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1

Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium

Brusic, Vladimir, Gottardo, Raphael, Kleinstein, Steven H, Davis, Mark M, Davis, Mark M, Hafler, David A, Quill, Helen, Palucka, A Karolina, Poland, Gregory A, Pulendran, Bali, Reinherz, Ellis L, Stua

Journal:

Nature Biotechnology

Year:

2014

Language:

english

File:

PDF, 534 KB

english, 2014

2

Germinal Center B Cell and T Follicular Helper Cell Development Initiates in the Interfollicular Zone

Steven M. Kerfoot, Gur Yaari, Jaymin R. Patel, Kody L. Johnson, David G. Gonzalez, Steven H. Kleinstein, Ann M. Haberman

Journal:

Year:

2011

Language:

english

File:

PDF, 3.49 MB

english, 2011

3

Toward Quantitative Simulation of Germinal Center Dynamics: Biological and Modeling Insights from Experimental Validation

STEVEN H. KLEINSTEIN, JASWINDER PAL SINGH

Journal:

Journal of Theoretical Biology

Year:

2001

Language:

english

File:

PDF, 893 KB

english, 2001

4

Cell subset prediction for blood genomic studies

Christopher R Bolen, Mohamed Uduman, Steven H Kleinstein

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 921 KB

english, 2011

5

Gene Expression Gradients along the Tonotopic Axis of the Chicken Auditory Epithelium

Corey S. Frucht, Mohamed Uduman, Steven H. Kleinstein, Joseph Santos-Sacchi, Dhasakumar S. Navaratnam

Journal:

Journal of the Association for Research in Otolaryngology

Year:

2011

Language:

english

File:

PDF, 310 KB

english, 2011

6

Two levels of protection for the B cell genome during somatic hypermutation

Liu, Man, Duke, Jamie L., Richter, Daniel J., Vinuesa, Carola G., Goodnow, Christopher C., Kleinstein, Steven H., Schatz, David G.

Journal:

Year:

2008

Language:

english

File:

PDF, 694 KB

english, 2008

7

Somatic hypermutation targeting is influenced by location within the immunoglobulin V region

Reuma Magori Cohen, Steven H. Kleinstein, Yoram Louzoun

Journal:

Molecular Immunology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

8

Lambda and alpha interferons inhibit hepatitis B virus replication through a common molecular mechanism but with different in vivo activities

Nicole E. Pagliaccetti, Esther N. Chu, Christopher R. Bolen, Steven H. Kleinstein, Michael D. Robek

Journal:

Year:

2010

Language:

english

File:

PDF, 1.09 MB

english, 2010

9

PS2-108. Infection with Hepatitis C down-regulates the expression of cytokine genes in peripheral blood

Milton W. Taylor, Christopher R. Bolen, Steven H. Kleinstein, Leonid Brodsky

Journal:

Year:

2011

Language:

english

File:

PDF, 42 KB

english, 2011

10

Definition of Germinal-Center B Cell Migration In Vivo Reveals Predominant Intrazonal Circulation Patterns

Anja E. Hauser, Tobias Junt, Thorsten R. Mempel, Michael W. Sneddon, Steven H. Kleinstein, Sarah E. Henrickson, Ulrich H. von Andrian, Mark J. Shlomchik, Ann M. Haberman

Journal:

Year:

2007

Language:

english

File:

PDF, 2.03 MB

english, 2007

11

Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+ Cell Properties during Viral Infection

Heather D. Marshall, Anmol Chandele, Yong Woo Jung, Hailong Meng, Amanda C. Poholek, Ian A. Parish, Rachel Rutishauser, Weiguo Cui, Steven H. Kleinstein, Joe Craft, Susan M. Kaech

Journal:

Year:

2011

Language:

english

File:

PDF, 1.33 MB

english, 2011

12

The Blood Transcriptional Signature of Chronic Hepatitis C Virus Is Consistent with an Ongoing Interferon-Mediated Antiviral Response

Bolen, Christopher R., Robek, Michael D., Brodsky, Leonid, Schulz, Vincent, Lim, Joseph K., Taylor, Milton W., Kleinstein, Steven H.

Journal:

Journal of Interferon & Cytokine Research

Year:

2013

Language:

english

File:

PDF, 616 KB

english, 2013

13

Coregulation mapping based on individual phenotypic variation in response to virus infection

German Nudelman, Yongchao Ge, Jianzhong Hu, Madhu Kumar, Jeremy Seto, Jamie L Duke, Steven H Kleinstein, Fernand Hayot, Stuart C Sealfon, James G Wetmur

Journal:

Immunome Research

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

14

Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression

Bolen, Christopher R., Ding, Siyuan, Robek, Michael D., Kleinstein, Steven H.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.83 MB

english, 2014

15

CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype

Zuccarino-Catania, Griselda V, Sadanand, Saheli, Weisel, Florian J, Tomayko, Mary M, Meng, Hailong, Kleinstein, Steven H, Good-Jacobson, Kim L, Shlomchik, Mark J

Journal:

Nature Immunology

Year:

2014

Language:

english

File:

PDF, 1.00 MB

english, 2014

16

Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis

Wu, Yu-Chang B., James, Louisa K., Vander Heiden, Jason A., Uduman, Mohamed, Durham, Stephen R., Kleinstein, Steven H., Kipling, David, Gould, Hannah J.

Journal:

Journal of Allergy and Clinical Immunology

Year:

2014

Language:

english

File:

PDF, 2.13 MB

english, 2014

17

Immune Markers Associated with Host Susceptibility to Infection with West Nile Virus

Qian, Feng, Thakar, Juilee, Yuan, Xiaoling, Nolan, Melissa, Murray, Kristy O., Lee, William T., Wong, Susan J., Meng, Hailong, Fikrig, Erol, Kleinstein, Steven H., Montgomery, Ruth R.

Journal:

Viral Immunology

Year:

2014

Language:

english

File:

PDF, 405 KB

english, 2014

18

[IEEE 2006 Winter Simulation Conference - Monterey, CA, USA (2006.12.3-2006.12.6)] Proceedings of the 2006 Winter Simulation Conference - Nonuniform Sampling for Global Optimization of Kinetic Rate Constants in Biological Pathways

Kleinstein, Steven, Bottino, Dean, Georgieva, Anna, Sarangapani, Ramesh, Lett, G.

Year:

2006

Language:

english

File:

PDF, 310 KB

english, 2006

19

[IEEE 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Washington, D.C., USA (2009.11.1-2009.11.4)] 2009 IEEE International Conference on Bioinformatics and Biomedicine - Activated Germinal-Center B Cells Undergo Directed Migration

O'Connor, Mark J., Hauser, Anja E., Haberman, Ann M., Kleinstein, Steven H.

Year:

2009

Language:

english

File:

PDF, 415 KB

english, 2009

20

Overcoming NS1-Mediated Immune Antagonism Involves Both Interferon-Dependent and Independent Mechanisms

Thakar, Juilee, Schmid, Sonja, Duke, Jamie L., García-Sastre, Adolfo, Kleinstein, Steven H.

Journal:

Journal of Interferon & Cytokine Research

Year:

2013

Language:

english

File:

PDF, 471 KB

english, 2013

21

Determinism and stochasticity during maturation of the zebrafish antibody repertoire

Ning Jiang, Joshua A. Weinstein, Lolita Penland, Richard A. White III, Daniel S. Fisher, Stephen R. Quake and Steven H. Kleinstein

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.59 MB

english, 2011

22

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

Gadala-Maria, Daniel, Yaari, Gur, Uduman, Mohamed, Kleinstein, Steven H.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 794 KB

english, 2015

23

Analysis of gene–environment interactions in postnatal development of the mammalian intestine

Rakoff-Nahoum, Seth, Kong, Yong, Kleinstein, Steven H., Subramanian, Sathish, Ahern, Philip P., Gordon, Jeffrey I., Medzhitov, Ruslan

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

24

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

Gupta, Namita T., Vander Heiden, Jason A., Uduman, Mohamed, Gadala-Maria, Daniel, Yaari, Gur, Kleinstein, Steven H.

Journal:

Year:

2015

Language:

english

File:

PDF, 80 KB

english, 2015

25

Salmonella Typhimurium Type III Secretion Effectors Stimulate Innate Immune Responses in Cultured Epithelial Cells

Bruno, Vincent M., Hannemann, Sebastian, Lara-Tejero, María, Flavell, Richard A., Kleinstein, Steven H., Galán, Jorge E., Isberg, Ralph R.

Journal:

Year:

2009

Language:

english

File:

PDF, 624 KB

english, 2009

26

The center for expanded data annotation and retrieval

Musen, Mark A., Bean, Carol A., Cheung, Kei-Hoi, Dumontier, Michel, Durante, Kim A., Gevaert, Olivier, Gonzalez-Beltran, Alejandra, Khatri, Purvesh, Kleinstein, Steven H., O’Connor, Martin J., Pouliot

Journal:

Journal of the American Medical Informatics Association

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

27

Getting Started in Computational Immunology

Kleinstein, Steven H., Troyanskaya, Olga

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 622 KB

english, 2008

28

Production of IL-10 by CD4+ regulatory T cells during the resolution of infection promotes the maturation of memory CD8+ T cells

Laidlaw, Brian J, Cui, Weiguo, Amezquita, Robert A, Gray, Simon M, Guan, Tianxia, Lu, Yisi, Kobayashi, Yasushi, Flavell, Richard A, Kleinstein, Steven H, Craft, Joe, Kaech, Susan M

Journal:

Nature Immunology

Year:

2015

Language:

english

File:

PDF, 2.28 MB

english, 2015

29

Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation

Di Niro, Roberto, Lee, Seung-Joo, Vander Heiden, Jason A., Elsner, Rebecca A., Trivedi, Nikita, Bannock, Jason M., Gupta, Namita T., Kleinstein, Steven H., Vigneault, Francois, Gilbert, Tamara J., Mef

Journal:

Year:

2015

Language:

english

File:

PDF, 2.60 MB

english, 2015

30

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales

Yaari, Gur, Benichou, Jennifer I. C., Vander Heiden, Jason A., Kleinstein, Steven H., Louzoun, Yoram

Journal:

Philosophical Transactions Biological Sciences

Year:

2015

Language:

english

File:

PDF, 508 KB

english, 2015

31

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors

Sprecher, Emmett, Sarkar, Sudipa, Kleinstein, Steven H., Narayan, Murli, Winer, Eric, Tuck, David, Lezon-Geyda, Kimberly, Krop, Ian, Harris, Lyndsay

Year:

2011

Language:

english

File:

PDF, 748 KB

english, 2011

32

Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses

Ho, Ping-Chih, Bihuniak, Jessica Dauz, Macintyre, Andrew N., Staron, Matthew, Liu, Xiaojing, Amezquita, Robert, Tsui, Yao-Chen, Cui, Guoliang, Micevic, Goran, Perales, Jose C., Kleinstein, Steven H.,

Journal:

Year:

2015

Language:

english

File:

PDF, 2.98 MB

english, 2015

33

Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism

Thakar, Juilee, Hartmann, Boris M., Marjanovic, Nada, Sealfon, Stuart C., Kleinstein, Steven H.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.31 MB

english, 2015

34

Practical guidelines for B-cell receptor repertoire sequencing analysis

Yaari, Gur, Kleinstein, Steven H.

Journal:

Genome Medicine

Year:

2015

Language:

english

File:

PDF, 1.73 MB

english, 2015

35

Characterization of diabetogenic CD8+ T cells: immune therapy with metabolic blockade

Garyu, Justin W., Uduman, Mohamed, Stewart, Alex, Rui, Jinxiu, Deng, Songyan, Shenson, Jared, Staron, Matt M., Kaech, Susan M., Kleinstein, Steven H., Herold, Kevan C.

Journal:

Journal of Biological Chemistry

Year:

2016

Language:

english

File:

PDF, 1.24 MB

english, 2016

36

Recurrent genetic defects in classical Hodgkin lymphoma cell lines

Hudnall, S. David, Meng, Hailong, Lozovatsky, Larissa, Li, Peining, Strout, Matthew, Kleinstein, Steven H.

Journal:

Leukemia and Lymphoma

Year:

2016

Language:

english

File:

PDF, 1.30 MB

english, 2016

37

Activated germinal centre B cells undergo directed migration

O'Connor, Mark J., Hauser, Anja E., Haberman, Ann M., Kleinstein, Steven H.

Journal:

International Journal of Data Mining and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.52 MB

english, 2011

38

Age-associated vascular inflammation promotes monocytosis during atherogenesis

Du, Wei, Wong, Christine, Song, Yang, Shen, Hua, Mori, Daniel, Rotllan, Noemi, Price, Nathan, Dobrian, Anca D., Meng, Hailong, Kleinstein, Steven H., Fernandez-Hernando, Carlos, Goldstein, Daniel R.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.91 MB

english, 2016

39

Solving Immunology?

Vodovotz, Yoram, Xia, Ashley, Read, Elizabeth L., Bassaganya-Riera, Josep, Hafler, David A., Sontag, Eduardo, Wang, Jin, Tsang, John S., Day, Judy D., Kleinstein, Steven H., Butte, Atul J., Altman, Ma

Journal:

Trends in Immunology

Year:

2017

Language:

english

File:

PDF, 1.67 MB

english, 2017

40

Corrigendum: Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection

Bohannon, Caitlin, Powers, Ryan, Satyabhama, Lakshmipriyadarshini, Cui, Ang, Tipton, Christopher, Michaeli, Miri, Skountzou, Ioanna, Mittler, Robert S., Kleinstein, Steven H., Mehr, Ramit, Lee, France

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 128 KB

english, 2016

41

Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data

Gupta, Namita T., Adams, Kristofor D., Briggs, Adrian W., Timberlake, Sonia C., Vigneault, Francois, Kleinstein, Steven H.

Journal:

The Journal of Immunology

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

42

Generation of Long-Lived Bone Marrow Plasma Cells Secreting Antibodies Specific for the HIV-1 gp41 Membrane-Proximal External Region in the Absence of Polyreactivity

Donius, Luke R., Cheng, Yuxing, Choi, Jaewon, Sun, Zhen-Yu J., Hanson, Melissa, Zhang, Michael, Gierahn, Todd M., Marquez, Susanna, Uduman, Mohammed, Kleinstein, Steven H., Irvine, Darrell, Love, J. C

Journal:

Journal of Virology

Year:

2016

Language:

english

File:

PDF, 3.80 MB

english, 2016

43

Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8 + T Cell Terminal Differentiation and Loss of Multipotency

Gray, Simon M., Amezquita, Robert A., Guan, Tianxia, Kleinstein, Steven H., Kaech, Susan M.

Journal:

Year:

2017

Language:

english

File:

PDF, 3.97 MB

english, 2017

44

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

Maman, Yaakov, Teng, Grace, Seth, Rashu, Kleinstein, Steven H., Schatz, David G.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 4.21 MB

english, 2016

45

Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection

Bohannon, Caitlin, Powers, Ryan, Satyabhama, Lakshmipriyadarshini, Cui, Ang, Tipton, Christopher, Michaeli, Miri, Skountzou, Ioanna, Mittler, Robert S., Kleinstein, Steven H., Mehr, Ramit, Lee, Franci

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.58 MB

english, 2016

46

Interleukin-10 from CD4 + follicular regulatory T cells promotes the germinal center response

Laidlaw, Brian J., Lu, Yisi, Amezquita, Robert A., Weinstein, Jason S., Vander Heiden, Jason A., Gupta, Namita T., Kleinstein, Steven H., Kaech, Susan M., Craft, Joe

Journal:

Science Immunology

Year:

2017

Language:

english

File:

PDF, 1.68 MB

english, 2017

47

Multiple network-constrained regressions expand insights into influenza vaccination responses

Avey, Stefan, Mohanty, Subhasis, Wilson, Jean, Zapata, Heidi, Joshi, Samit R., Siconolfi, Barbara, Tsang, Sui, Shaw, Albert C., Kleinstein, Steven H.

Journal:

Year:

2017

Language:

english

File:

PDF, 452 KB

english, 2017

48

[ACM Press Companion of the The Web Conference 2018 - Lyon, France (2018.04.23-2018.04.27)] Companion of the The Web Conference 2018 on The Web Conference 2018 - WWW '18 - CEDAR

Musen, Mark A., Sansone, Susanna-Assunta, Cheung, Kei-Hoi, Kleinstein, Steven H., Crafts, Morgan, Schürer, Stephan C., Graybeal, John

Year:

2018

Language:

english

File:

PDF, 753 KB

english, 2018

49

Gene Expression Analysis of Forskolin Treated Basilar Papillae Identifies MicroRNA181a as a Mediator of Proliferation

Frucht, Corey S., Uduman, Mohamed, Duke, Jamie L., Kleinstein, Steven H., Santos-Sacchi, Joseph, Navaratnam, Dhasakumar S., Ravasi, Timothy

Journal:

Year:

2010

Language:

english

File:

PDF, 755 KB

english, 2010

50

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

Nouri, Nima, Kleinstein, Steven H

Journal:

Year:

2018

Language:

english

File:

PDF, 985 KB

english, 2018