2013; 288(2): 1065-78.
Hsieh Scott I, Castruita Madeli, Malasarn Davin, Urzica Eugen, Erde Jonathan, Page M Dudley, Yamasaki Hiroaki, Casero David, Pellegrini Matteo, Merchant Sabeeha S, Loo Joseph A   The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii Molecular & cellular proteomics : MCP, 2013; 12(1): 65-86.
Malasarn Davin, Kropat Janette, Hsieh Scott I, Finazzi Giovanni, Casero David, Loo Joseph A, Pellegrini Matteo, Wollman Francis-André, Merchant Sabeeha S   Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii The Journal of biological chemistry, 2013; 288(15): 10672-83.
Prabhudesai Shubhangi, Sinha Sharmistha, Attar Aida, Kotagiri Aswani, Fitzmaurice Arthur G, Lakshmanan Rajeswari, Lakshmanan Ravi, Ivanova Magdalena I, Loo Joseph A, Klärner Frank-Gerrit, Schrader Thomas, Stahl Mark, Bitan Gal, Bronstein Jeff M   A novel "molecular tweezer" inhibitor of α-synuclein neurotoxicity in vitro and in vivo Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics, 2012; 9(2): 464-76.
Zhu Weidong, Phan Quynh T, Boontheung Pinmanee, Solis Norma V, Loo Joseph A, Filler Scott G   EGFR and HER2 receptor kinase signaling mediate epithelial cell invasion by Candida albicans during oropharyngeal infection Proceedings of the National Academy of Sciences of the United States of America, 2012; 109(35): 14194-9.
Page M Dudley, Allen Michael D, Kropat Janette, Urzica Eugen I, Karpowicz Steven J, Hsieh Scott I, Loo Joseph A, Merchant Sabeeha S   Fe sparing and Fe recycling contribute to increased superoxide dismutase capacity in iron-starved Chlamydomonas reinhardtii The Plant cell, 2012; 24(6): 2649-65.
Rohlin Lars, Leon Deborah R, Kim Unmi, Loo Joseph A, Ogorzalek Loo Rachel R, Gunsalus Robert P   Identification of the major expressed S-layer and cell surface-layer-related proteins in the model methanogenic archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A Archaea (Vancouver, B.C.), 2012; 2012(5): 873589.
Shirasaki Dyna I, Greiner Erin R, Al-Ramahi Ismael, Gray Michelle, Boontheung Pinmanee, Geschwind Daniel H, Botas Juan, Coppola Giovanni, Horvath Steve, Loo Joseph A, Yang X William   Network organization of the huntingtin proteomic interactome in mammalian brain Neuron, 2012; 75(1): 41-57.
Urzica Eugen I, Casero David, Yamasaki Hiroaki, Hsieh Scott I, Adler Lital N, Karpowicz Steven J, Blaby-Haas Crysten E, Clarke Steven G, Loo Joseph A, Pellegrini Matteo, Merchant Sabeeha S   Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage The Plant cell, 2012; 24(10): 3921-48.
Chiu May L, Ytterberg A Jimmy, Ogorzalek Loo Rachel R, Loo Joseph A, Monbouquette Harold G   Characterization of morphine-glucose-6-phosphate dehydrogenase conjugates by mass spectrometry Bioconjugate chemistry, 2011; 22(8): 1595-604.
Zhang Lifeng, Pang Eric, Loo Rachel R Ogorzalek, Rao Jianyu, Go Vay-Liang W, Loo Joseph A, Lu Qing-Yi   Concomitant inhibition of HSP90, its mitochondrial localized homologue TRAP1 and HSP27 by green tea in pancreatic cancer HPAF-II cells Proteomics, 2011; 11(24): 4638-47.
Ferguson Carly N, Benchaar Sabrina A, Miao Zhixin, Loo Joseph A, Chen Hao   Direct ionization of large proteins and protein complexes by desorption electrospray ionization-mass spectrometry Analytical chemistry, 2011; 83(17): 6468-73.
Sinha Sharmistha, Lopes Dahabada H J, Du Zhenming, Pang Eric S, Shanmugam Akila, Lomakin Aleksey, Talbiersky Peter, Tennstaedt Annette, McDaniel Kirsten, Bakshi Reena, Kuo Pei-Yi, Ehrmann Michael, Benedek George B, Loo Joseph A, Klärner Frank-Gerrit, Schrader Thomas, Wang Chunyu, Bitan Gal   Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins Journal of the American Chemical Society, 2011; 133(42): 16958-69.
Castruita Madeli, Casero David, Karpowicz Steven J, Kropat Janette, Vieler Astrid, Hsieh Scott I, Yan Weihong, Cokus Shawn, Loo Joseph A, Benning Christoph, Pellegrini Matteo, Merchant Sabeeha S   Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps The Plant cell, 2011; 23(4): 1273-92.
Schneider Rachel E, Brown Mark T, Shiflett April M, Dyall Sabrina D, Hayes Richard D, Xie Yongming, Loo Joseph A, Johnson Patricia J   The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes International journal for parasitology, 2011; 41(13-14): 1421-34.
Yin Sheng, Loo Joseph A   Top-Down Mass Spectrometry of Supercharged Native Protein-Ligand Complexes International journal of mass spectrometry, 2011; 300(2-3): 118-122.
Kang Xuedong, Li Ning, Wang Meiying, Boontheung Pinmanee, Sioutas Constantinos, Harkema Jack R, Bramble Lori A, Nel Andre E, Loo Joseph A   Adjuvant effects of ambient particulate matter monitored by proteomics of bronchoalveolar lavage fluid Proteomics, 2010; 10(3): 520-31.
Ryan Christopher M, Souda Puneet, Halgand Frederic, Wong David T, Loo Joseph A, Faull Kym F, Whitelegge Julian P   Confident assignment of intact mass tags to human salivary cystatins using top-down Fourier-transform ion cyclotron resonance mass spectrometry Journal of the American Society for Mass Spectrometry, 2010; 21(6): 908-17.
Peng Ivory X, Ogorzalek Loo Rachel R, Margalith Eli, Little Mark W, Loo Joseph A   Electrospray-assisted laser desorption ionization mass spectrometry (ELDI-MS) with an infrared laser for characterizing peptides and proteins The Analyst, 2010; 135(4): 767-72.
Yin Sheng, Loo Joseph A   Elucidating the site of protein-ATP binding by top-down mass spectrometry Journal of the American Society for Mass Spectrometry, 2010; 21(6): 899-907.
Loo Joseph A   Focus in honor of Dr. Neil Kelleher, recipient of the 2009 Biemann Medal Journal of the American Society for Mass Spectrometry, 2010; 21(6): i-iii.
Chatterjee Debalina, Ytterberg A Jimmy, Son Sang Uk, Loo Joseph A, Garrell Robin L   Integration of protein processing steps on a droplet microfluidics platform for MALDI-MS analysis Analytical chemistry, 2010; 82(5): 2095-101.
Grintsevich Elena E, Galkin Vitold E, Orlova Albina, Ytterberg A Jimmy, Mikati Mouna M, Kudryashov Dmitri S, Loo Joseph A, Egelman Edward H, Reisler Emil   Mapping of drebrin binding site on F-actin Journal of molecular biology, 2010; 398(4): 542-54.
Thevis Mario, Thomas Andreas, Kohler Maxie, Beuck Simon, Möller Ines, Schäfer Mathias, Rodchenkov Grigory, Yin Sheng, Loo Joseph A, Geyer Hans, Schänzer Wilhelm   Mass spectrometry-based characterization of new drugs and methods of performance manipulation in doping control analysis European journal of mass spectrometry (Chichester, England), 2010; 16(3): 301-12.
Halgand Frédéric, Zabrouskov Vlad, Bassilian Sara, Souda Puneet, Wong David T, Loo Joseph A, Faull Kym F, Whitelegge Julian P   Micro-heterogeneity of human saliva Peptide P-C characterized by high-resolution top-down Fourier-transform mass spectrometry Journal of the American Society for Mass Spectrometry, 2010; 21(5): 868-77.
Razani Bahram, Zarnegar Brian, Ytterberg A Jimmy, Shiba Travis, Dempsey Paul W, Ware Carl F, Loo Joseph A, Cheng Genhong   Negative feedback in noncanonical NF-kappaB signaling modulates NIK stability through IKKalpha-mediated phosphorylation Science signaling, 2010; 3(123): ra41.
Lomeli Shirley H, Peng Ivory X, Yin Sheng, Loo Rachel R Ogorzalek, Loo Joseph A   New reagents for increasing ESI multiple charging of proteins and protein complexes Journal of the American Society for Mass Spectrometry, 2010; 21(1): 127-31.
Loo Joseph A   Outstanding JASMS Manuscript Reviewers, 2009-2010 Journal of the American Society for Mass Spectrometry, 2010; .
Sun Qingyu, Yin Sheng, Loo Joseph A, Julian Ryan R   Radical directed dissociation for facile identification of iodotyrosine residues using electrospray ionization mass spectrometry Analytical chemistry, 2010; 82(9): 3826-33.
Senturia Rachel, Faller Michael, Yin Sheng, Loo Joseph A, Cascio Duilio, Sawaya Michael R, Hwang Daniel, Clubb Robert T, Guo Feng   Structure of the dimerization domain of DiGeorge critical region 8 Protein science : a publication of the Protein Society, 2010; 19(7): 1354-65.
Maji Samir K, Ogorzalek Loo Rachel R, Inayathullah Mohammed, Spring Sean M, Vollers Sabrina S, Condron Margaret M, Bitan Gal, Loo Joseph A, Teplow David B   Amino acid position-specific contributions to amyloid beta-protein oligomerization The Journal of biological chemistry, 2009; 284(35): 23580-91.
Mosessian Sherly, Avliyakulov Nuraly K, Mulholland David J, Boontheung Pinmanee, Loo Joseph A, Wu Hong   Analysis of PTEN complex assembly and identification of heterogeneous nuclear ribonucleoprotein C as a component of the PTEN-associated complex The Journal of biological chemistry, 2009; 284(44): 30159-66.
Pesek Joseph J, Matyska Maria T, Loo Joseph A, Fischer Steven M, Sana Theodore R   Analysis of hydrophilic metabolites in physiological fluids by HPLC-MS using a silica hydride-based stationary phase Journal of separation science, 2009; 32(13): 2200-8.
Averette Kathleen M, Pratt Matthew R, Yang Yanan, Bassilian Sara, Whitelegge Julian P, Loo Joseph A, Muir Tom W, Bradley Kenneth A   Anthrax lethal toxin induced lysosomal membrane permeabilization and cytosolic cathepsin release is Nlrp1b/Nalp1b-dependent PloS one, 2009; 4(11): e7913.
Lu Qing-Yi, Yang Yanan, Jin Yu Sheng, Zhang Zuo-Feng, Heber David, Li Frederick P, Dubinett Steven M, Sondej Melissa A, Loo Joseph A, Rao Jian Yu   Effects of green tea extract on lung cancer A549 cells: proteomic identification of proteins associated with cell migration Proteomics, 2009; 9(3): 757-67.
Ly Tony, Yin Sheng, Loo Joseph A, Julian Ryan R   Electron-induced dissociation of protonated peptides yields backbone fragmentation consistent with a hydrogen-deficient radical Rapid communications in mass spectrometry : RCM, 2009; 23(13): 2099-101.
Lu Kan V, Zhu Shaojun, Cvrljevic Anna, Huang Tiffany T, Sarkaria Shawn, Ahkavan David, Dang Julie, Dinca Eduard B, Plaisier Seema B, Oderberg Isaac, Lee Yohan, Chen Zugen, Caldwell Jeremy S, Xie Yongmin, Loo Joseph A, Seligson David, Chakravari Arnab, Lee Francis Y, Weinmann Roberto, Cloughesy Timothy F, Nelson Stanley F, Bergers Gabriele, Graeber Thomas, Furnari Frank B, James C David, Cavenee Webster K, Johns Terrance G, Mischel Paul S   Fyn and SRC are effectors of oncogenic epidermal growth factor receptor signaling in glioblastoma patients Cancer research, 2009; 69(17): 6889-98.
Nie Minghua, Xie Yongming, Loo Joseph A, Courey Albert J   Genetic and proteomic evidence for roles of Drosophila SUMO in cell cycle control, Ras signaling, and early pattern formation PloS one, 2009; 4(6): e5905.
Sondej Melissa, Denny Patricia A, Xie Yongming, Ramachandran Prasanna, Si Yan, Takashima Jona, Shi Wenyuan, Wong David T, Loo Joseph A, Denny Paul C   Glycoprofiling of the Human Salivary Proteome Clinical proteomics, 2009; 5(1): 52-68.
Lomeli Shirley H, Yin Sheng, Ogorzalek Loo Rachel R, Loo Joseph A   Increasing charge while preserving noncovalent protein complexes for ESI-MS Journal of the American Society for Mass Spectrometry, 2009; 20(4): 593-6.
Yin Sheng, Loo Joseph A   Mass spectrometry detection and characterization of noncovalent protein complexes Methods in molecular biology (Clifton, N.J.), 2009; 492(3): 273-82.
Zhang Lifeng, Wang Meiying, Kang Xuedong, Boontheung Pinmanee, Li Ning, Nel Andre E, Loo Joseph A   Oxidative stress and asthma: proteome analysis of chitinase-like proteins and FIZZ1 in lung tissue and bronchoalveolar lavage fluid Journal of proteome research, 2009; 8(4): 1631-8.
Sohn Chang Ho, Chung Cheol K, Yin Sheng, Ramachandran Prasanna, Loo Joseph A, Beauchamp J L   Probing the mechanism of electron capture and electron transfer dissociation using tags with variable electron affinity Journal of the American Chemical Society, 2009; 131(15): 5444-59.
Loo Joseph A   Rantings of an associate editor: a plea to manuscript reviewers Journal of the American Society for Mass Spectrometry, 2009; 20(4): i-ii.
Tienson Heather L, Dabir Deepa V, Neal Sonya E, Loo Rachel, Hasson Samuel A, Boontheung Pinmanee, Kim Sung-Kun, Loo Joseph A, Koehler Carla M   Reconstitution of the mia40-erv1 oxidative folding pathway for the small tim proteins Molecular biology of the cell, 2009; 20(15): 3481-90.
Leary Julie A, Loo Joseph A   Report of the 2008 ASMS Fall Workshop: protein-protein and protein-ligand interactions Journal of the American Society for Mass Spectrometry, 2009; 20(5): R1-2.
Zhang Zhiwen, Gildersleeve Jeff, Yang Yu-Ying, Xu Ran, Loo Joseph A, Uryu Sean, Wong Chi-Huey, Schultz Peter G   Retraction Science (New York, N.Y.), 2009; 326(5957): 1187.
Francoleon Deborah R, Boontheung Pinmanee, Yang Yanan, Kin UnMi, Ytterberg A Jimmy, Denny Patricia A, Denny Paul C, Loo Joseph A, Gunsalus Robert P, Loo Rachel R Ogorzalek   S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei Journal of proteome research, 2009; 8(4): 1972-82.
Kim Hugh I, Kim Hyungjun, Pang Eric S, Ryu Ernest K, Beegle Luther W, Loo Joseph A, Goddard William A, Kanik Isik   Structural characterization of unsaturated phosphatidylcholines using traveling wave ion mobility spectrometry Analytical chemistry, 2009; 81(20): 8289-97.
Tao Lei, Kaddis Catherine S, Ogorzalek Loo Rachel R, Grover Gregory N, Loo Joseph A, Maynard Heather D   Synthetic approach to homodimeric protein-polymer conjugates Chemical communications (Cambridge, England), 2009; 20(16): 2148-50.
Yan Weihong, Apweiler Rolf, Balgley Brian M, Boontheung Pinmanee, Bundy Jonathan L, Cargile Benjamin J, Cole Steve, Fang Xueping, Gonzalez-Begne Mireya, Griffin Timothy J, Hagen Fred, Hu Shen, Wolinsky Lawrence E, Lee Cheng S, Malamud Daniel, Melvin James E, Menon Rajasree, Mueller Michael, Qiao Renli, Rhodus Nelson L, Sevinsky Joel R, States David, Stephenson James L, Than Shawn, Yates John R, Yu Weixia, Xie Hongwei, Xie Yongming, Omenn Gilbert S, Loo Joseph A, Wong David T   Systematic comparison of the human saliva and plasma proteomes Proteomics. Clinical applications, 2009; 3(1): 116-134.
Lomenick Brett, Hao Rui, Jonai Nao, Chin Randall M, Aghajan Mariam, Warburton Sarah, Wang Jianing, Wu Raymond P, Gomez Fernando, Loo Joseph A, Wohlschlegel James A, Vondriska Thomas M, Pelletier Jerry, Herschman Harvey R, Clardy Jon, Clarke Catherine F, Huang Jing   Target identification using drug affinity responsive target stability (DARTS) Proceedings of the National Academy of Sciences of the United States of America, 2009; 106(51): 21984-9.
Gonzalez Oscar, Fontanes Vanessa, Raychaudhuri Santanu, Loo Rachel, Loo Joseph, Arumugaswami Vaithilingaraja, Sun Ren, Dasgupta Asim, French Samuel W   The heat shock protein inhibitor Quercetin attenuates hepatitis C virus production Hepatology (Baltimore, Md.), 2009; 50(6): 1756-64.
Claypool Steven M, Oktay Yavuz, Boontheung Pinmanee, Loo Joseph A, Koehler Carla M   Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane The Journal of cell biology, 2008; 182(5): 937-50.
Kudryashov Dmitri S, Durer Zeynep A Oztug, Ytterberg A Jimmy, Sawaya Michael R, Pashkov Inna, Prochazkova Katerina, Yeates Todd O, Loo Rachel R Ogorzalek, Loo Joseph A, Satchell Karla J Fullner, Reisler Emil   Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin Proceedings of the National Academy of Sciences of the United States of America, 2008; 105(47): 18537-42.
Grintsevich Elena E, Benchaar Sabrina A, Warshaviak Dora, Boontheung Pinmanee, Halgand Frédéric, Whitelegge Julian P, Faull Kym F, Loo Rachel R Ogorzalek, Sept David, Loo Joseph A, Reisler Emil   Mapping the cofilin binding site on yeast G-actin by chemical cross-linking Journal of molecular biology, 2008; 377(2): 395-409.
Yin Sheng, Xie Yongming, Loo Joseph A   Mass spectrometry of protein-ligand complexes: enhanced gas-phase stability of ribonuclease-nucleotide complexes Journal of the American Society for Mass Spectrometry, 2008; 19(8): 1199-208.
Chen Haiyan, Boontheung Pinmanee, Loo Rachel R Ogorzalek, Xie Yongming, Loo Joseph A, Rao Jian-yu, Collins Michael D   Proteomic analysis to characterize differential mouse strain sensitivity to cadmium-induced forelimb teratogenesis Birth defects research. Part A, Clinical and molecular teratology, 2008; 82(4): 187-99.
Peng Ivory X, Ogorzalek Loo Rachel R, Shiea Jentaie, Loo Joseph A   Reactive-electrospray-assisted laser desorption/ionization for characterization of peptides and proteins Analytical chemistry, 2008; 80(18): 6995-7003.
Hu Shen, Arellano Martha, Boontheung Pinmanee, Wang Jianghua, Zhou Hui, Jiang Jiang, Elashoff David, Wei Roger, Loo Joseph A, Wong David T   Salivary proteomics for oral cancer biomarker discovery Clinical cancer research : an official journal of the American Association for Cancer Research, 2008; 14(19): 6246-52.
Claypool Steven M, Boontheung Pinmanee, McCaffery J Michael, Loo Joseph A, Koehler Carla M   The cardiolipin transacylase, tafazzin, associates with two distinct respiratory components providing insight into Barth syndrome Molecular biology of the cell, 2008; 19(12): 5143-55.
Denny Paul, Hagen Fred K, Hardt Markus, Liao Lujian, Yan Weihong, Arellanno Martha, Bassilian Sara, Bedi Gurrinder S, Boontheung Pinmannee, Cociorva Daniel, Delahunty Claire M, Denny Trish, Dunsmore Jason, Faull Kym F, Gilligan Joyce, Gonzalez-Begne Mireya, Halgand Frédéric, Hall Steven C, Han Xuemei, Henson Bradley, Hewel Johannes, Hu Shen, Jeffrey Sherry, Jiang Jiang, Loo Joseph A, Ogorzalek Loo Rachel R, Malamud Daniel, Melvin James E, Miroshnychenko Olga, Navazesh Mahvash, Niles Richard, Park Sung Kyu, Prakobphol Akraporn, Ramachandran Prasanna, Richert Megan, Robinson Sarah, Sondej Melissa, Souda Puneet, Sullivan Mark A, Takashima Jona, Than Shawn, Wang Jianghua, Whitelegge Julian P, Witkowska H Ewa, Wolinsky Lawrence, Xie Yongming, Xu Tao, Yu Weixia, Ytterberg Jimmy, Wong David T, Yates John R, Fisher Susan J   The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions Journal of proteome research, 2008; 7(5): 1994-2006.
Faller Michael, Matsunaga Michio, Yin Sheng, Loo Joseph A, Guo Feng   Heme is involved in microRNA processing Nature structural & molecular biology, 2007; 14(1): 23-9.
Benchaar Sabrina A, Xie Yongming, Phillips Martin, Loo Rachel R Ogorzalek, Galkin Vitold E, Orlova Albina, Thevis Mario, Muhlrad Andras, Almo Steven C, Loo Joseph A, Egelman Edward H, Reisler Emil   Mapping the interaction of cofilin with subdomain 2 on actin Biochemistry, 2007; 46(1): 225-33.
Loo Rachel R Ogorzalek, Loo Joseph A   Matrix-assisted laser desorption/ionization-mass spectrometry of hydrophobic proteins in mixtures using formic acid, perfluorooctanoic acid, and sorbitol Analytical chemistry, 2007; 79(3): 1115-25.
Kaddis Catherine S, Loo Joseph A   Native protein MS and ion mobility large flying proteins with ESI Analytical chemistry, 2007; 79(5): 1778-84.
Thevis Mario, Loo Joseph A, Loo Rachel R Ogorzalek, Schänzer Wilhelm   Recommended criteria for the mass spectrometric identification of target peptides and proteins ( Rapid communications in mass spectrometry : RCM, 2007; 21(3): 297-304.
Lee Nathan V, Sato Makoto, Annis Douglas S, Loo Joseph A, Wu Lily, Mosher Deane F, Iruela-Arispe M Luisa   ADAMTS1 mediates the release of antiangiogenic polypeptides from TSP1 and 2 The EMBO journal, 2006; 25(22): 5270-83.
Hu Shen, Loo Joseph A, Wong David T   Human Body Fluid Proteome Analysis Proteomics, 2006; 6(23): 6326-53.
Hu S, Li Y, Wang J, Xie Y, Tjon K, Wolinsky L, Ogorzalek Loo RR, Loo JA, and Wong DT.   Human Saliva Proteome and Transcriptome, J Dent Res, 2006; 85: 1129-1133.
Ramachandran Prasanna, Boontheung Pinmannee, Xie Yongming, Sondej Melissa, Wong David T, Loo Joseph A   Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry Journal of proteome research, 2006; 5(6): 1493-503.
Skaggs Brian J, Gorre Mercedes E, Ryvkin Ann, Burgess Michael R, Xie Yongming, Han Yun, Komisopoulou Evangelia, Brown Lauren M, Loo Joseph A, Landaw Elliot M, Sawyers Charles L, Graeber Thomas G   Phosphorylation of the ATP-binding loop directs oncogenicity of drug-resistant BCR-ABL mutants Proceedings of the National Academy of Sciences of the United States of America, 2006; 103(51): 19466-71.
Poderycki Michael J, Kickhoefer Valerie A, Kaddis Catherine S, Raval-Fernandes Sujna, Johansson Erik, Zink Jeffrey I, Loo Joseph A, Rome Leonard H   The vault exterior shell is a dynamic structure that allows incorporation of vault-associated proteins into its interior Biochemistry, 2006; 45(39): 12184-93.
Xie Yongming, Zhang Jennifer, Yin Sheng, Loo Joseph A   Top-down ESI-ECD-FT-ICR mass spectrometry localizes noncovalent protein-ligand binding sites Journal of the American Chemical Society, 2006; 128(45): 14432-3.
Leikina Eugenia, Delanoe-Ayari Helene, Melikov Kamran, Cho Myoung-Soon, Chen Andrew, Waring Alan J, Wang Wei, Xie Yongming, Loo Joseph A, Lehrer Robert I, Chernomordik Leonid V   Carbohydrate-binding molecules inhibit viral fusion and entry by crosslinking membrane glycoproteins Nature immunology, 2005; 6(10): 995-1001.
Divakaruni Arun V, Loo Rachel R Ogorzalek, Xie Yongming, Loo Joseph A, Gober James W   The cell-shape protein MreC interacts with extracytoplasmic proteins including cell wall assembly complexes in Caulobacter crescentus Proceedings of the National Academy of Sciences of the United States of America, 2005; 102(51): 18602-7.
Gomes Aldrin V, Zong Chenggong, Edmondson Ricky D, Berhane Beniam T, Wang Guang-Wu, Le Steven, Young Glen, Zhang Jun, Vondriska Thomas M, Whitelegge Julian P, Jones Richard C, Joshua Irving G, Thyparambil Sheeno, Pantaleon Dawn, Qiao Joe, Loo Joseph, Ping Peipei   The murine cardiac 26S proteasome: an organelle awaiting exploration Annals of the New York Academy of Sciences, 2005; 1047(7): 197-207.
Hu Shen, Wang Jianghua, Meijer Jiska, Ieong Sonya, Xie Yongming, Yu Tianwei, Zhou Hui, Henry Sharon, Vissink Arjan, Pijpe Justin, Kallenberg Cees, Elashoff David, Loo Joseph A, Wong David T   Salivary proteomic and genomic biomarkers for primary Sjögren's syndrome Arthritis and rheumatism, 2007; 56(11): 3588-600.
Jung EunMi Juliana, Avliyakulov Nuraly K, Boontheung Pinmanee, Loo Joseph A, Nel Andre E   Pro-oxidative DEP chemicals induce heat shock proteins and an unfolding protein response in a bronchial epithelial cell line as determined by DIGE analysis Proteomics, 2007; 7(21): 3906-18.
Januszyk Kurt, Li Patrick Wai-Lun, Villareal Valerie, Branciforte Dan, Wu Haihong, Xie Yongming, Feigon Juli, Loo Joseph A, Martin Sandra L, Clubb Robert T   Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1 The Journal of biological chemistry, 2007; 282(34): 24893-904.
Hu Shen, Loo Joseph A, Wong David T   Human saliva proteome analysis and disease biomarker discovery Expert review of proteomics, 2007; 4(4): 531-8.
Allan Christopher M, Hill Shauna, Morvaridi Susan, Saiki Ryoichi, Johnson Jarrett S, Liau Wei-Siang, Hirano Kathleen, Kawashima Tadashi, Ji Ziming, Loo Joseph A, Shepherd Jennifer N, Clarke Catherine F   A conserved START domain coenzyme Q-binding polypeptide is required for efficient Q biosynthesis, respiratory electron transport, and antioxidant function in Saccharomyces cerevisiae Biochimica et biophysica acta, 2013; 1831(4): 776-91.
Kaddis Catherine S, Lomeli Shirley H, Yin Sheng, Berhane Beniam, Apostol Marcin I, Kickhoefer Valerie A, Rome Leonard H, Loo Joseph A   Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility Journal of the American Society for Mass Spectrometry, 2007; 18(7): 1206-16.
Loo Joseph A, Neff Joyce L   Outstanding JASMS manuscript reviewers, 2011-2012 Journal of the American Society for Mass Spectrometry, 2013; 24(3): 315.
Liu Bin, Yang Yonghui, Chernishof Vasili, Loo Rachel R Ogorzalek, Jang Hyunduk, Tahk Samuel, Yang Randy, Mink Sheldon, Shultz David, Bellone Clifford J, Loo Joseph A, Shuai Ke   Proinflammatory stimuli induce IKKalpha-mediated phosphorylation of PIAS1 to restrict inflammation and immunity Cell, 2007; 129(5): 903-14.
Hu Shen, Loo Joseph A, Wong David T   Human saliva proteome analysis Annals of the New York Academy of Sciences, 2007; 1098(5): 323-9.
Hu Shen, Yu Tianwei, Xie Yongming, Yang Yanan, Li Yang, Zhou Xiaofeng, Tsung Stephanie, Loo Rachel R, Loo Joseph R, Wong David T   Discovery of oral fluid biomarkers for human oral cancer by mass spectrometry Cancer genomics & proteomics, 2007; 4(2): 55-64.
Peng Ivory X, Shiea Jentaie, Ogorzalek Loo Rachel R, Loo Joseph A   Electrospray-assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins Rapid communications in mass spectrometry : RCM, 2007; 21(16): 2541-6.
Moon Hyejin, Wheeler Aaron R, Garrell Robin L, Loo Joseph A, Kim Chang-Jin Cj   An integrated digital microfluidic chip for multiplexed proteomic sample preparation and analysis by MALDI-MS Lab on a chip, 2006; 6(9): 1213-9.
Nelson Wyatt C, Peng Ivory, Lee Geun-An, Loo Joseph A, Garrell Robin L, Kim Chang-Jin C J   Incubated protein reduction and digestion on an electrowetting-on-dielectric digital microfluidic chip for MALDI-MS Analytical chemistry, 2010; 82(23): 9932-7.
Leuchter Andrew F, Cook Ian A, Hamilton Steven P, Narr Katherine L, Toga Arthur, Hunter Aimee M, Faull Kym, Whitelegge Julian, Andrews Anne M, Loo Joseph, Way Baldwin, Nelson Stanley F, Horvath Steven, Lebowitz Barry D   Biomarkers to predict antidepressant response Current psychiatry reports, 2010; 12(6): 553-62.
Arellano-Garcia Martha E, Li Roger, Liu Xiaojun, Xie Yongming, Yan Xiaofei, Loo Joseph A, Hu Shen   Identification of tetranectin as a potential biomarker for metastatic oral cancer International journal of molecular sciences, 2010; 11(9): 3106-21.
Tao Lei, Kaddis Catherine S, Loo Rachel R Ogorzalek, Grover Gregory N, Loo Joseph A, Maynard Heather D   Synthesis of Maleimide-End Functionalized Star Polymers and Multimeric Protein-Polymer Conjugates Macromolecules, 2009; 42(21): 8028-8033.
Ramachandran Prasanna, Boontheung Pinmanee, Pang Eric, Yan Weihong, Wong David T, Loo Joseph A   Comparison of N-linked Glycoproteins in Human Whole Saliva, Parotid, Submandibular, and Sublingual Glandular Secretions Identified using Hydrazide Chemistry and Mass Spectrometry Clinical proteomics, 2008; 4(3-4): 80-104.
Mathivanan Suresh, Ahmed Mukhtar, Ahn Natalie G, Alexandre Hainard, Amanchy Ramars, Andrews Philip C, Bader Joel S, Balgley Brian M, Bantscheff Marcus, Bennett Keiryn L, Björling Erik, Blagoev Blagoy, Bose Ron, Brahmachari Samir K, Burlingame Alma S, Bustelo Xosé R, Cagney Gerard, Cantin Greg T, Cardasis Helene L, Celis Julio E, Chaerkady Raghothama, Chu Feixia, Cole Philip A, Costello Catherine E, Cotter Robert J, Crockett David, DeLany James P, De Marzo Angelo M, DeSouza Leroi V, Deutsch Eric W, Dransfield Eric, Drewes Gerard, Droit Arnaud, Dunn Michael J, Elenitoba-Johnson Kojo, Ewing Rob M, Van Eyk Jennifer, Faca Vitor, Falkner Jayson, Fang Xiangming, Fenselau Catherine, Figeys Daniel, Gagné Pierre, Gelfi Cecilia, Gevaert Kris, Gimble Jeffrey M, Gnad Florian, Goel Renu, Gromov Pavel, Hanash Samir M, Hancock William S, Harsha H C, Hart Gerald, Hays Faith, He Fuchu, Hebbar Prashantha, Helsens Kenny, Hermeking Heiko, Hide Winston, Hjernø Karin, Hochstrasser Denis F, Hofmann Oliver, Horn David M, Hruban Ralph H, Ibarrola Nieves, James Peter, Jensen Ole N, Jensen Pia Hønnerup, Jung Peter, Kandasamy Kumaran, Kheterpal Indu, Kikuno Reiko F, Korf Ulrike, Körner Roman, Kuster Bernhard, Kwon Min-Seok, Lee Hyoung-Joo, Lee Young-Jin, Lefevre Michael, Lehvaslaiho Minna, Lescuyer Pierre, Levander Fredrik, Lim Megan S, Löbke Christian, Loo Joseph A, Mann Matthias, Martens Lennart, Martinez-Heredia Juan, McComb Mark, McRedmond James, Mehrle Alexander, Menon Rajasree, Miller Christine A, Mischak Harald, Mohan S Sujatha, Mohmood Riaz, Molina Henrik, Moran Michael F, Morgan James D, Moritz Robert, Morzel Martine, Muddiman David C, Nalli Anuradha, Navarro J Daniel, Neubert Thomas A, Ohara Osamu, Oliva Rafael, Omenn Gilbert S, Oyama Masaaki, Paik Young-Ki, Pennington Kyla, Pepperkok Rainer, Periaswamy Balamurugan, Petricoin Emanuel F, Poirier Guy G, Prasad T S Keshava, Purvine Samuel O, Rahiman B Abdul, Ramachandran Prasanna, Ramachandra Y L, Rice Robert H, Rick Jens, Ronnholm Ragna H, Salonen Johanna, Sanchez Jean-Charles, Sayd Thierry, Seshi Beerelli, Shankari Kripa, Sheng Shi Jun, Shetty Vivekananda, Shivakumar K, Simpson Richard J, Sirdeshmukh Ravi, Siu K W Michael, Smith Jeffrey C, Smith Richard D, States David J, Sugano Sumio, Sullivan Matthew, Superti-Furga Giulio, Takatalo Maarit, Thongboonkerd Visith, Trinidad Jonathan C, Uhlen Mathias, Vandekerckhove Joël, Vasilescu Julian, Veenstra Timothy D, Vidal-Taboada José-Manuel, Vihinen Mauno, Wait Robin, Wang Xiaoyue, Wiemann Stefan, Wu Billy, Xu Tao, Yates John R, Zhong Jun, Zhou Ming, Zhu Yunping, Zurbig Petra, Pandey Akhilesh   Human Proteinpedia enables sharing of human protein data Nature biotechnology, 2008; 26(2): 164-7.
Whitelegge Julian P, Zabrouskov Vlad, Halgand Frederic, Souda Puneet, Bassilian Sara, Yan Weihong, Wolinsky Larry, Loo Joseph A, Wong David T W, Faull Kym F   Protein-Sequence Polymorphisms and Post-translational Modifications in Proteins from Human Saliva using Top-Down Fourier-transform Ion Cyclotron Resonance Mass Spectrometry International journal of mass spectrometry, 2007; 268(2-3): 190-197.