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1

Cand1 Promotes Assembly of New SCF Complexes through Dynamic Exchange of F Box Proteins

Pierce, Nathan W., Lee, J. Eugene, Liu, Xing, Sweredoski, Michael J., Graham, Robert L.J., Larimore, Elizabeth A., Rome, Michael, Zheng, Ning, Clurman, Bruce E., Hess, Sonja, Shan, Shu-ou, Deshaies, R

Journal:

Year:

2013

Language:

english

File:

PDF, 1.36 MB

english, 2013

2

Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain

Schaefer, Kathryn N., Geil, Wendy M., Sweredoski, Michael J., Moradian, Annie, Hess, Sonja, Barton, Jacqueline K.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.07 MB

english, 2015

3

Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes

Renata, Hans, Lewis, Russell D., Sweredoski, Michael J., Moradian, Annie, Hess, Sonja, Wang, Z. Jane, Arnold, Frances H.

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 722 KB

english, 2016

4

Nitric Oxide Modulates Endonuclease III Redox Activity by a 800 mV Negative Shift upon [Fe 4 S 4 ] Cluster Nitrosylation

Ekanger, Levi A., Oyala, Paul H., Moradian, Annie, Sweredoski, Michael J., Barton, Jacqueline K.

Journal:

Journal of the American Chemical Society

Year:

2018

Language:

english

File:

PDF, 1.07 MB

english, 2018

5

Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1

Tara A Gomez, Natalie Kolawa, Marvin Gee, Michael J Sweredoski, Raymond J Deshaies

Journal:

Year:

2011

Language:

english

File:

PDF, 2.25 MB

english, 2011

6

Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data

Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi

Journal:

Data Mining and Knowledge Discovery

Year:

2005

Language:

english

File:

PDF, 223 KB

english, 2005

7

DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks

Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi

Journal:

Data Mining and Knowledge Discovery

Year:

2006

Language:

english

File:

PDF, 203 KB

english, 2006

8

Click Chemistry Facilitates Formation of Reporter Ions and Simplified Synthesis of Amine-Reactive Multiplexed Isobaric Tags for Protein Quantification

Sohn, Chang Ho, Lee, J. Eugene, Sweredoski, Michael J., Graham, Robert L.J., Smith, Geoffrey T., Hess, Sonja, Czerwieniec, Gregg, Loo, Joseph A., Deshaies, Raymond J., Beauchamp, J. L.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

9

Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions

Sohn, Chang Ho, Agnew, Heather D., Lee, J. Eugene, Sweredoski, Michael J., Graham, Robert L.J., Smith, Geoffrey T., Hess, Sonja, Czerwieniec, Gregg, Loo, Joseph A., Heath, James R.

Journal:

Analytical Chemistry

Year:

2012

Language:

english

File:

PDF, 545 KB

english, 2012

10

A comparative computational analysis of nonautonomousHelitronelements between maize and rice

Michael Sweredoski, Leah DeRose-Wilson, Brandon S Gaut

Journal:

Year:

2008

Language:

english

File:

PDF, 1.11 MB

english, 2008

11

Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT)

Jennifer J. L. Hodas, Anne Nehring, Nicole Höche, Michael J. Sweredoski, Rainer Pielot, Sonja Hess, David A. Tirrell, Daniela C. Dieterich, Erin M. Schuman

Journal:

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

12

Characterization of the Mycobacterium tuberculosis Proteome by Liquid Chromatography Mass Spectrometry-based Proteomics Techniques: A Comprehensive Resource for Tuberculosis Research

Bell, Christina, Smith, Geoffrey T., Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 2.58 MB

english, 2012

13

Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers

Kalli, Anastasia, Smith, Geoffrey T., Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 3.10 MB

english, 2013

14

Comprehensive Profiling of N-Linked Glycosylation Sites in HeLa Cells Using Hydrazide Enrichment

Malerod, Helle, Graham, Robert L. J., Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 2.35 MB

english, 2013

15

O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins

Smith, Geoffrey T., Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of Proteomics

Year:

2014

Language:

english

File:

PDF, 935 KB

english, 2014

16

Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni

Jang, Kyoung-Soon, Sweredoski, Michael J., Graham, Robert L.J., Hess, Sonja, Clemons, William M.

Journal:

Journal of Proteomics

Year:

2014

Language:

english

File:

PDF, 328 KB

english, 2014

17

Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture

Bagert, J. D., Xie, Y. J., Sweredoski, M. J., Qi, Y., Hess, S., Schuman, E. M., Tirrell, D. A.

Journal:

Molecular & Cellular Proteomics

Year:

2014

Language:

english

File:

PDF, 812 KB

english, 2014

18

Degradation of the Deubiquitinating Enzyme USP33 Is Mediated by p97 and the Ubiquitin Ligase HERC2

Chan, Nickie C., den Besten, Willem, Sweredoski, Michael J., Hess, Sonja, Deshaies, Raymond J., Chan, David C.

Journal:

Journal of Biological Chemistry

Year:

2014

Language:

english

File:

PDF, 1.98 MB

english, 2014

19

Data-Dependent Middle-Down Nano-Liquid Chromatography–Electron Capture Dissociation-Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones

Kalli, Anastasia, Sweredoski, Michael J., Hess, Sonja

Journal:

Analytical Chemistry

Year:

2013

Language:

english

File:

PDF, 2.45 MB

english, 2013

20

Prometastatic GPCR CD97 Is a Direct Target of Tumor Suppressor microRNA-126

Lu, Ying Y., Sweredoski, Michael J., Huss, David, Lansford, Rusty, Hess, Sonja, Tirrell, David A.

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 761 KB

english, 2014

21

SCRATCH: a protein structure and structural feature prediction server

Cheng, J., Randall, A. Z., Sweredoski, M. J., Baldi, P.

Journal:

Nucleic Acids Research

Year:

2005

Language:

english

File:

PDF, 252 KB

english, 2005

22

The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications

Moradian, Annie, Kalli, Anastasia, Sweredoski, Michael J., Hess, Sonja

Journal:

Year:

2014

Language:

english

File:

PDF, 271 KB

english, 2014

23

Cell-specific proteomic analysis in Caenorhabditis elegans

Yuet, Kai P., Doma, Meenakshi K., Ngo, John T., Sweredoski, Michael J., Graham, Robert L. J., Moradian, Annie, Hess, Sonja, Schuman, Erin M., Sternberg, Paul W., Tirrell, David A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

24

Phosphorylation of Synaptic GTPase-activating Protein (synGAP) by Ca 2+ /Calmodulin-dependent Protein Kinase II (CaMKII) and Cyclin-dependent Kinase 5 (CDK5) Alters the Ratio of Its GAP Activity toward Ras and Rap GTPases

Walkup, Ward G., Washburn, Lorraine, Sweredoski, Michael J., Carlisle, Holly J., Graham, Robert L., Hess, Sonja, Kennedy, Mary B.

Journal:

Journal of Biological Chemistry

Year:

2015

Language:

english

File:

PDF, 3.60 MB

english, 2015

25

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling

Sweredoski, M. J., Donovan, K. J., Nguyen, B. D., Shaka, A.J., Baldi, P.

Journal:

Year:

2007

Language:

english

File:

PDF, 564 KB

english, 2007

26

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

McHugh, Colleen A., Chen, Chun-Kan, Chow, Amy, Surka, Christine F., Tran, Christina, McDonel, Patrick, Pandya-Jones, Amy, Blanco, Mario, Burghard, Christina, Moradian, Annie, Sweredoski, Michael J., S

Journal:

Year:

2015

Language:

english

File:

PDF, 17.37 MB

english, 2015

27

Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy

Chan, N. C., Salazar, A. M., Pham, A. H., Sweredoski, M. J., Kolawa, N. J., Graham, R. L. J., Hess, S., Chan, D. C.

Journal:

Human Molecular Genetics

Year:

2011

Language:

english

File:

PDF, 533 KB

english, 2011

28

COBEpro: a novel system for predicting continuous B-cell epitopes

Sweredoski, M. J., Baldi, P.

Journal:

Protein Engineering Design and Selection

Year:

2008

Language:

english

File:

PDF, 241 KB

english, 2008

29

Identification of secreted bacterial proteins by noncanonical amino acid tagging

Mahdavi, A., Szychowski, J., Ngo, J. T., Sweredoski, M. J., Graham, R. L. J., Hess, S., Schneewind, O., Mazmanian, S. K., Tirrell, D. A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 911 KB

english, 2014

30

Activation of p107 by Fibroblast Growth Factor, Which Is Essential for Chondrocyte Cell Cycle Exit, Is Mediated by the Protein Phosphatase 2A/B55 Holoenzyme

Kurimchak, A., Haines, D. S., Garriga, J., Wu, S., De Luca, F., Sweredoski, M. J., Deshaies, R. J., Hess, S., Grana, X.

Journal:

Molecular and Cellular Biology

Year:

2013

Language:

english

File:

PDF, 2.21 MB

english, 2013

31

Novel Proteomic Tools Reveal Essential Roles of SRP and Importance of Proper Membrane Protein Biogenesis

Zhang, D., Sweredoski, M. J., Graham, R. L. J., Hess, S., Shan, S.-o.

Journal:

Molecular & Cellular Proteomics

Year:

2012

Language:

english

File:

PDF, 3.40 MB

english, 2012

32

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

Sweredoski, M. J., Baldi, P.

Journal:

Year:

2008

Language:

english

File:

PDF, 78 KB

english, 2008

33

Protein Interaction Profiling of the p97 Adaptor UBXD1 Points to a Role for the Complex in Modulating ERGIC-53 Trafficking

Haines, D. S., Lee, J. E., Beauparlant, S. L., Kyle, D. B., den Besten, W., Sweredoski, M. J., Graham, R. L. J., Hess, S., Deshaies, R. J.

Journal:

Molecular & Cellular Proteomics

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

34

TMBpro: secondary structure, -contact and tertiary structure prediction of transmembrane -barrel proteins

Randall, A., Cheng, J., Sweredoski, M., Baldi, P.

Journal:

Year:

2008

Language:

english

File:

PDF, 185 KB

english, 2008

35

High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics

Sweredoski, Michael J., Moradian, Annie, Raedle, Matthias, Franco, Catarina, Hess, Sonja

Journal:

Analytical Chemistry

Year:

2015

Language:

english

File:

PDF, 1.16 MB

english, 2015

36

ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome

Porras-Yakushi, Tanya R., Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2015

Language:

english

File:

PDF, 565 KB

english, 2015

37

Vectored antibody gene delivery mediates long-term contraception

Li, Juan, Olvera, Alejandra I., Akbari, Omar S., Moradian, Annie, Sweredoski, Michael J., Hess, Sonja, Hay, Bruce A.

Journal:

Current Biology

Year:

2015

Language:

english

File:

PDF, 486 KB

english, 2015

38

JNK associated leucine zipper protein functions as a docking platform for Polo like kinase 1 and regulation of the associating transcription factor Forkhead box protein K1

Ramkumar, Poornima, Lee, Clement M., Moradian, Annie, Sweredoski, Michael J., Hess, Sonja, Sharrocks, Andrew D., Haines, Dale S., Reddy, E. Premkumar

Journal:

Journal of Biological Chemistry

Year:

2015

Language:

english

File:

PDF, 2.15 MB

english, 2015

39

High resolution data-independent acquisition with electron transfer dissociation mass spectrometry: Multiplexed analysis of post-translationally modified proteins

Sweredoski, Michael J., Pekar Second, Tonya, Broeker, Jenny, Moradian, Annie, Hess, Sonja

Journal:

International Journal of Mass Spectrometry

Year:

2015

Language:

english

File:

PDF, 1.61 MB

english, 2015

40

Perturbations to the Ubiquitin Conjugate Proteome in Yeast ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition

Kolawa, N., Sweredoski, M. J., Graham, R. L. J., Oania, R., Hess, S., Deshaies, R. J.

Journal:

Molecular & Cellular Proteomics

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

41

The Steady-State Repertoire of Human SCF Ubiquitin Ligase Complexes Does Not Require Ongoing Nedd8 Conjugation

Lee, J. E., Sweredoski, M. J., Graham, R. L. J., Kolawa, N. J., Smith, G. T., Hess, S., Deshaies, R. J.

Journal:

Molecular & Cellular Proteomics

Year:

2011

Language:

english

File:

PDF, 601 KB

english, 2011

42

F-box Protein FBXL16 Binds PP2A-B55 and Regulates Differentiation of Embryonic Stem Cells along the FLK1+ Lineage

Honarpour, N., Rose, C. M., Brumbaugh, J., Anderson, J., Graham, R. L. J., Sweredoski, M. J., Hess, S., Coon, J. J., Deshaies, R. J.

Journal:

Molecular & Cellular Proteomics

Year:

2014

Language:

english

File:

PDF, 1.19 MB

english, 2014

43

Textbook of Radiographic Positioning and Related Anatomy

Sweredoski, Ray

Journal:

Year:

1984

Language:

english

File:

PDF, 95 KB

english, 1984

44

Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi

Bagert, John D., van Kessel, Julia C., Sweredoski, Michael J., Feng, Lihui, Hess, Sonja, Bassler, Bonnie L., Tirrell, David A.

Journal:

Chemical Science

Year:

2016

Language:

english

File:

PDF, 1.38 MB

english, 2016

45

Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon

Nguyen, T. Van, Lee, J. Eugene, Sweredoski, Michael J., Yang, Seung-Joo, Jeon, Seung-Je, Harrison, Joseph S., Yim, Jung-Hyuk, Lee, Sang Ghil, Handa, Hiroshi, Kuhlman, Brian, Jeong, Ji-Seon, Reitsma, J

Journal:

Year:

2016

Language:

english

File:

PDF, 3.31 MB

english, 2016

46

An engineered aminoacyl-tRNA synthetase for cell-selective analysis of mammalian protein synthesis

Mahdavi, Alborz, Hamblin, Graham D, Jindal, Granton A, Bagert, John D., Dong, Cathy, Sweredoski, Michael J., Hess, Sonja, Schuman, Erin M., Tirrell, David A.

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 687 KB

english, 2016

47

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) – an Introduction for Biologists

L.J. Graham, Robert, J. Sweredoski, Michael, Hess, Sonja

Journal:

Current Proteomics

Year:

2011

Language:

english

File:

PDF, 261 KB

english, 2011

48

Middle-down electron capture dissociation and electron transfer dissociation for histone analysis

Moradian, Annie, Franco, Catarina, Sweredoski, Michael J., Hess, Sonja

Journal:

Journal of Analytical Science & Technology

Year:

2015

Language:

english

File:

PDF, 2.55 MB

english, 2015

49

Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap–High-Energy Collision Induced Dissociation MS 3 Scan

Liu, Jane M., Sweredoski, Michael J., Hess, Sonja

Journal:

Analytical Chemistry

Year:

2016

Language:

english

File:

PDF, 980 KB

english, 2016

50

Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system

Sung, M.-K., Reitsma, J. M., Sweredoski, M. J., Hess, S., Deshaies, R. J.

Journal:

Molecular Biology of the Cell

Year:

2016

Language:

english

File:

PDF, 6.69 MB

english, 2016