U.S. Department of Energy

Pacific Northwest National Laboratory

Josh Adkins

Professional Title: 
Biological Sciences Associate Division Director

Dr. Joshua Adkins' research focuses on the comprehensive characterization of biomolecules through space (associated proteins, structural determinants and localization) and time (before and after treatment, cell cycle, day-night cycle, and evolutionary changes) to better understand biological systems. Of particular interest are highly challenging biological studies that require bridging the gaps between technology development and application. In recent years, this interest has led him to use host-microbe interactions as tractable model systems. These studies have ranged single cultured pathogens, such as isolated Salmonella to studies of dynamic host response, such as changes in lung fluid with viral infection. Dr. Adkins is an Associate-Director for the Biological Sciences Division leading the Integrative Omics group, Integrative Omics Projects. He has also been the Director of the recently completed Center for Systems Biology of EnteroPathogens. In his roles, he leads and collaborates with talented and multidisciplinary teams comprised of scientists from PNNL, universities, and other research organizations whose aims are to better understand a broad range of biological questions from environmental biology, pathogens, and human performance and health.


2006--Laboratory Director's Award for Early Career Exceptional Achievement
2004--2006 Inaugural candidate, PNNL Scientist and Engineer Development Program
2003--Outstanding Performance Award, Biological Science Division, PNNL
2002--Kownin Award, College of Natural Sciences, Colorado State University

Research Interests: 

Integrative Omics
Proteomics and Metabolomics
Systems Biology
Dynamic Biological Systems
Human Health (Performance and Infectious Disease)
Environmental Biology
Protein Structure and Function

Professional Memberships and Activities: 

American Chemical Society
American Association for the Advancement of Science


See the most current complete list here: https://scholar.google.com/citations?user=hn5pO48AAAAJ&hl=en


  • Hosseinzadeh P, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, F Pardo-Avila, SA Rettie, DE Kim, DA Silva, YM Ibrahim, IK Webb, JR Cort, JN Adkins, G Varani, and D Baker. 2017. "Comprehensive computational design of ordered peptide macrocycles." Science 358(6369):1461-1466.  doi:10.1126/science.aap7577
  • Merkley ED, LH Sego, A Lin, OP Leiser, BLD Kaiser, JN Adkins, PS Keim, DM Wagner, and HW Kreuzer. 2017. "Protein Abundances can Distinguish Between Naturally-occurring and Laboratory Strains of Yersinia pestis, the Causative Agent of Plague." PLoS One 12(8):e0183478.  doi:10.1371/journal.pone.0183478
  • Negretti NM, CR Gourley, GCD Clair, JN Adkins, and M Konkel. 2017. "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." Scientific Reports 7:15455.  doi:10.1038/s41598-017-15379-5
  • Tan K, BLD Kaiser, R Wu, M Cuff, Y Fan, L Bigelow, R Jedrzejczak, JN Adkins, JR Cort, G Babnigg, and A Joachimiak. 2017. "Insights into PG-binding, conformational change, and dimerization of the OmpAC-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi." The Protein Society 26(9):1738-1748.  doi:10.1002/pro.3209
  • Waters EM, JK Rudkin, S Coughlan, GCD Clair, JN Adkins, S Gore, G Xia, NS Black, T Downing, E O'Neill, A Kadioglu, and JP O'Gara. 2017. "Redeploying ß-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections." The Journal of Infectious Disease 215(1):80-87.  doi:10.1093/infdis/jiw461


  • Sontag RL, ES Nakayasu, RN Brown, GS Niemann, MA Sydor, O Sanchez, C Ansong, SY Lu, H Choi, D Valleau, KK Weitz, A Savchenko, E Cambronne, and JN Adkins. 2016. "Identification of novel host interactors of effectors secreted by Salmonella and Citrobacter: SrfH regulates host kinase ERK2 phosphorylation." mSystems 1(4):e00032-15. doi:10.1128/mSystems.00032-15
  • Bayles BR, KA Brauman, JN Adkins, BF Allan, AM Ellis, TL Goldberg, CD Golden, DS Grigsby-Toussaint, SS Myers, SA Ofosky, TH Ricketts, and JB Ristaino. 2016. "Ecosystem Services Connect Environmental Change to Human Health Outcomes." ECOHEALTH 13(3):443-449. doi:10.1007/s10393-016-1137-5
  • Conlon BP, SE Rowe, AV Brown-Gandt, AS Nuxoll, NP Donegan, EA Zalis, GCD Clair, JN Adkins, AL Cheung, and K Lewis. 2016. "Persister formation in Staphylococcus aureus is associated with ATP depletion." Nature Microbiology 1:16051. doi:10.1038/nmicrobiol.2016.51
  • Oxford KL, JP Wendler, JE McDermott, RA White, III, JD Powell, JM Jacobs, JN Adkins, and KM Waters. 2016. "The Landscape of Viral Proteomics and Its Potential to Impact Human Health." Expert Review of Proteomics 13(6):579-591.  doi:10.1080/14789450.2016.1184091


  • Sontag RL, C Mihai, G Orr, A Savchenko, T Skarina, H Cui, JR Cort, JN Adkins, and RN Brown. 2015. "Electroporation of Functional Bacterial Effectors into Mammalian Cells." Journal of Visualized Experiments 95:Article No. e52296.  doi:10.3791/52296
  • Elfenbein JR, LA Knodler, ES Nakayasu, C Ansong, HM Brewer, L Bogomolnaya, LG Adams, M McClelland, JN Adkins, and HL Andrews-Polymenis. 2015. "Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens." PLoS Genetics 11(9):e1005472. doi:10.1371/journal.pgen.1005472
  • Li J, CC Overall, ES Nakayasu, AS Kidwai, MB Jones, R Johnson, NT Nguyen, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6:Artcle No. 27.  doi:10.3389/fmicb.2015.00027
  • Li J, CC Overall, R Johnson, MB Jones, JE McDermott, F Heffron, JN Adkins, and E Cambronne. 2015. "ChIP-Seq Analysis of the s E Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response." PLoS One 10(9):Article No. e0138466.  doi:10.1371/journal.pone.0138466
  • Li J, ES Nakayasu, CC Overall, R Johnson, AS Kidwai, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14(4):1716-1726. doi:10.1021/pr5010423
  • Nakayasu ES, MA Sydor, RN Brown, RL Sontag, T Sobreira, GW Slysz, DR Humphrys, T Skarina, O Onoprienko, R Di Leo, BLD Kaiser, J Li, C Ansong, E Cambronne, RD Smith, A Savchenko, and JN Adkins. 2015. "Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis." Journal of Proteome Research 14(9):4029-4038.  doi:10.1021/acs.jproteome.5b00574
  • Payne SH, ME Monroe, CC Overall, GR Kiebel, MG Degan, BC Gibbons, GM Fujimoto, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2015. "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." Scientific Data 2:Art. No. 150041.  doi:10.1038/sdata.2015.41
  • Suh MJ, A Tovchigrechko, V Thovari, MA Rolfe, M Torralba, J Wang, JN Adkins, BJM Webb-Robertson, W Osborne, F Cogen, P Kaplowitz, TO Metz, KE Nelson, R Madupu, and R Pieper. 2015. "Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes." Journal of Proteome Research 14(8):3123-3135.  doi:10.1021/acs.jproteome.5b00052


  • Brown JN, HM Brewer, CD Nicora, KK Weitz, MJ Morris, AJ Skabelund, JN Adkins, RD Smith, JH Cho, and R Gelinas. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7:Article No. 58.  doi:10.1186/1755-8794-7-58
  • Shen Y, L Pasa-Tolic, EW Robinson, JN Adkins, and RD Smith. 2014. "New challenges for proteomics technologies: a mini perspective review." Austin Journal of Proteomics, Bioinformatics & Genomics 1(1):Article No. 3. 
  • Eletsky A, K Michalska, S Houliston, Q Zhang, MD Daily, X Xu, H Cui, A Yee, A Lemak, B Wu, M Garcia, MC Burnet, KM Meyer, UK Aryal, O Sanchez, C Ansong, R Xiao, T Acton, JN Adkins, G Montelione, A Joachimiak, CH Arrowsmith, A Savchenko, T Szyperski, and JR Cort. 2014. "Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO." PLoS One 9(7):Article No. e101787. doi:10.1371/journal.pone.0101787
  • Kronewitter SR, I Marginean, JT Cox, R Zhao, CD Hagler, AK Shukla, TS Carlson, JN Adkins, DG Camp, II, RJ Moore, KD Rodland, and RD Smith. 2014. "Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry." Analytical Chemistry 86(17):8700-10.  doi:10.1021/ac501839b
  • Lu J, R Wu, JN Adkins, A Joachimiak, and M Glover. 2014. "Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability." Biochemistry 53(36):5810-9.  doi:10.1021/bi500244m
  • Merkley ED, S Rysavy, A Kahraman, RP Hafen, V Daggett, and JN Adkins. 2014. "Distance Restraints from Crosslinking Mass Spectrometry: Mining a Molecular Dynamics Simulation Database to Evaluate Lysine-Lysine Distances." Protein Science 23(6):747-759. doi:10.1002/pro.2458
  • Nakayasu ES, S Wu, MA Sydor, AK Shukla, KK Weitz, RJ Moore, KK Hixson, JS Kim, VA Petyuk, ME Monroe, L Pasa-Tolic, W Qian, RD Smith, JN Adkins, and C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014:Article No. 730725.  doi:10.1155/2014/730725
  • Zaborin A, J Defazio, M Kade, BLD Kaiser, N Belogortseva, DG Camp, II, RD Smith, JN Adkins, SM Kim, A Alverdy, D Goldfeld, M Firestone, J Collier, B Jabri, M Tirrell, O Zaborina, and JC Alverdy. 2014. "Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens." Antimicrobial Agents and Chemotherapy 58(2):966.  doi:10.1128/AAC.02183-13


  • Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, AR Ollodart, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133.  doi:10.1016/j.chembiol.2012.11.008
  • Ansong C, S Wu, D Meng, X Liu, HM Brewer, BLD Kaiser, ES Nakayasu, JR Cort, PA Pevzner, RD Smith, F Heffron, JN Adkins, and L Pasa-Tolic. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110(25):10153-10158.  doi:10.1073/pnas.1221210110
  • Kim YM, B Schmidt, AS Kidwai, MB Jones, BL Deatherage, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, and JN Adkins. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9(6):1522-1534. doi:10.1039/C3MB25598K
  • Ansong C, AC Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K Mcateer, BL Deatherage, JL DuBois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, and JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9(1):44-54.  doi:10.1039/C2MB25287B 
  • Conlon BP, ES Nakayasu, LE Fleck, MD LaFleur, VM Isabella, K Coleman, SN Leonard, RD Smith, JN Adkins, and K Lewis. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503(7476):365-370.  doi:10.1038/nature12790
  • Kaiser BLD, J Li, JA Sanford, YM Kim, SR Kronewitter, MB Jones, C Peterson, SN Peterson, BC Frank, SO Purvine, JN Brown, TO Metz, RD Smith, F Heffron, and JN Adkins. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8(6):Article No. e67155.  doi:10.1371/journal.pone.0067155
  • Kidwai AS, IT Mushamiri, G Niemann, RN Brown, JN Adkins, and F Heffron. 2013. "Diverse Secreted Effectors Are Required for Salmonella Persistence in a Mouse Infection Model." PLoS One 8(8):e70753.  doi:10.1371/journal.pone.0070753
  • Latif H, JA Lerman, VA Portnoy, Y Tarasova, H Nagarajan, AC Rutledge, RD Smith, JN Adkins, DH Lee, Y Qiu, and K Zengler. 2013. "The Genome Organization of Thermotoga maritima Reflects Its Lifestyle." PLoS Genetics 9(4):Article No. e1003485. doi:10.1371/journal.pgen.1003485
  • Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking ." Journal of the American Society for Mass Spectrometry 24(3):444-449. doi:10.1007/s13361-012-0565-x
  • Merkley ED, JR Cort, and JN Adkins. 2013. "Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze." Journal of Structural and Functional Genomics 14(3):77-90.  doi:10.1007/s10969-013-9160-z
  • Michalska K, RN Brown, H Li, R Jedrzejczak, G Niemann, F Heffron, JR Cort, JN Adkins, G Babnigg, and A Joachimiak. 2013. "New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium." Journal of Structural and Functional Genomics 14(1):1-10. doi:10.1007/s10969-013-9151-0
  • Nakayasu ES, C Ansong, JN Brown, F Yang, D Lopez-Ferrer, W Qian, RD Smith, and JN Adkins. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24(8):1214-1223. doi:10.1007/s13361-013-0619-8
  • Nakayasu ES, R Tempel, XA Cambronne, VA Petyuk, MB Jones, MA Gritsenko, ME Monroe, F Yang, RD Smith, JN Adkins, and F Heffron. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12(11):3297-3309. doi:10.1074/mcp.M113.029850
  • Nakayasu ES, RN Brown, C Ansong, MA Sydor, S Imtiaz, C Mihai, RL Sontag, KK Hixson, ME Monroe, T Sobreira, G Orr, VA Petyuk, F Yang, RD Smith, and JN Adkins. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12(8):2136-2147.  doi:10.1074/mcp.M112.026138
  • Niemann G, RN Brown, IT Mushamiri, NT Nguyen, R Taiwo, A Stufkens, RD Smith, JN Adkins, JE McDermott, and F Heffron. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195(10):2119-2125.  doi:10.1128/JB.00024-13
  • Schmidt B, A Ebrahim, TO Metz, JN Adkins, BO Palsson, and DR Hyduke. 2013. "GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data." Bioinformatics 29(22):2900-2908.  doi:10.1093/bioinformatics/btt493
  • Wang J, BJM Webb-Robertson, MM Matzke, SM Varnum, JN Brown, RM Riensche, JN Adkins, JM Jacobs, JR Hoidal, MB Scholand, JG Pounds, MR Blackburn, KD Rodland, and JE McDermott. 2013. "A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers 35(5):513-523.  doi:10.1155/2013/613529


  • Brown RN, JA Sanford, JH Park, BL Deatherage, BL Champion, RD Smith, F Heffron, and JN Adkins. 2012. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions." International Journal of Proteomics 2012:Article ID 123076.  doi:10.1155/2012/123076
  • Bordbar A, ML Mo, ES Nakayasu, AC Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins, and BO Palsson. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8:Article No. 558.  doi:10.1038/msb.2012.21
  • Lerman JA, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, AC Rutledge, RD Smith, JN Adkins, K Zengler, and BO Palsson. 2012. "In silico method for modelling metabolism and gene product expression at genome scale." Nature Communications 3:Article No. 929. doi:10.1038/ncomms1928
  • Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131.  doi:10.1186/1471-2164-13-131
  • Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11(7):3520-32.  doi:10.1021/pr3002996
  • Rutledge AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7(3):Article No. E33903.  doi:10.1371/journal.pone.0033903


  • Ansong C, N Tolic, SO Purvine, S Porwollik, MB Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, S Peterson, F Heffron, M Mcclelland, and JN Adkins. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12:Art. No. 433. doi:10.1186/1471-2164-12-433
  • McDermott JE, AL Corrigan, ES Peterson, CS Oehmen, G Niemann, E Cambronne, D Sharp, JN Adkins, R Samudrala, and F Heffron. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria ." Infection and Immunity 79(1):23-32. doi:10.1128/IAI.00537-10
  • McDermott JE, H Yoon, ES Nakayasu, TO Metz, DR Hyduke, AS Kidwai, BO Palsson, JN Adkins, and F Heffron. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2:121. doi:10.3389/fmicb.2011.00121
  • McDermott JE, MN Archuleta, BD Thrall, JN Adkins, and KM Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6(2):e14673. doi:10.1371/journal.pone.0014673
  • Aderem A, JN Adkins, C Ansong, J Galagan, S Kaiser, MJ Korth, GL Law, JE McDermott, S Proll, C Rosenberger, G Schoolnik, and MG Katze. 2011. "A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm." mBio 2(1):Article No. e00325.  doi:10.1128/mBio.00325-10
  • Charusanti P, S Chauhan, K Mcateer, JA Lerman, DR Hyduke, VL Motin, C Ansong, JN Adkins, and BO Palsson. 2011. "An Experimentally-Supported Genome-Scale Metabolic Network Reconstruction for Yersinia pestis CO92." BMC Systems Biology 5:Article No. 163. doi:10.1186/1752-0509-5-163
  • Du X, SM Chowdhury, NP Manes, S Wu, MU Mayer, JN Adkins, GA Anderson, and RD Smith. 2011. "Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry." Journal of Proteome Research 10(3):923-931.  doi:10.1021/pr100848a
  • Heffron F, G Niemann, H Yoon, AS Kidwai, RN Brown, JE McDermott, RD Smith, and JN Adkins. 2011. "Salmonella-secreted Virulence Factors." Chapter 10 in Salmonella: From Genome to Function, ed. S Porwollik, pp. 187-223.  Caister Academic Press, Norfolk, United Kingdom. 
  • Niemann G, RN Brown, JK Gustin, A Stufkens, AS Shaikh-Kidwai, J Li, JE McDermott, HM Brewer, AA Schepmoes, RD Smith, JN Adkins, and F Heffron. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79(1):33-43. doi:10.1128/IAI.00771-10
  • Schutzer SE, TE Angel, T Liu, AA Schepmoes, TRW Clauss, JN Adkins, DG Camp, II, BK Holland, J Bergquist, PK Coyle, RD Smith, BA Fallon, and B Natelson. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6(2):Article No. e17287.  doi:10.1371/journal.pone.0017287
  • Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83(16):6135-6140.  doi:10.1021/ac2009806
  • Thiele I, DR Hyduke, B Steeb, G Fankam, DK Allen, S Bazzani, P Charusanti, FC Chen, RM Fleming, CA Hsiung, SC De Keersmaecker, YC Liao, K Marchal, ML Mo, E Ozdemir, A Raghunathan, JL Reed, SI Shin, S Sigurbjornsdottir, J Steinmann, S Sudarsan, N Swainston, IM Thijs, K Zengler, BO Palsson, JN Adkins, and D Bumann. 2011. "A community effort towards a knowledge--base and mathematical model of the human pathogen Salmonella Typhimurium LT2 ." BMC Systems Biology 5:Article No. 8.  doi:10.1186/1752-0509-5-8
  • Yoon H, C Ansong, JN Adkins, and F Heffron. 2011. "Discovery of Salmonella Virulence Factors Translocated via Outer Membrane Vesicles to Murine Macrophages." Infection and Immunity 79(6):2182-92.  doi:10.1128/IAI.01277-10
  • Yoon H, C Ansong, JE McDermott, MA Gritsenko, RD Smith, F Heffron, and JN Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella ." BMC Systems Biology 5:Article No. 100.  doi:10.1186/1752-0509-5-100


  • Adkins JN, H Mottaz, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chapter 2 in Peptidomics: Methods and Protocols, Methods in Molecular Biology, vol. 615, ed. Mikhail Soloviev, pp. 13-27.  Humana Press, Inc., New York, NY. 
  • Auberry KJ, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, and RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3(1):1-4. 
  • Brown JN, R Estep, D Lopez-Ferrer, HM Brewer, TRW Clauss, NP Manes, M O'Connor, H Li, JN Adkins, S Wong, and RD Smith. 2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9(12):2760-2771. doi:10.1074/mcp.M110.001875
  • Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458.  doi:10.1039/c0mb00097c
  • Jung HJ, SO Purvine, H Kim, VA Petyuk, SW Hyung, ME Monroe, DG Mun, KC Kim, JM Park, SJ Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp, II, MH Yu, RD Smith, and SW Lee. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82(20):8510-8518. doi:10.1021/ac101388b
  • Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390. doi:10.1038/msb.2010.47
  • Rana GSJB, TP York, JS Edmiston, BK Zedler, JG Pounds, JN Adkins, RD Smith, Z Liu, G Li, BT Webb, EL Murrelle, and JW Flora. 2010. "Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD) ." Analytical and Bioanalytical Chemistry 397:1809-1819. doi:10.1007/s00216-010-3742-4
  • Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarr�a-Miranda, S Choudhury, I Gorton, DK Gracio, TD Halter, N Jaitly, JR Johnson, RT Kouzes, MC Macduff, A Marquez, ME Monroe, CS Oehmen, WA Pike, C Scherrer, O Villa, BJM Webb-Robertson, PD Whitney, and N Zuljevic. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, vol. 79, ed. M Zelkowitz, pp. 1-70.  Academic Press Inc., San Diego, CA. 
  • Shah AR, N Jaitly, N Zuljevic, ME Monroe, AV Liyu, AD Polpitiya, JN Adkins, ME Belov, GA Anderson, RD Smith, and I Gorton. 2010. "An architecture for real time data acquisition and online signal processing for high throughput tandem mass spectrometry." In 5th IEEE International Conference on e-Science, pp. 88 - 93.  IEEE, Piscataway, NJ.  doi:10.1109/e-Science.2009.21
  • Singhal M, AR Shah, RN Brown, and JN Adkins. 2010. "Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions." In ACM-BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology  , pp. 537-545.  Association for Computing Machinery, New York. doi:10.1145/1854776.1854878


  • Chowdhury SM, X Du, N Tolic, S Wu, RJ Moore, MU Mayer, RD Smith, and JN Adkins. 2009. "Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry." Analytical Chemistry 81(13):5524-5532.  doi:10.1021/ac900853k
  • Ansong C, H Yoon, S Porwollik, H Mottaz-Brewer, BO Petritis, N Jaitly, JN Adkins, M Mcclelland, F Heffron, and RD Smith. 2009. "Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation." PLoS One 4(3):e4809.  doi:10.1371/journal.pone.0004809
  • Chowdhury SM, L Shi, H Yoon, C Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, and RD Smith. 2009. "A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis ." Journal of Proteome Research 8(3):1504-1514 . 
  • Jaitly N, AM Mayampurath, KA Littlefield, JN Adkins, GA Anderson, and RD Smith. 2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10:87. doi:10.1186/1471-2105-10-87
  • Karpievitch Y, JR Stanley, T Taverner, J Huang, JN Adkins, C Ansong, F Heffron, TO Metz, W Qian, H Yoon, RD Smith, and AR Dabney. 2009. "A statistical framework for protein quantitation in bottom-up MS-based proteomics ." Bioinformatics 25(16):2028-2034. doi:10.1093/bioinformatics/btp362
  • Karpievitch Y, JR Stanley, T Taverner, J Huang, JN Adkins, C Ansong, F Heffron, TO Metz, W Qian, H Yoon, RD Smith, and AR Dabney. 2009. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25(16):2028-2034. 
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233.  doi:10.1128/IAI.00063-09


  • Ansong C, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7(1):50-62. 
  • Manes NP, RD Estep, HM Mottaz, RJ Moore, TRW Clauss, ME Monroe, X Du, JN Adkins, S Wong, and RD Smith. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 3:960-8.  doi:10.1021/pr070432+
  • Pounds JG, JW Flora, JN Adkins, KM Lee, GSJB Rana, T Sengupta, RD Smith, and WJ McKinney. 2008. "Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry." Journal of Chromatography B 864(1-2):95-101. 
  • Ansong C, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, and RD Smith. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7(2):546-557.  doi:10.1021/pr070434u
  • Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295. 
  • Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, and MS Lipton. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3(2):e1542.  doi:10.1371/journal.pone.0001542
  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 18O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24.  doi:10.1021/pr7007785 
  • Du X, F Yang, NP Manes, DL Stenoien, ME Monroe, JN Adkins, DJ States, SO Purvine, DG Camp, II, and RD Smith. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications ." Journal of Proteome Research 7(6):2195-2203.  doi:10.1021/pr070510t
  • Du X, SJ Callister, NP Manes, JN Adkins, RA Alexandridis, X Zeng, JH Roh, WE Smith, TJ Donohue, S Kaplan, RD Smith, and MS Lipton. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7(7):2595-2604.  doi:10.1021/pr0704837
  • Ham BM, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, DJ Orton, JN Adkins, DG Camp, II, SS Rossie, and RD Smith. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7(6):2215-2221. 
  • Mayampurath AM, N Jaitly, SO Purvine, ME Monroe, KJ Auberry, JN Adkins, and RD Smith. 2008. "DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24(7):1021-1023. doi:10.1093/bioinformatics/btn063
  • Monroe ME, JL Shaw, DS Daly, JN Adkins, and RD Smith. 2008. "MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32(3):215-217. doi:10.1016/j.compbiolchem.2008.02.006
  • Petyuk VA, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, W Qian, DG Camp, II, and RD Smith. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content ." Analytical Chemistry 80(3):693-706.  doi:10.1021/ac701863d
  • Polpitiya AD, W Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp, II, GA Anderson, and RD Smith. 2008. " DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24(13):1556-1558.  doi:10.1093/bioinformatics/btn217
  • Rodland KD, JN Adkins, C Ansong, SM Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, and F Heffron. 2008. "Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella." Future Microbiology 3(6):625-634. 
  • Rodland KD, JN Adkins, C Ansong, SM Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, and F Heffron. 2008. "Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella." Future Microbiology 3(6):625-634. doi:10.2217/17460913.3.6.625
  • Shen Y, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, W Qian, JN Adkins, RJ Moore, and RD Smith. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80(6):1871-82.  doi:10.1021/ac702328x
  • Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525.  doi:10.1021/ac801376g


  • Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23(13):1705-1707.  doi:10.1093/bioinformatics/btm132
  • Gupta N, S Tanner, N Jaitly, JN Adkins, MS Lipton, R Edwards, MF Romine, A Osterman, V Bafna, RD Smith, and PA Pevzner. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Research 17(9):1362-1377.  doi:0.1101/gr.6427907
  • Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6(4):717-727. doi:10.1074/mcp.M600282-MCP200 
  • Monroe ME, N Tolic, N Jaitly, JL Shaw, JN Adkins, and RD Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23(15- August 2007):2021-2023.  doi:10.1093/bioinformatics/btm281
  • Petyuk VA, W Qian, MH Chin, HH Wang, EA Livesay, ME Monroe, JN Adkins, N Jaitly, DJ Anderson, DG Camp, II, DJ Smith, and RD Smith. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17(3):328-336. doi:10.1101/gr.5799207 
  • Yang F, N Jaitly, H Jayachandran, Q Lou, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, II, HR Udseth, RD Smith, and SS Rossie. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6(11):4489-4497.  doi:10.1021/pr070068e 


  • Adkins JN, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TRW Clauss, SO Purvine, KD Rodland, F Heffron, and RD Smith. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5(8):1450-1461.  doi:10.1074/mcp.M600139-MCP200 
  • Callister SJ, RC Barry, JN Adkins, ET Johnson, W Qian, BJM Webb-Robertson, RD Smith, and MS Lipton. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5(2):277-286.  doi:10.1021/pr050300l
  • Ding YHR, KK Hixson, CS Giometti, A Stanley, A Esteve-Nunez, T Khare, SL Tollaksen, W Zhu, JN Adkins, MS Lipton, RD Smith, T Mester, and DR Lovley. 2006. "The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions." Biochimica et Biophysica Acta--Proteins and Proteomics 1764(7):1198-1206. doi:10.1016/j.bbapap.2006.04.017 
  • Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725.  doi:10.1074/mcp.M500301-MCP200 
  • Hixson KK, JN Adkins, SE Baker, RJ Moore, RD Smith, SL McCutchen-Maloney, and MS Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics ." Journal of Proteome Research 5(11):3008-3017. 
  • Jaitly N, ME Monroe, VA Petyuk, TRW Clauss, JN Adkins, and RD Smith. 2006. "Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline." Analytical Chemistry 78(21):7397-7409. 
  • Petritis K, LJ Kangas, B Yan, ME Monroe, EF Strittmatter, W Qian, JN Adkins, RJ Moore, Y Xu, MS Lipton, DG Camp, II, and RD Smith. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78(14):5026-5039.  doi:10.1021/ac060143p
  • Shi L, JN Adkins, JR Coleman, AA Schepmoes, A Dohnalkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, HH Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, and TC Squier. 2006. "Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from RAW 264.7 Macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages." Journal of Biological Chemistry 281:29131-29140.  doi:10.1074/jbc.M604640200
  • Tolmachev AV, ME Monroe, N Jaitly, VA Petyuk, JN Adkins, and RD Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78(24):8374-8385. doi:10.1021/ac0606251
  • Webb-Robertson BJM, WR Cannon, JN Adkins, and DK Gracio. 2006. "The Challenge of Proteomic Data from Molecular Signals to Biological Networks and Disease." In Pacific Symposium On Biocomputing 2006, pp. 212-218.  World Scientific, , Singapore. 
  • Yang F, DL Stenoien, EF Strittmatter, JH Wang, L Ding, MS Lipton, ME Monroe, CD Nicora, MA Gritsenko, K Tang, R Fang, JN Adkins, DG Camp, II, DJ Chen, and RD Smith. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation ." Journal of Proteome Research 5(5):1252-1260. 


  • Norbeck AD, ME Monroe, JN Adkins, KK Anderson, DS Daly, and RD Smith. 2005. "The utility of accurate mass and LC elution time information in the analysis of complex proteomes." Journal of the American Society for Mass Spectrometry 16(8):1239-1249. 
  • Adkins JN, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp, II, F Vitzthum, KD Rodland, RC Zangar, RD Smith, and JG Pounds. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5(13):3454-3466.  doi:10.1002/pmic.200401333
  • Ahram M, EF Strittmatter, ME Monroe, JN Adkins, JC Hunter, JH Miller, and DL Springer. 2005. "Identification of shed proteins from Chinese hamster ovary cells: Application of statistical confidence using human and mouse protein databases." Proteomics 5(7):1815-1826. 
  • Ahram M, JN Adkins, DL Auberry, DS Wunschel, and DL Springer. 2005. "A Proteomic Approach to Characterize Protein Shedding." Proteomics 5(1):123-131. doi:10.1002/pmic.200400912
  • Edberg DD, JN Adkins, DL Springer, and RC Reeves. 2005. "Dynamic and Differential in vivo Modifications of the Isoform HMGA1a and HMGA1b Chromatin Proteins." Journal of Biological Chemistry 280(10):8961-8973.  doi:10.1074/jbc.M407348200
  • Haab BB, BH Geierstanger, G Michailidis, F Vitzthum, S Forrester, R Okon, P Saviranta, A Brinker, M Sorette, L Perlee, S Suresh, G Drwal, JN Adkins, and GS Omenn. 2005. "Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data." Proteomics 5(13):3278-3291. 
  • Jacobs JM, JN Adkins, W Qian, T Liu, Y Shen, DG Camp, II, and RD Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4(4):1073-1085.  doi:10.1021/pr0500657
  • Kapp E, F Schutz, LM Connolly, JA Chakel, JE Meza, CA Miller, D Fenyo, JK Eng, JN Adkins, G Omenn, and R Simpson. 2005. "An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and Specificity analysis." Proteomics 5(13):3475-3490. 
  • Markillie LM, CT Lin, JN Adkins, DL Auberry, EA Hill, BS Hooker, PA Moore, RJ Moore, L Shi, HS Wiley, and V Kery. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4(2):268-274.  doi:10.1021/pr049847a
  • Omenn G, DJ States, M Adamski, TW Blackwell, R Menon, H Hermjakob, R Apweiler, BB Haab, R Simpson, J Eddes, E Kapp, R Moritz, DW Chan, AJ Rai, A Admon, R Aebersold, JK Eng, WS Hancock, SA Hefta, H Meyer, YK Paik, JS Yoo, P Ping, JG Pounds, JN Adkins, X Qian, R Wang, V Wasinger, CY Wu, X Zhao, R Zeng, A Archakov, A Tsugita, I Beer, A Pandey, M Pisano, P Andrews, H Tammen, DW Speicher, and SM Hanash. 2005. "Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database ." Proteomics 5(13):3226-3245. 
  • Springer DL, M Ahram, JN Adkins, LE Kathmann, and JH Miller. 2005. "Characterization of Medium Conditioned by Irradiated Cells Using Proteome-Wide, High-Throughput Mass Spectrometry." Radiation Research 164(5):651-654. 


  • Anderson LN, M Polanski, R Peiper, T Gatlin, R Tiramalai, T Conrads, T Veenstra, JN Adkins, JG Pounds, R Fagan, and A Lobley. 2004. "The Human Plasma Proteome: A Nonredundant List Developed by Combination of Four Separate Sources ." Molecular & Cellular Proteomics. MCP 3(4):311-326.  doi:10.1074/mcp.M300127-MCP200


  • Springer DL, DL Auberry, M Ahram, JN Adkins, JM Feldhaus, JH Wahl, DM Wunsch, and KD Rodland. 2003. "Characterization of Plasma Membrane Proteins from Ovarian Cancer Cells Using Mass Spectrometry ." Disease Markers 19(4-5):219-228. 


  • Adkins JN, SM Varnum, KJ Auberry, RJ Moore, N Angell, RD Smith, DL Springer, and JG Pounds. 2002. "Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Molecular & Cellular Proteomics. MCP 1(12):947-955. 
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