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1

A Deep Learning Approach to Antibiotic Discovery

Stokes, Jonathan M., Yang, Kevin, Swanson, Kyle, Jin, Wengong, Cubillos-Ruiz, Andres, Donghia, Nina M., MacNair, Craig R., French, Shawn, Carfrae, Lindsey A., Bloom-Ackerman, Zohar, Tran, Victoria M.,

Journal:

Year:

2020

Language:

english

File:

PDF, 3.50 MB

english, 2020

2

ER Stress Sensor XBP1 Controls Anti-tumor Immunity by Disrupting Dendritic Cell Homeostasis

Cubillos-Ruiz, Juan R., Silberman, Pedro C., Rutkowski, Melanie R., Chopra, Sahil, Perales-Puchalt, Alfredo, Song, Minkyung, Zhang, Sheng, Bettigole, Sarah E., Gupta, Divya, Holcomb, Kevin, Ellenson,

Journal:

Year:

2015

Language:

english

File:

PDF, 3.03 MB

english, 2015

3

Tumorigenic and Immunosuppressive Effects of Endoplasmic Reticulum Stress in Cancer

Cubillos-Ruiz, Juan R., Bettigole, Sarah E., Glimcher, Laurie H.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.46 MB

english, 2017

4

Endoplasmic Reticulum Stress Responses in Intratumoral Immune Cells: Implications for Cancer Immunotherapy

Song, Minkyung, Cubillos-Ruiz, Juan R.

Journal:

Trends in Immunology

Year:

2019

Language:

english

File:

PDF, 2.53 MB

english, 2019

5

A Deep Learning Approach to Antibiotic Discovery

Stokes, Jonathan M., Yang, Kevin, Swanson, Kyle, Jin, Wengong, Cubillos-Ruiz, Andres, Donghia, Nina M., MacNair, Craig R., French, Shawn, Carfrae, Lindsey A., Bloom-Ackermann, Zohar, Tran, Victoria M.

Journal:

Year:

2020

File:

PDF, 5.56 MB

2020

6

Antifungal mechanisms by which a novel Pseudomonas aeruginosa phenazine toxin kills Candida albicans in biofilms

Diana K. Morales, Nicholas J. Jacobs, Sathish Rajamani, Malathy Krishnamurthy, Juan R. Cubillos-Ruiz, Deborah A. Hogan

Journal:

Molecular Microbiology

Year:

2010

Language:

english

File:

PDF, 1.13 MB

english, 2010

7

Nanomolecular targeting of dendritic cells for ovarian cancer therapy

Cubillos-Ruiz, Juan R, Fiering, Steven, Conejo-Garcia, Jose R

Journal:

Future Oncology

Year:

2009

Language:

english

File:

PDF, 870 KB

english, 2009

8

Analysis of the genetic variation inMycobacterium tuberculosisstrains by multiple genome alignments

Andrés Cubillos-Ruiz, Juan Morales, Mercedes María Zambrano

Journal:

BMC Research Notes

Year:

2008

Language:

english

File:

PDF, 367 KB

english, 2008

9

Imaging secondary metabolism ofStreptomycessp. Mg1 during cellular lysis and colony degradation of competingBacillus subtilis

Sarah R. Barger, B. Chris Hoefler, Andrés Cubillos-Ruiz, William K. Russell, David H. Russell, Paul D. Straight

Journal:

Antonie van Leeuwenhoek

Year:

2012

Language:

english

File:

PDF, 826 KB

english, 2012

10

IS-seq: a novel high throughput survey of in vivo IS6110transposition in multipleMycobacterium tuberculosisgenomes

Reyes, Alejandro, Sandoval, Andrea, Cubillos-Ruiz, Andrés, Varley, Katherine E, Hernández-Neuta, Ivan, Samper, Sofía, Martín, Carlos, García, María, Ritacco, Viviana, López, Lucelly, Robledo, Jaime, Z

Journal:

Year:

2012

Language:

english

File:

PDF, 681 KB

english, 2012

11

Avirulent Toxoplasma gondii Generates Therapeutic Antitumor Immunity by Reversing Immunosuppression in the Ovarian Cancer Microenvironment

Baird, J. R., Fox, B. A., Sanders, K. L., Lizotte, P. H., Cubillos-Ruiz, J. R., Scarlett, U. K., Rutkowski, M. R., Conejo-Garcia, J. R., Fiering, S., Bzik, D. J.

Journal:

Cancer Research

Year:

2013

Language:

english

File:

PDF, 1.17 MB

english, 2013

12

Ovarian cancer progression is controlled by phenotypic changes in dendritic cells

Scarlett, U. K., Rutkowski, M. R., Rauwerdink, A. M., Fields, J., Escovar-Fadul, X., Baird, J., Cubillos-Ruiz, J. R., Jacobs, A. C., Gonzalez, J. L., Weaver, J., Fiering, S., Conejo-Garcia, J. R.

Journal:

Journal of Experimental Medicine

Year:

2012

Language:

english

File:

PDF, 3.10 MB

english, 2012

13

In situ Stimulation of CD40 and Toll-like Receptor 3 Transforms Ovarian Cancer-Infiltrating Dendritic Cells from Immunosuppressive to Immunostimulatory Cells

Scarlett, U. K., Cubillos-Ruiz, J. R., Nesbeth, Y. C., Martinez, D. G., Engle, X., Gewirtz, A. T., Ahonen, C. L., Conejo-Garcia, J. R.

Journal:

Cancer Research

Year:

2009

Language:

english

File:

PDF, 895 KB

english, 2009

14

Reprogramming Tumor-Associated Dendritic Cells In Vivo Using miRNA Mimetics Triggers Protective Immunity against Ovarian Cancer

Cubillos-Ruiz, J. R., Baird, J. R., Tesone, A. J., Rutkowski, M. R., Scarlett, U. K., Camposeco-Jacobs, A. L., Anadon-Arnillas, J., Harwood, N. M., Korc, M., Fiering, S. N., Sempere, L. F., Conejo-Gar

Journal:

Cancer Research

Year:

2012

Language:

english

File:

PDF, 860 KB

english, 2012

15

Genomic Signatures of the Haarlem Lineage of Mycobacterium tuberculosis: Implications of Strain Genetic Variation in Drug and Vaccine Development

Cubillos-Ruiz, A., Sandoval, A., Ritacco, V., Lopez, B., Robledo, J., Correa, N., Hernandez-Neuta, I., Zambrano, M. M., Del Portillo, P.

Journal:

Journal of Clinical Microbiology

Year:

2010

Language:

english

File:

PDF, 1.31 MB

english, 2010

16

Nitrate reductase assay for the rapid detection of pyrazinamide resistance in Mycobacterium tuberculosis using nicotinamide

Martin, A., Cubillos-Ruiz, A., Von Groll, A., Del Portillo, P., Portaels, F., Palomino, J. C.

Journal:

Journal of Antimicrobial Chemotherapy

Year:

2007

Language:

english

File:

PDF, 90 KB

english, 2007

17

CCL5-Mediated Endogenous Antitumor Immunity Elicited by Adoptively Transferred Lymphocytes and Dendritic Cell Depletion

Nesbeth, Y., Scarlett, U., Cubillos-Ruiz, J., Martinez, D., Engle, X., Turk, M.-J., Conejo-Garcia, J. R.

Journal:

Cancer Research

Year:

2009

Language:

english

File:

PDF, 833 KB

english, 2009

18

CD4+ T Cells Elicit Host Immune Responses to MHC Class II- Ovarian Cancer through CCL5 Secretion and CD40-Mediated Licensing of Dendritic Cells

Nesbeth, Y. C., Martinez, D. G., Toraya, S., Scarlett, U. K., Cubillos-Ruiz, J. R., Rutkowski, M. R., Conejo-Garcia, J. R.

Journal:

The Journal of Immunology

Year:

2010

Language:

english

File:

PDF, 1.18 MB

english, 2010

19

Depletion of Dendritic Cells Delays Ovarian Cancer Progression by Boosting Antitumor Immunity

Huarte, E., Cubillos-Ruiz, J. R., Nesbeth, Y. C., Scarlett, U. K., Martinez, D. G., Buckanovich, R. J., Benencia, F., Stan, R. V., Keler, T., Sarobe, P., Sentman, C. L., Conejo-Garcia, J. R.

Journal:

Cancer Research

Year:

2008

Language:

english

File:

PDF, 714 KB

english, 2008

20

BH3-only proteins are part of a regulatory network that control the sustained signalling of the unfolded protein response sensor IRE1α

Rodriguez, Diego A, Zamorano, Sebastian, Lisbona, Fernanda, Rojas-Rivera, Diego, Urra, Hery, Cubillos-Ruiz, Juan R, Armisen, Ricardo, Henriquez, Daniel R, H Cheng, Emily, Letek, Michal, Vaisar, Tomas,

Journal:

The EMBO Journal

Year:

2012

Language:

english

File:

PDF, 2.25 MB

english, 2012

21

IL-21 induces antiviral microRNA-29 in CD4 T cells to limit HIV-1 infection

Adoro, Stanley, Cubillos-Ruiz, Juan R., Chen, Xi, Deruaz, Maud, Vrbanac, Vladimir D., Song, Minkyung, Park, Suna, Murooka, Thomas T., Dudek, Timothy E., Luster, Andrew D., Tager, Andrew M., Streeck, H

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.26 MB

english, 2015

22

Targeting abnormal ER stress responses in tumors: A new approach to cancer immunotherapy

Cubillos-Ruiz, Juan R., Glimcher, Laurie H.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.64 MB

english, 2015

23

Good things come in small packages

Cubillos-Ruiz, Juan R., Sempere, Lorenzo F., Conejo-Garcia, Jose R.

Journal:

Year:

2012

Language:

english

File:

PDF, 597 KB

english, 2012

24

It never rains but it pours

Cubillos-Ruiz, Juan R., Conejo-Garcia, Jose R.

Journal:

Year:

2011

Language:

english

File:

PDF, 653 KB

english, 2011

25

Blocking ovarian cancer progression by targeting tumor microenvironmental leukocytes

Cubillos-Ruiz, Juan R., Rutkowski, Melanie, Conejo-Garcia, José R.

Journal:

Year:

2010

Language:

english

File:

PDF, 759 KB

english, 2010

26

Molecular Pathways: Immunosuppressive Roles of IRE1 -XBP1 Signaling in Dendritic Cells of the Tumor Microenvironment

Cubillos-Ruiz, J. R., Bettigole, S. E., Glimcher, L. H.

Journal:

Clinical Cancer Research

Year:

2016

File:

PDF, 5.95 MB

2016

27

Molecular Pathways: Immunosuppressive Roles of IRE1 -XBP1 Signaling in Dendritic Cells of the Tumor Microenvironment

Cubillos-Ruiz, J. R., Bettigole, S. E., Glimcher, L. H.

Journal:

Clinical Cancer Research

Year:

2016

Language:

english

File:

PDF, 5.95 MB

english, 2016

28

State-of-the-art of regulatory dendritic cells in cancer

Conejo-Garcia, Jose R., Rutkowski, Melanie R., Cubillos-Ruiz, Juan R.

Journal:

Pharmacology & Therapeutics

Year:

2016

Language:

english

File:

PDF, 1.07 MB

english, 2016

29

Reprogramming immune responses via microRNA modulation

Cubillos-Ruiz, Juan R., Rutkowski, Melanie R, Tchou, Julia, Conejo-Garcia, Jose R.

Journal:

microRNA Diagnostics and Therapeutics

Year:

2014

Language:

english

File:

PDF, 469 KB

english, 2014

30

935 Potential role of an IRE1α/XBP1 inhibitor in preventing therapeutic failure of intravesical BCG in bladder cancer

Lewicki, P., Liu, H., Golombos, D., O'Malley, P., Cubillos-Ruiz, J., Scherr, D.

Journal:

European Urology Supplements

Year:

2016

Language:

english

File:

PDF, 200 KB

english, 2016

31

1053 Endoplasmic reticulum stress as a putative mechanism for attenuated response to intravesical BCG in bladder cancer

Lewicki, P., Liu, H., O’, Malley P., Golombos, D., Cubillos-Ruiz, J., Scherr, D.

Journal:

European Urology Supplements

Year:

2016

Language:

english

File:

PDF, 200 KB

english, 2016

32

Dendritic cell rehab: new strategies to unleash therapeutic immunity in ovarian cancer

Chae, Chang-Suk, Teran-Cabanillas, Eli, Cubillos-Ruiz, Juan R.

Journal:

Cancer Immunology, Immunotherapy

Year:

2017

Language:

english

File:

PDF, 1.06 MB

english, 2017

33

Unfolding anti-tumor immunity: ER stress responses sculpt tolerogenic myeloid cells in cancer

Cubillos-Ruiz, Juan R., Mohamed, Eslam, Rodriguez, Paulo C.

Journal:

Journal for ImmunoTherapy of Cancer

Year:

2017

Language:

english

File:

PDF, 1.04 MB

english, 2017

34

Evolutionary radiation of lanthipeptides in marine cyanobacteria

Cubillos-Ruiz, Andres, Berta-Thompson, Jessie W., Becker, Jamie W., van der Donk, Wilfred A., Chisholm, Sallie W.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 2.15 MB

english, 2017

35

Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells

Read, Robert W, Berube, Paul M, Biller, Steven J, Neveux, Iva, Cubillos-Ruiz, Andres, Chisholm, Sallie W, Grzymski, Joseph J

Journal:

The ISME Journal

Year:

2017

Language:

english

File:

PDF, 1.31 MB

english, 2017

36

Adoptive dendritic cell transfer following platinum-based chemotherapy extends overall host survival in a preclinical model of metastatic ovarian cancer

Buskwofie, A., Teran-Cabanillas, E., Sandoval Medina, T., Cubillos-Ruiz, J.R.

Journal:

Gynecologic Oncology

Year:

2018

Language:

english

File:

PDF, 555 KB

english, 2018

37

Endoplasmic Reticulum Stress Sensor IRE1α Enhances IL-23 Expression by Human Dendritic Cells

Márquez, Saioa, Fernández, José Javier, Terán-Cabanillas, Eli, Herrero, Carmen, Alonso, Sara, Azogil, Alicia, Montero, Olimpio, Iwawaki, Takao, Cubillos-Ruiz, Juan R., Fernández, Nieves, Crespo, Maria

Journal:

Frontiers in Immunology

Year:

2017

Language:

english

File:

PDF, 5.39 MB

english, 2017

38

PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis

Ramos, Yusibeska, Rocha, Jorge, Hael, Ana L., van Gestel, Jordi, Vlamakis, Hera, Cywes-Bentley, Colette, Cubillos-Ruiz, Juan R., Pier, Gerald B., Gilmore, Michael S., Kolter, Roberto, Morales, Diana K

Journal:

Year:

2019

Language:

english

File:

PDF, 19.57 MB

english, 2019

39

Dendritic Cell Metabolism and Function in Tumors

Giovanelli, Paolo, Sandoval, Tito A., Cubillos-Ruiz, Juan R.

Journal:

Trends in Immunology

Year:

2019

Language:

english

File:

PDF, 1.42 MB

english, 2019

40

Dendritic Cell Metabolism and Function in Tumors

Giovanelli, Paolo, Sandoval, Tito A., Cubillos-Ruiz, Juan R.

Journal:

Trends in Immunology

Year:

2019

File:

PDF, 1.42 MB

2019

41

CD3+ and CD8+ tumor-infiltrating lymphocytes (TILs) as markers of improved prognosis in high-grade serous ovarian cancer

Kahn, R.M., Matrai, C., Quinn, A.S., Talukdar, N., McIntire, P., Cubillos-Ruiz, J.R., Frey, M.K., Caputo, T.A., Holcomb, K.M., Chapman-Davis, E.

Journal:

Gynecologic Oncology

Year:

2019

File:

PDF, 115 KB

2019

42

Dietary Fructose Alters the Composition, Localization and Metabolism of Gut Microbiota in Association with Worsening Colitis

Montrose, David C., Nishiguchi, Ryohei, Basu, Srijani, Staab, Hannah A., Zhou, Xi Kathy, Wang, Hanhan, Meng, Lingsong, Johncilla, Melanie, Cubillos-Ruiz, Juan R., Morales, Diana K., Wells, Martin T.,

Journal:

CMGH Cellular and Molecular Gastroenterology and Hepatology

Year:

2020

File:

PDF, 17.55 MB

2020

43

IRE1Î±-XBP1 Signaling as a Mechanism of Resistance to Immunotherapy in Ovarian Cancer

Zhou, Z.N., Sandoval, T.A., Chae, C.S., Cubillos-Ruiz, J.R.

Journal:

Gynecologic Oncology

Year:

2020

File:

PDF, 460 KB

2020

44

Intratumoral XBP1s expression and its association with T cell infiltration and patient outcomes in ovarian carcinoma

Kahn, R.M., Cubillos-Ruiz, J.R., Matrai, C., Quinn, A.S., Christos, P.J., Askin, G., Litvin, D., Goyal, A., Frey, M.K., Caputo, T.A., Holcomb, K.M., Chapman-Davis, E.

Journal:

Gynecologic Oncology

Year:

2020

File:

PDF, 59 KB

2020

45

Endoplasmic reticulum stress signals in the tumour and its microenvironment

Chen, Xi, Cubillos-Ruiz, Juan R.

Journal:

Nature Reviews Cancer

Year:

2020

File:

PDF, 2.28 MB

2020

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