Research Output

2020

Computational deconvolution of tumor-infiltrating immune components with bulk tumor gene expression data

Li, B., Li, T., Liu, J. S. & Liu, X. S., Jan 1 2020, Methods in Molecular Biology. Humana Press Inc., p. 249-262 14 p. (Methods in Molecular Biology; vol. 2120).

Research output: Chapter in Book/Report/Conference proceedingChapter

Investigation of antigen-specific T-cell receptor clusters in human cancers

Zhang, H., Liu, L., Zhang, J., Chen, J., Ye, J., Shukla, S., Qiao, J., Zhan, X., Chen, H., Wu, C. J., Fu, Y. X. & Li, B., Mar 15 2020, In : Clinical Cancer Research. 26, 6, p. 1359-1371 13 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

TRA-1-60-positive/CD45low cells found in the peripheral blood of prostate cancer patients with metastatic disease – A proof-of-concept study

Schäfer, C., Ju, Y., Tak, Y., Vazquez, C., Han, S. J., Tan, E., Shay, J. W., Holmqvist, M., Danuser, G., Schopperle, W. M. & Bubley, G., Jan 2020, In : Heliyon. 6, 1, e03263.

Research output: Contribution to journalArticle

Open Access
2019

Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21

Kim, D. S., Camacho, C. V., Nagari, A., Malladi, V. S., Challa, S. & Kraus, W. L., Sep 19 2019, In : Molecular cell. 75, 6, p. 1270-1285.e14

Research output: Contribution to journalArticle

11 Scopus citations

A multi-modal data resource for investigating topographic heterogeneity in patient-derived xenograft tumors

Rajaram, S., Roth, M. A., Malato, J., VandenBerg, S., Hann, B., Atreya, C. E., Altschuler, S. J. & Wu, L. F., Oct 31 2019, In : Scientific data. 6, 1, 1 p.

Research output: Contribution to journalArticle

Open Access

An image-based assay to quantify changes in proliferation and viability upon drug treatment in 3D microenvironments

Murali, V. S., Chang, B. J., Fiolka, R., Danuser, G., Cobanoglu, M. C. & Welf, E. S., May 28 2019, In : BMC Cancer. 19, 1, 502.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth

David, A. F., Roudot, P., Legant, W. R., Betzig, E., Danuser, G. & Gerlich, D. W., Jan 1 2019, In : Journal of Cell Biology. 218, 7, p. 2150-2168 19 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Automated profiling of growth cone heterogeneity defines relations between morphology and motility

Bagonis, M. M., Fusco, L., Pertz, O. & Danuser, G., Jan 1 2019, In : Journal of Cell Biology. 218, 1, p. 350-379 30 p.

Research output: Contribution to journalArticle

1 Scopus citations

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

Hashimoto, H., Wang, Z., Garry, G. A., Malladi, V. S., Botten, G. A., Ye, W., Zhou, H., Osterwalder, M., Dickel, D. E., Visel, A., Liu, N., Bassel-Duby, R. & Olson, E. N., Jul 3 2019, In : Cell Stem Cell. 25, 1, p. 69-86.e5

Research output: Contribution to journalArticle

4 Scopus citations

Distinct expression patterns of carbonic anhydrase IX in clear cell, microcystic, and angiomatous meningiomas

Chkheidze, R., Cimino, P. J., Hatanpaa, K. J., White, C. L., Ferreira, M., Piccirillo, S. G. M., Li, L., Rajaram, S., Nyagilo, J. O., Burns, D. K., Raisanen, J. M. & Cai, C., Dec 1 2019, In : Journal of neuropathology and experimental neurology. 78, 12, p. 1081-1088 8 p.

Research output: Contribution to journalArticle

Enhanced Dendritic Actin Network Formation in Extended Lamellipodia Drives Proliferation in Growth-Challenged Rac1 P29S Melanoma Cells

Mohan, A. S., Dean, K. M., Isogai, T., Kasitinon, S. Y., Murali, V. S., Roudot, P., Groisman, A., Reed, D. K., Welf, E. S., Han, S. J., Noh, J. & Danuser, G., May 6 2019, In : Developmental cell. 49, 3, p. 444-460.e9

Research output: Contribution to journalArticle

2 Scopus citations

Erratum: Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community (Database : the journal of biological databases and curation (2017) 2017 PII: baz035)

Saha, S., Hosmani, P. S., Villalobos-Ayala, K., Miller, S., Shippy, T., Flores, M., Rosendale, A., Cordola, C., Bell, T., Mann, H., DeAvila, G., DeAvila, D., Moore, Z., Buller, K., Ciolkevich, K., Nandyal, S., Mahoney, R., Voorhis, J. V., Dunlevy, M., Farrow, D. & 28 others, Hunter, D., Morgan, T., Shore, K., Guzman, V., Izsak, A., Dixon, D. E., Cridge, A., Cano, L., Cao, X., Jiang, H., Leng, N., Johnson, S., Cantarel, B. L., Richards, S., English, A., Shatters, R. G., Childers, C., Chen, M. J., Hunter, W., Cilia, M., Mueller, L. A., Munoz-Torres, M., Nelson, D., Poelchau, M. F., Benoit, J. B., Wiersma-Koch, H., D'Elia, T. & Brown, S. J., Jan 1 2019, In : Database : the journal of biological databases and curation. 2019

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

GEAMP, a novel gastroesophageal junction carcinoma cell line derived from a malignant pleural effusion

Zhang, W., Williams, T. A., Bhagwath, A. S., Hiermann, J. S., Peacock, C. D., Watkins, D. N., Ding, P., Park, J. Y., Montgomery, E. A., Forastiere, A. A., Jie, C., Cantarel, B. L., Pham, T. H. & Wang, D. H., Jan 1 2019, In : Laboratory Investigation.

Research output: Contribution to journalArticle

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L., Aug 1 2019, In : Nature biotechnology. 37, 8, p. 907-915 9 p.

Research output: Contribution to journalArticle

39 Scopus citations

Human pancreatic cancer cell exosomes, but not human normal cell exosomes, act as an initiator in cell transformation

Stefanius, K., Servage, K., de Souza Santos, M., Gray, H. F., Toombs, J. E., Chimalapati, S., Kim, M. S., Malladi, V. S., Brekken, R. & Orth, K., May 28 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Identification and characterization of an alternative cancer-derived PD-L1 splice variant

Hassounah, N. B., Malladi, V. S., Huang, Y., Freeman, S. S., Beauchamp, E. M., Koyama, S., Souders, N., Martin, S., Dranoff, G., Wong, K. K., Pedamallu, C. S., Hammerman, P. S. & Akbay, E. A., Mar 13 2019, In : Cancer Immunology, Immunotherapy. 68, 3, p. 407-420 14 p.

Research output: Contribution to journalArticle

3 Scopus citations

Immune receptor repertoires in pediatric and adult acute myeloid leukemia

Zhang, J., Hu, X., Wang, J., Sahu, A. D., Cohen, D., Song, L., Ouyang, Z., Fan, J., Wang, B., Fu, J., Gu, S., Sade-Feldman, M., Hacohen, N., Li, W., Ying, X., Li, B. & Liu, X. S., Nov 26 2019, In : Genome Medicine. 11, 1, 73.

Research output: Contribution to journalArticle

Open Access

Landscape of B cell immunity and related immune evasion in human cancers

Hu, X., Zhang, J., Wang, J., Fu, J., Li, T., Zheng, X., Wang, B., Gu, S., Jiang, P., Fan, J., Ying, X., Zhang, J., Carroll, M. C., Wucherpfennig, K. W., Hacohen, N., Zhang, F., Zhang, P., Liu, J. S., Li, B. & Liu, X. S., Mar 1 2019, In : Nature genetics. 51, 3, p. 560-567 8 p.

Research output: Contribution to journalArticle

11 Scopus citations

Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution

Chakraborty, T., Driscoll, M. K., Jeffery, E., Murphy, M. M., Roudot, P., Chang, B. J., Vora, S., Wong, W. M., Nielson, C. D., Zhang, H., Zhemkov, V., Hiremath, C., De La Cruz, E. D., Yi, Y., Bezprozvanny, I., Zhao, H., Tomer, R., Heintzmann, R., Meeks, J. P., Marciano, D. K. & 4 others, Morrison, S. J., Danuser, G., Dean, K. M. & Fiolka, R., Nov 1 2019, In : Nature methods. 16, 11, p. 1109-1113 5 p.

Research output: Contribution to journalArticle

3 Scopus citations

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes

Blakeley-Ruiz, J. A., Erickson, A. R., Cantarel, B., Xiong, W., Adams, R., Jansson, J. K., Fraser, C. M. & Hettich, R. L., Feb 11 2019, In : Microbiome. 7, 1, 18.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Nuclear positioning facilitates amoeboid migration along the path of least resistance

Renkawitz, J., Kopf, A., Stopp, J., de Vries, I., Driscoll, M. K., Merrin, J., Hauschild, R., Welf, E. S., Danuser, G., Fiolka, R. & Sixt, M., Apr 25 2019, In : Nature. 568, 7753, p. 546-550 5 p.

Research output: Contribution to journalArticle

19 Scopus citations

Open collaborative writing with manubot

Himmelstein, D. S., Rubinetti, V., Slochower, D. R., Hu, D., Malladi, V. S., Greene, C. S. & Gitter, A., Jun 2019, In : PLoS Computational Biology. 15, 6, e1007128.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers (Nature Genetics, (2019), 51, 3, (560-567), 10.1038/s41588-018-0339-x)

Hu, X., Zhang, J., Wang, J., Fu, J., Li, T., Zheng, X., Wang, B., Gu, S., Jiang, P., Fan, J., Ying, X., Zhang, J., Carroll, M. C., Wucherpfennig, K. W., Hacohen, N., Zhang, F., Zhang, P., Liu, J. S., Li, B. & Liu, X. S., Jun 1 2019, In : Nature genetics. 51, 6, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Robust and automated detection of subcellular morphological motifs in 3D microscopy images

Driscoll, M. K., Welf, E. S., Jamieson, A. R., Dean, K. M., Isogai, T., Fiolka, R. & Danuser, G., Oct 1 2019, In : Nature methods. 16, 10, p. 1037-1044 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Spatiotemporal dynamics of GEF-H1 activation controlled by microtubule- and Src-mediated pathways

Azoitei, M. L., Noh, J., Marston, D. J., Roudot, P., Marshall, C. B., Daugird, T. A., Lisanza, S. L., Sandí, M. J., Ikura, M., Sondek, J., Rottapel, R., Hahn, K. M. & Danuser, G., Sep 2 2019, In : The Journal of cell biology. 218, 9, p. 3077-3097 21 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Suppression of Myeloid Cell Arginase Activity leads to Therapeutic Response in a NSCLC Mouse Model by Activating Anti-Tumor Immunity

Miret, J. J., Kirschmeier, P., Koyama, S., Zhu, M., Li, Y. Y., Naito, Y., Wu, M., Malladi, V. S., Huang, W., Walker, W., Palakurthi, S., Dranoff, G., Hammerman, P. S., Pecot, C. V., Wong, K. K. & Akbay, E. A., Feb 6 2019, In : Journal for ImmunoTherapy of Cancer. 7, 1, 504.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding

Li, S., Chen, K., Zhang, Y., Barnes, S. D., Jaichander, P., Zheng, Y., Hassan, M., Malladi, V. S., Skapek, S. X., Xu, L., Bassel-Duby, R., Olson, E. N. & Liu, N., Jun 1 2019, In : Genes & development. 33, 11-12, p. 626-640 15 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Universal light-sheet generation with field synthesis

Chang, B. J., Kittisopikul, M., Dean, K. M., Roudot, P., Welf, E. S. & Fiolka, R., Mar 1 2019, In : Nature methods. 16, 3, p. 235-238 4 p.

Research output: Contribution to journalArticle

7 Scopus citations

Using Mothur to Determine Bacterial Community Composition and Structure in 16S Ribosomal RNA Datasets

Chappidi, S., Villa, E. C. & Cantarel, B. L., Jan 1 2019, In : Current Protocols in Bioinformatics. 67, 1, e83.

Research output: Contribution to journalArticle

Open Access
2018

Analysis of PD1, PDL1, PDL2 expression and T cells infiltration in 1014 gastric cancer patients

Xing, X., Guo, J., Wen, X., Ding, G., Li, B., Dong, B., Feng, Q., Li, S., Zhang, J., Cheng, X., Guo, T., Du, H., Hu, Y., Wang, X., Li, L., Li, Q., Xie, M., Li, L., Gao, X., Shan, F. & 5 others, Li, Z., Ying, X., Zhou, T., Wang, J. & Ji, J., Mar 4 2018, In : OncoImmunology. 7, 3, e1356144.

Research output: Contribution to journalArticle

26 Scopus citations

A noncanonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells

Srinivasan, S., Burckhardt, C. J., Bhave, M., Chen, Z., Chen, P. H., Wang, X., Danuser, G. & Schmid, S. L., Apr 18 2018, In : PLoS Biology. 16, 4, e2005377.

Research output: Contribution to journalArticle

4 Scopus citations

A sparse-to-dense method for 3D optical flow estimation in 3D light-microscopy image sequences

Manandhar, S., Bouthemy, P., Welf, E., Roudot, P. & Kervrann, C., May 23 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. IEEE Computer Society, p. 952-956 5 p. (Proceedings - International Symposium on Biomedical Imaging; vol. 2018-April).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Evaluation of immune repertoire inference methods from RNA-seq data

Hu, X., Zhang, J., Liu, J. S., Li, B. & Liu, X. S., Nov 9 2018, In : Nature Biotechnology. 36, 11, 1 p.

Research output: Contribution to journalArticle

2 Scopus citations

Imaging, tracking and computational analyses of virus entry and egress with the cytoskeleton

Wang, I. H., Burckhardt, C. J., Yakimovich, A. & Greber, U. F., Apr 2018, In : Viruses. 10, 4, 166.

Research output: Contribution to journalReview article

Open Access
21 Scopus citations

Inhibition of epithelial cell migration and Src/FAK signaling by SIRT3

Lee, J. J., van de Ven, R. A. H., Zaganjor, E., Ng, M. R., Barakat, A., Demmers, J. J. P. G., Finley, L. W. S., Gonzalez Herrera, K. N., Hung, Y. P., Harris, I. S., Jeong, S. M., Danuser, G., McAllister, S. S. & Haigis, M. C., Jul 3 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 27, p. 7057-7062 6 p.

Research output: Contribution to journalArticle

8 Scopus citations

Profiling cellular morphodynamics by spatiotemporal spectrum decomposition

Ma, X., Dagliyan, O., Hahn, K. M. & Danuser, G., Aug 1 2018, In : PLoS Computational Biology. 14, 8, e1006321.

Research output: Contribution to journalArticle

4 Scopus citations

Regulation of Clathrin-Mediated Endocytosis

Mettlen, M., Chen, P. H., Srinivasan, S., Danuser, G. & Schmid, S. L., Jun 20 2018, In : Annual Review of Biochemistry. 87, p. 871-896 26 p.

Research output: Contribution to journalReview article

42 Scopus citations

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

Jiang, P., Gu, S., Pan, D., Fu, J., Sahu, A., Hu, X., Li, Z., Traugh, N., Bu, X., Li, B., Liu, J., Freeman, G. J., Brown, M. A., Wucherpfennig, K. W. & Liu, X. S., Oct 1 2018, In : Nature Medicine. 24, 10, p. 1550-1558 9 p.

Research output: Contribution to journalArticle

95 Scopus citations

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration

Wang, Z., Cao, S., Morris, J. S., Ahn, J., Liu, R., Tyekucheva, S., Gao, F., Li, B., Lu, W., Tang, X., Wistuba, I. I., Bowden, M., Mucci, L., Loda, M., Parmigiani, G., Holmes, C. C. & Wang, W., Nov 30 2018, In : iScience. 9, p. 451-460 10 p.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Cornwell, M. I., Vangala, M., Taing, L., Herbert, Z., Köster, J., Li, B., Sun, H., Li, T., Zhang, J., Qiu, X., Pun, M., Jeselsohn, R., Brown, M., Liu, X. S. & Long, H. W., Apr 12 2018, In : BMC Bioinformatics. 19, 1, 135.

Research output: Contribution to journalArticle

20 Scopus citations
2017

Adaptive robust regression with continuous Gaussian scale mixture errors

Seo, B., Noh, J., Lee, T. & Yoon, Y. J., Mar 1 2017, In : Journal of the Korean Statistical Society. 46, 1, p. 113-125 13 p.

Research output: Contribution to journalArticle

4 Scopus citations

A method for measuring the distribution of the shortest telomeres in cells and tissues

Lai, T. P., Zhang, N., Noh, J., Mender, I., Tedone, E., Huang, E., Wright, W. E., Danuser, G. & Shay, J. W., Dec 1 2017, In : Nature Communications. 8, 1, 1356.

Research output: Contribution to journalArticle

25 Scopus citations

A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis

Cepika, A. M., Banchereau, R., Segura, E., Ohouo, M., Cantarel, B., Goller, K., Cantrell, V., Ruchaud, E., Gatewood, E., Nguyen, P., Gu, J., Anguiano, E., Zurawski, S., Baisch, J. M., Punaro, M., Baldwin, N., Obermoser, G., Palucka, K., Banchereau, J., Amigorena, S. & 1 others, Pascual, V., Nov 1 2017, In : Journal of Experimental Medicine. 214, 11, p. 3449-3466 18 p.

Research output: Contribution to journalArticle

11 Scopus citations

Cell forces meet cell metabolism

Isogai, T., Park, J. S. & Danuser, G., May 31 2017, In : Nature Cell Biology. 19, 6, p. 591-593 3 p.

Research output: Contribution to journalReview article

3 Scopus citations

Cistrome cancer: A web resource for integrative gene regulation modeling in cancer

Mei, S., Meyer, C. A., Zheng, R., Qin, Q., Wu, Q., Jiang, P., Li, B., Shi, X., Wang, B., Fan, J., Shih, C., Brown, M., Zang, C. & Liu, X. S., Nov 1 2017, In : Cancer research. 77, 21, p. e19-e22

Research output: Contribution to journalArticle

17 Scopus citations

Clonality analysis of synchronous gastro-oesophageal junction carcinoma and distal gastric cancer by whole-exome sequencing

Xing, X., Jia, S., Wu, J., Feng, Q., Dong, B., Li, B., Jia, Y., Shan, F., Li, Y., Zhang, Y., Hu, Y., Wang, X., Liu, X., Yu, W., Zhang, L., Bu, Z., Wu, A., Li, Z. & Ji, J., Oct 2017, In : Journal of Pathology. 243, 2, p. 165-175 11 p.

Research output: Contribution to journalArticle

7 Scopus citations

Combination therapy targeting BCL6 and phospho-STAT3 defeats intratumor heterogeneity in a subset of non-small cell lung cancers

Deb, D., Rajaram, S., Larsen, J. E., Dospoy, P. D., Marullo, R., Li, L. S., Avila, K., Xue, F., Cerchietti, L., Minna, J. D., Altschuler, S. J. & Wu, L. F., Jun 1 2017, In : Cancer Research. 77, 11, p. 3070-3081 12 p.

Research output: Contribution to journalArticle

11 Scopus citations