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1

Non-Atopic Individuals Exhibit a Distinct Immune Reactivity Patterns in Response to Timothy Grass Pollen in and out-of-Season

Hinz, Denise, Seumois, Gregory, Greenbaum, Jason, White, Brandie, Schulten, Veronique M., Broide, David H., Sidney, John, Oseroff, Carla, Wambre, Erik R., James, Eddie A., Kwok, William W., Vijayanand

Journal:

Journal of Allergy and Clinical Immunology

Year:

2016

Language:

english

File:

PDF, 126 KB

english, 2016

2

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

Jason Greenbaum, John Sidney, Jolan Chung, Christian Brander, Bjoern Peters, Alessandro Sette

Journal:

Year:

2011

Language:

english

File:

PDF, 553 KB

english, 2011

3

A Subset Of Novel Timothy Grass Antigens Is Associated With Marked Th1/Th2 Shifts Following Specific Immunotherapy

Schulten, Veronique M., Tripple, Victoria, Sidney, John, Greenbaum, Jason, Frazier, April, Alam, Rafeul, Broide, David H., Grey, Howard, Peters, Bjoern, Sette, Alessandro

Journal:

Journal of Allergy and Clinical Immunology

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

4

A Systematic Analysis Of Pollen Transcriptomes From Plant Allergens Reveals Conserved Targets Of Immune Responses

Peters, Bjoern, Greenbaum, Jason, Schulten, Veronique M., Baker, Denise, Frazier, April, Sette, Alessandro, Wallner, Michael, Hofer, Heidi

Journal:

Journal of Allergy and Clinical Immunology

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

5

Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy

Schulten, Véronique, Tripple, Victoria, Sidney, John, Greenbaum, Jason, Frazier, April, Alam, Rafeul, Broide, David, Peters, Bjoern, Sette, Alessandro

Journal:

Journal of Allergy and Clinical Immunology

Year:

2014

Language:

english

File:

PDF, 1.15 MB

english, 2014

6

Immunological consequences of intragenus conservation of Mycobacterium tuberculosis T-cell epitopes

Lindestam Arlehamn, Cecilia S., Paul, Sinu, Mele, Federico, Huang, Charlie, Greenbaum, Jason A., Vita, Randi, Sidney, John, Peters, Bjoern, Sallusto, Federica, Sette, Alessandro

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 990 KB

english, 2015

7

Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals

Schulten, Véronique, Greenbaum, Jason A., Hauser, Michael, McKinney, Denise M., Sidney, John, Kolla, Ravi, Lindestam Arlehamn, Cecilia S., Oseroff, Carla, Alam, Rapheul, Broide, David H., Ferreira, Fa

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 796 KB

english, 2013

8

A Multivalent and Cross-Protective Vaccine Strategy against Arenaviruses Associated with Human Disease

Kotturi, Maya F., Botten, Jason, Sidney, John, Bui, Huynh-Hoa, Giancola, Lori, Maybeno, Matt, Babin, Josie, Oseroff, Carla, Pasquetto, Valerie, Greenbaum, Jason A., Peters, Bjoern, Ting, Joey, Do, Dan

Journal:

Year:

2009

Language:

english

File:

PDF, 750 KB

english, 2009

9

Memory T Cells in Latent Mycobacterium tuberculosis Infection Are Directed against Three Antigenic Islands and Largely Contained in a CXCR3+CCR6+ Th1 Subset

Lindestam Arlehamn, Cecilia S., Gerasimova, Anna, Mele, Federico, Henderson, Ryan, Swann, Justine, Greenbaum, Jason A., Kim, Yohan, Sidney, John, James, Eddie A., Taplitz, Randy, McKinney, Denise M.,

Journal:

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

10

Immunodominance in allergic T-cell reactivity to Japanese cedar in different geographic cohorts

Oseroff, Carla, Pham, John, Frazier, April, Hinz, Denise, Sidney, John, Paul, Sinu, Greenbaum, Jason A., Vita, Randi, Peters, Bjoern, Schulten, Véronique, Sette, Alessandro

Journal:

Annals of Allergy, Asthma & Immunology

Year:

2016

Language:

english

File:

PDF, 998 KB

english, 2016

11

Predicting T cell recognition of MHC class I restricted neoepitopes

Koşaloğlu-Yalçın, Zeynep, Lanka, Manasa, Frentzen, Angela, Logandha Ramamoorthy Premlal, Ashmitaa, Sidney, John, Vaughan, Kerrie, Greenbaum, Jason, Robbins, Paul, Gartner, Jared, Sette, Alessandro, Pe

Journal:

Year:

2018

Language:

english

File:

PDF, 4.44 MB

english, 2018

12

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

Schmiedel, Benjamin J., Singh, Divya, Madrigal, Ariel, Valdovino-Gonzalez, Alan G., White, Brandie M., Zapardiel-Gonzalo, Jose, Ha, Brendan, Altay, Gokmen, Greenbaum, Jason A., McVicker, Graham, Seumo

Journal:

Year:

2018

Language:

english

File:

PDF, 9.17 MB

english, 2018

13

A Magnetic Data Correction Workflow for Sparse, FourâDimensional Data

Aitken, Alan R. A., Ramos, Lara N., Roberts, Jason L., Greenbaum, Jamin S., Jong, Lenneke M., Young, Duncan A., Blankenship, Donald D.

Journal:

Journal of Geophysical Research: Solid Earth

Year:

2020

File:

PDF, 5.73 MB

2020

14

Spectrum of sequence variation in the FANCG gene: An International Fanconi Anemia Registry (IFAR) study

Arleen D. Auerbach, Jason Greenbaum, Kanan Pujara, Sat Dev Batish, Marco A. Bitencourt, Indira Kokemohr, Hildegard Schneider, Stephan Lobitzc, Ricardo Pasquini, Philip F. Giampietro, Helmut Hanenberg,

Journal:

Year:

2003

Language:

english

File:

PDF, 214 KB

english, 2003

15

Spectrum of sequence variation in the FANCG gene: An International Fanconi Anemia Registry (IFAR) study

Arleen D. Auerbach, Jason Greenbaum, Kanan Pujara, Sat Dev Batish, Marco A. Bitencourt, Indira Kokemohr, Hildegard Schneider, Stephan Lobitz, Ricardo Pasquini, Philip F. Giampietro, Helmut Hanenberg,

Journal:

Year:

2003

Language:

english

File:

PDF, 54 KB

english, 2003

16

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

Jason A. Greenbaum, Pernille Haste Andersen, Martin Blythe, Huynh-Hoa Bui, Raul E. Cachau, James Crowe, Matthew Davies, A. S. Kolaskar, Ole Lund, Sherrie Morrison, Brendan Mumey, Yanay Ofran, Jean-Luc

Journal:

Journal of Molecular Recognition

Year:

2007

Language:

english

File:

PDF, 223 KB

english, 2007

17

Mapping nucleic acid structure by hydroxyl radical cleavage

Thomas D Tullius, Jason A Greenbaum

Journal:

Current Opinion in Chemical Biology

Year:

2005

Language:

english

File:

PDF, 235 KB

english, 2005

18

Morphology of PI–PEO block copolymers for lithium batteries

Chenchen Xue, Mary Ann B. Meador, Lei Zhu, Jason J. Ge, Stephen Z.D. Cheng, Sirina Putthanarat, R.K. Eby, Ameesh Khalfan, George D. Bennett, Steve G. Greenbaum

Journal:

Year:

2006

Language:

english

File:

PDF, 2.40 MB

english, 2006

19

Lithium-7 nuclear magnetic resonance and Ti K-edge X-ray absorption spectroscopic investigation of electrochemical lithium insertion in Li4/3+xTi5/3O4

Fabio Ronci, P.E Stallworth, Faisal Alamgir, Theanne Schiros, Jason Van Sluytman, Xiaodong Guo, Priscilla Reale, Steve Greenbaum, Marten denBoer, Bruno Scrosati

Journal:

Journal of Power Sources

Year:

2003

Language:

english

File:

PDF, 167 KB

english, 2003

20

A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes

Young, Duncan A., Wright, Andrew P., Roberts, Jason L., Warner, Roland C., Young, Neal W., Greenbaum, Jamin S., Schroeder, Dustin M., Holt, John W., Sugden, David E., Blankenship, Donald D.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.55 MB

english, 2011

21

Functional expression and characterization of Schistosoma mansoni cathepsin B and its trans-activation by an endogenous asparaginyl endopeptidase

Mohammed Sajid, James H McKerrow, Elizabeth Hansell, Mary A Mathieu, Kimberley D Lucas, Ivy Hsieh, Doron Greenbaum, Matthew Bogyo, Jason P Salter, Kee C Lim, Christopher Franklin, Jea-Hyoun Kim, Conor

Journal:

Molecular and Biochemical Parasitology

Year:

2003

Language:

english

File:

PDF, 360 KB

english, 2003

22

An Evidenced-Based Approach to Radiographic Assessment of Cervical Spine Injuries in the Emergency Department

Jason Greenbaum, Nathan Walters, Phillip D. Levy

Journal:

The Journal of Emergency Medicine

Year:

2009

Language:

english

File:

PDF, 112 KB

english, 2009

23

Query enhancement through the practical application of ontology: the IEDB and OBI

Randi Vita, James A Overton, Jason A Greenbaum…

Journal:

Journal of Biomedical Semantics

Year:

2013

Language:

english

File:

PDF, 420 KB

english, 2013

24

Novel Grass Pollen Antigens Contribute to the Stimulation of Th2 Cytokines in Allergic Individuals

Schulten, Veronique M., Greenbaum, Jason, Kolla, Ravi, Arlehamn-Lindestam, Cecilia, Oseroff, Carla, Alam, Rafeul, Broide, David H., Grey, Howard, Sette, Alessandro, Peters, Bjoern

Journal:

Journal of Allergy and Clinical Immunology

Year:

2013

Language:

english

File:

PDF, 39 KB

english, 2013

25

Photoinduced Surface Potential Change of Bacteriorhodopsin Mutant D96N Measured by Scanning Surface Potential Microscopy

Lee, Ida, Greenbaum, Elias, Budy, Stephen, Hillebrecht, Jason R., Birge, Robert R., Stuart, Jeffrey A.

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 856 KB

english, 2006

26

Meta-analysis of All Immune Epitope Data in the Flavivirus Genus: Inventory of Current Immune Epitope Data Status in the Context of Virus Immunity and Immunopathology

Vaughan, Kerrie, Greenbaum, Jason, Blythe, Martin, Peters, Bjoern, Sette, Alessandro

Journal:

Viral Immunology

Year:

2010

Language:

english

File:

PDF, 791 KB

english, 2010

27

X-ray Absorption Spectroscopy Investigation of the Sub-Nanoscale Strain in Thin-Film Lithium Ion Battery Cathodes

Alamgir, Faisal M., Vansluytman, Jason, Carter, Daniel, Whitacre, Jay, Kao, Chi-Chang, Greenbaum, Steve, Denboer, Marten

Journal:

MRS Proceedings

Year:

2004

Language:

english

File:

PDF, 248 KB

english, 2004

28

Dengue Virus Evolution under a Host-Targeted Antiviral

Plummer, Emily, Buck, Michael D., Sanchez, Marisa, Greenbaum, Jason A., Turner, Julia, Grewal, Rajvir, Klose, Brennan, Sampath, Aruna, Warfield, Kelly L., Peters, Bjoern, Ramstedt, Urban, Shresta, Suj

Journal:

Journal of Virology

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

29

IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis

Krause, Petra, Morris, Venetia, Greenbaum, Jason A., Park, Yoon, Bjoerheden, Unni, Mikulski, Zbigniew, Muffley, Tracy, Shui, Jr-Wen, Kim, Gisen, Cheroutre, Hilde, Liu, Yun-Cai, Peters, Bjoern, Kronenb

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

30

Towards Defining Molecular Determinants Recognized by Adaptive Immunity in Allergic Disease: An Inventory of the Available Data

Vaughan, Kerrie, Greenbaum, Jason, Kim, Yohan, Vita, Randi, Chung, Jo, Peters, Bjoern, Broide, David, Goodman, Richard, Grey, Howard, Sette, Alessandro

Journal:

Journal of Allergy (Hindawi Publishing Corporation)

Year:

2010

Language:

english

File:

PDF, 186 KB

english, 2010

31

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

McKinney, Denise M., Fu, Zheng, Le, Lucas, Greenbaum, Jason A., Peters, Bjoern, Sette, Alessandro

Journal:

Human Immunology

Year:

2015

Language:

english

File:

PDF, 667 KB

english, 2015

32

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

Calis, Jorg J. A., Maybeno, Matt, Greenbaum, Jason A., Weiskopf, Daniela, De Silva, Aruna D., Sette, Alessandro, KeÅŸmir, Can, Peters, Bjoern, Asquith, Becca

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 686 KB

english, 2013

33

[ACM Press the 5th ACM Conference - Newport Beach, California (2014.09.20-2014.09.23)] Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14 - The interplay of sequence conservation and T cell immune recognition

Bresciani, Anne, Greenbaum, Jason, Arlehamn, Cecilia S. Lindestam, Sette, Alessandro, Nielsen, Morten, Peters, Bjoern

Year:

2014

Language:

english

File:

PDF, 357 KB

english, 2014

34

An extensive subglacial lake and canyon system in Princess Elizabeth Land, East Antarctica

Jamieson, Stewart S.R., Ross, Neil, Greenbaum, Jamin S., Young, Duncan A., Aitken, Alan R.A., Roberts, Jason L., Blankenship, Donald D., Bo, Sun, Siegert, Martin J.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

35

T-cell epitope conservation across allergen species is a major determinant of immunogenicity

Westernberg, Luise, Schulten, Véronique, Greenbaum, Jason A., Natali, Sara, Tripple, Victoria, McKinney, Denise M., Frazier, April, Hofer, Heidi, Wallner, Michael, Sallusto, Federica, Sette, Alessandr

Journal:

Journal of Allergy and Clinical Immunology

Year:

2016

Language:

english

File:

PDF, 2.33 MB

english, 2016

36

A Systematic Analysis of Pollen Transcriptomes from Plant Allergens Reveals Conserved Targets of Immune Responses

Sternberg, Luise, Greenbaum, Jason, Schulten, Veronique M., Tripple, Victoria, Baker, Denise, Frazier, April, Hofer, Heidi, Wallner, Michael, Sette, Alessandro, Peters, Bjoern

Journal:

Journal of Allergy and Clinical Immunology

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

37

Land-ice elevation changes from photon-counting swath altimetry: first applications over the Antarctic ice sheet

Young, Duncan A., Lindzey, Laura E., Blankenship, Donald D., Greenbaum, Jamin S., Garcia De Gorordo, Alvaro, Kempf, Scott D., Roberts, Jason L., Warner, Roland C., Van Ommen, Tas, Siegert, Martin J.,

Journal:

Journal of Glaciology

Year:

2015

Language:

english

File:

PDF, 5.41 MB

english, 2015

38

T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

Bresciani, Anne, Paul, Sinu, Schommer, Nina, Dillon, Myles B., Bancroft, Tara, Greenbaum, Jason, Sette, Alessandro, Nielsen, Morten, Peters, Bjoern

Journal:

Year:

2016

Language:

english

File:

PDF, 245 KB

english, 2016

39

Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity

Oseroff, Carla, Christensen, Lars H., Westernberg, Luise, Pham, John, Lane, Jerome, Paul, Sinu, Greenbaum, Jason, Stranzl, Thomas, Lund, Gitte, Hoof, Ilka, Holm, Jens, Würtzen, Peter A, Meno, Kåre H.,

Journal:

Clinical & Experimental Allergy

Year:

2016

Language:

english

File:

PDF, 934 KB

english, 2016

40

An automated benchmarking platform for MHC class II binding prediction methods

Andreatta, Massimo, Trolle, Thomas, Yan, Zhen, Greenbaum, Jason A, Peters, Bjoern, Nielsen, Morten

Journal:

Year:

2017

Language:

english

File:

PDF, 800 KB

english, 2017

41

Improved methods for predicting peptide binding affinity to MHC class II molecules

Jensen, Kamilla Kjaergaard, Andreatta, Massimo, Marcatili, Paolo, Buus, Søren, Greenbaum, Jason A., Yan, Zhen, Sette, Alessandro, Peters, Bjoern, Nielsen, Morten

Journal:

Year:

2018

Language:

english

File:

PDF, 1.18 MB

english, 2018

42

Development of Asthma in Inner-City Children: Possible Roles of MAIT Cells and Variation in the Home Environment

Chandra, Shilpi, Wingender, Gerhard, Greenbaum, Jason A., Khurana, Archana, Gholami, Amin M., Ganesan, Anusha-Preethi, Rosenbach, Michael, Jaffee, Katy, Gern, James E., Wood, Robert, O’Connor, George,

Journal:

The Journal of Immunology

Year:

2018

Language:

english

File:

PDF, 1.24 MB

english, 2018

43

Transcriptomic Analysis of CD4 + T Cells Reveals Novel Immune Signatures of Latent Tuberculosis

Burel, Julie G., Lindestam Arlehamn, Cecilia S., Khan, Nabeela, Seumois, Grégory, Greenbaum, Jason A., Taplitz, Randy, Gilman, Robert H., Saito, Mayuko, Vijayanand, Pandurangan, Sette, Alessandro, Pet

Journal:

The Journal of Immunology

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

44

Response to Comment on “Development of Asthma in Inner-City Children: Possible Roles of MAIT Cells and Variation in the Home Environment”

Chandra, Shilpi, Wingender, Gerhard, Greenbaum, Jason A., Kronenberg, Mitchell

Journal:

The Journal of Immunology

Year:

2018

Language:

english

File:

PDF, 1.12 MB

english, 2018

45

YAP and MRTF-A, transcriptional co-activators of RhoA-mediated gene expression, are critical for glioblastoma tumorigenicity

Yu, Olivia M., Benitez, Jorge A., Plouffe, Steven W., Ryback, Daniel, Klein, Andrea, Smith, Jeff, Greenbaum, Jason, Delatte, Benjamin, Rao, Anjana, Guan, Kun-Liang, Furnari, Frank B., Chaim, Olga Meir

Journal:

Year:

2018

Language:

english

File:

PDF, 4.19 MB

english, 2018

46

TiArA: A Virtual Appliance for the Analysis of Tiling Array Data

Greenbaum, Jason A., Assarsson, Erika, Chung, Jo L., Head, Steven, Sette, Alessandro, Peters, Bjoern, Ravasi, Timothy

Journal:

Year:

2010

Language:

english

File:

PDF, 735 KB

english, 2010

47

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data

Gerasimova, Anna, Chavez, Lukas, Li, Bin, Seumois, Gregory, Greenbaum, Jason, Rao, Anjana, Vijayanand, Pandurangan, Peters, Bjoern, Hsu, Yi-Hsiang

Journal:

Year:

2013

Language:

english

File:

PDF, 773 KB

english, 2013

48

IEDB-AR: immune epitope database—analysis resource in 2019

Dhanda, Sandeep Kumar, Mahajan, Swapnil, Paul, Sinu, Yan, Zhen, Kim, Haeuk, Jespersen, Martin Closter, Jurtz, Vanessa, Andreatta, Massimo, Greenbaum, Jason A, Marcatili, Paolo, Sette, Alessandro, Niel

Journal:

Nucleic Acids Research

Year:

2019

File:

PDF, 216 KB

2019

49

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Peters, Bjoern, Ruttenberg, Alan, Greenbaum, Jason, Courtot, Melanie, Brinkman, Ryan, Whetzel, Patricia, Schober, Daniel, Sansone, Susanna Assunta, Scheuerman, Richard, Rocca-Serra, Philippe

Journal:

Bioentrepreneur

Year:

2009

Language:

english

File:

PDF, 488 KB

english, 2009

50

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Peters, Bjoern, Ruttenberg, Alan, Greenbaum, Jason, Courtot, Melanie, Brinkman, Ryan, Whetzel, Patricia, Schober, Daniel, Sansone, Susanna Assunta, Scheuerman, Richard, Rocca-Serra, Philippe

Journal:

Bioentrepreneur

Year:

2009

File:

PDF, 488 KB

2009