Research Output

2020

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX

Shieh, K. R., Kratschmer, C., Maier, K. E., Greally, J. M., Levy, M. & Golden, A., May 1 2020, In : Bioinformatics (Oxford, England). 36, 9, p. 2905-2906 2 p.

Research output: Contribution to journalArticle

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

International 22q11.2 Brain and Behavior Consortium, Jan 2 2020, In : American Journal of Human Genetics. 106, 1, p. 26-40 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

FRS2α-dependent cell fate transition during endocardial cushion morphogenesis

Chen, D., Zhu, X., Kofler, N., Wang, Y., Zhou, B. & Simons, M., Feb 1 2020, In : Developmental Biology. 458, 1, p. 88-97 10 p.

Research output: Contribution to journalArticle

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

International 22q11.2DS Brain and Behavior Consortium, Jan 1 2020, (Accepted/In press) In : Molecular Psychiatry.

Research output: Contribution to journalArticle

2 Scopus citations

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV-negative cervical cancer

Van Arsdale, A., Patterson, N. E., Maggi, E. C., Agoni, L., Van Doorslaer, K., Harmon, B., Nevadunsky, N., Kuo, D. Y. S., Einstein, M. H., Lenz, J. & Montagna, C., Feb 1 2020, In : Genes Chromosomes and Cancer. 59, 2, p. 84-95 12 p.

Research output: Contribution to journalArticle

Roles of C/EBP class bZip proteins in the growth and cell competition of Rp (‘minute’) mutants in drosophila

Blanco, J., Cooper, J. C. & Baker, N. E., Jan 2020, In : eLife. 9, e50535.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access
2019

A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses

Andriani, G. A., Maggi, E., Piqué, D., Zimmerman, S. E., Lee, M., Quispe-Tintaya, W., Maslov, A., Campisi, J., Vijg, J., Mar, J. C. & Montagna, C., Dec 1 2019, In : Scientific reports. 9, 1, 10508.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Age is in the nucleus

Schumacher, B. & Vijg, J., Oct 1 2019, In : Nature Metabolism. 1, 10, p. 931-932 2 p.

Research output: Contribution to journalComment/debate

Aneuvis: Web-based exploration of numerical chromosomal variation in single cells

Piqué, D. G., Andriani, G. A., Maggi, E., Zimmerman, S. E., Greally, J. M., Montagna, C. & Mar, J. C., Jun 17 2019, In : BMC bioinformatics. 20, 1, 336.

Research output: Contribution to journalArticle

Open Access

A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma

Piqué, D. G., Montagna, C., Greally, J. M. & Mar, J. C., Apr 2 2019, In : British Journal of Cancer. 120, 7, p. 746-753 8 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila

Baker, N. E., Kiparaki, M. & Khan, C., Feb 1 2019, In : Developmental Biology. 446, 1, p. 17-19 3 p.

Research output: Contribution to journalComment/debate

2 Scopus citations

Ascorbic acid–induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma

Shenoy, N., Bhagat, T. D., Cheville, J., Lohse, C., Bhattacharyya, S., Tischer, A., Machha, V., Gordon-Mitchell, S., Choudhary, G., Wong, L. F., Gross, L. A., Ressigue, E., Leibovich, B., Boorjian, S. A., Steidl, U., Wu, X., Pradhan, K., Gartrell, B., Agarwal, B., Pagliaro, L. & 8 others, Suzuki, M., Greally, J. M., Rakheja, D., Houston Thompson, R., Susztak, K., Witzig, T., Zou, Y. & Verma, A., Apr 1 2019, In : Journal of Clinical Investigation. 129, 4, p. 1612-1625 14 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins

Vervoort, L., Demaerel, W., Rengifo, L. Y., Odrzywolski, A., Vergaelen, E., Hestand, M. S., Breckpot, J., Devriendt, K., Swillen, A., Mcdonald-Mcginn, D. M., Fiksinski, A. M., Zinkstok, J. R., Morrow, B. E., Heung, T., Vorstman, J. A. S., Bassett, A. S., Chow, E. W. C., Shashi, V. & Vermeesch, J. R., Nov 15 2019, In : Human molecular genetics. 28, 22, p. 3724-3733 10 p.

Research output: Contribution to journalArticle

Axon-Dependent Patterning and Maintenance of Somatosensory Dendritic Arbors

Ramirez-Suarez, N. J., Belalcazar, H. M., Salazar, C. J., Beyaz, B., Raja, B., Nguyen, K. C. Q., Celestrin, K., Fredens, J., Færgeman, N. J., Hall, D. H. & Bülow, H. E., Jan 28 2019, In : Developmental cell. 48, 2, p. 229-244.e4

Research output: Contribution to journalArticle

4 Scopus citations

CCL2 mobilizes ALIX to facilitate Gag-p6 mediated HIV-1 virion release

Ajasin, D. O., Rao, V. R., Wu, X., Ramasamy, S., Pujato, M., Ruiz, A. P., Fiser, A., Bresnick, A. R., Kalpana, G. V. & Prasad, V. R., Jun 2019, In : eLife. 8, e35546.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

Jaric, I., Rocks, D., Greally, J. M., Suzuki, M. & Kundakovic, M., Dec 1 2019, In : Nature communications. 10, 1, 2851.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Copy number variations in individuals with conotruncal heart defects reveal some shared developmental pathways irrespective of 22q11.2 deletion status

Xie, H. M., Taylor, D. M., Zhang, Z., McDonald-McGinn, D. M., Zackai, E. H., Stambolian, D., Hakonarson, H., Morrow, B. E., Emanuel, B. S. & Goldmuntz, E., Jan 1 2019, In : Birth Defects Research. 111, 13, p. 888-905 18 p.

Research output: Contribution to journalArticle

Open Access

Cytogenetic, genomic, and functional characterization of pituitary gonadotrope cell lines

Ruf-Zamojski, F., Ge, Y., Pincas, H., Shan, J., Song, Y., Hines, N., Kelley, K., Montagna, C., Nair, P., Toufaily, C., Bernard, D. J., Mellon, P. L., Nair, V., Turgeon, J. L. & Sealfon, S. C., May 1 2019, In : Journal of the Endocrine Society. 3, 5, p. 902-920 19 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance

Chen, K., Luan, X., Liu, Q., Wang, J., Chang, X., Snijders, A. M., Mao, J. H., Secombe, J., Dan, Z., Chen, J. H., Wang, Z., Dong, X., Qiu, C., Chang, X., Zhang, D., Celniker, S. E. & Liu, X., Apr 10 2019, In : Cell Host and Microbe. 25, 4, p. 537-552.e8

Research output: Contribution to journalArticle

10 Scopus citations

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1

Ji, Z., Kiparaki, M., Folgado, V., Kumar, A., Blanco, J., Rimesso, G., Chuen, J., Liu, Y., Zheng, D. & Baker, N. E., Jan 1 2019, In : PLoS genetics. 15, 12, e1008513.

Research output: Contribution to journalArticle

Open Access

Effect of diet in females (F1) from prenatally undernourished mothers on metabolism and liver function in the F2 progeny is sex-specific

Cissé, O., Fajardy, I., Delahaye, F., Dickes, A., Montel, V., Moitrot, E., Breton, C., Vieau, D. & Laborie, C., Sep 1 2019, In : European Journal of Nutrition. 58, 6, p. 2411-2423 13 p.

Research output: Contribution to journalArticle

Endocardially Derived Macrophages Are Essential for Valvular Remodeling

Shigeta, A., Huang, V., Zuo, J., Besada, R., Nakashima, Y., Lu, Y., Ding, Y., Pellegrini, M., Kulkarni, R. P., Hsiai, T., Deb, A., Zhou, B., Nakano, H. & Nakano, A., Mar 11 2019, In : Developmental cell. 48, 5, p. 617-630.e3

Research output: Contribution to journalArticle

5 Scopus citations

Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells

Nakahara, F., Borger, D. K., Wei, Q., Pinho, S., Maryanovich, M., Zahalka, A. H., Suzuki, M., Cruz, C. D., Wang, Z., Xu, C., Boulais, P. E., Ma’ayan, A., Greally, J. M. & Frenette, P. S., May 1 2019, In : Nature Cell Biology. 21, 5, p. 560-567 8 p.

Research output: Contribution to journalLetter

9 Scopus citations

Expressional artifact caused by a co-injection marker rol-6 in C. Elegans

Jin, H. Y., Emmons, S. W. & Kim, B., Jan 1 2019, In : PloS one. 14, 12, e0224533.

Research output: Contribution to journalArticle

Open Access

Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding

Johnston, A. D., Simões-Pires, C. A., Thompson, T. V., Suzuki, M. & Greally, J. M., Dec 1 2019, In : Nature communications. 10, 1, 3472.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Gata4 regulates hedgehog signaling and Gata6 expression for outflow tract development

Liu, J., Cheng, H., Xiang, M., Zhou, L., Wu, B., Moskowitz, I. P., Zhang, K. & Xie, L., May 1 2019, In : PLoS genetics. 15, 5, e1007711.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects

on behalf of the Pediatric Cardiac Genomics Consortium¶, Jan 1 2019, In : PloS one. 14, 7, e0219926.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Genetic variants associated with FDNY WTC-related sarcoidosis

Cleven, K. L., Ye, K., Zeig-Owens, R., Hena, K. M., Montagna, C., Shan, J., Hosgood, H. D., Jaber, N., Weiden, M. D., Colbeth, H. L., Goldfarb, D. G., Spivack, S. D. & Prezant, D. J., May 2 2019, In : International journal of environmental research and public health. 16, 10, 1830.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
Open Access

Inhibition of acetylation of histones 3 and 4 attenuates aortic valve calcification

Gu, J., Lu, Y., Deng, M., Qiu, M., Tian, Y., Ji, Y., Zong, P., Shao, Y., Zheng, R., Zhou, B., Sun, W. & Kong, X., Jul 1 2019, In : Experimental and Molecular Medicine. 51, 7, 79.

Research output: Contribution to journalArticle

Open Access

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data

Kong, Y., Rastogi, D., Seoighe, C., Greally, J. M. & Suzuki, M., Apr 1 2019, In : PLoS ONE. 14, 4, e0215987.

Research output: Contribution to journalArticle

Open Access

Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts

Bhagat, T. D., Von Ahgrens, D., Dawlaty, M., Zou, Y., Baddour, J., Achreja, A., Zhao, H., Yang, L., Patel, B., Kwak, C., Choudhary, G. S., Gordon-Mitchell, S., Alluri, S., Bhattacharyya, S., Sahu, S., Yu, Y., Bartenstein, M., Giricz, O., Suzuki, M., Sohal, D. & 12 others, Gupta, S., Guerrero, P., Batra, S., Goggins, M., Steidl, U., Greally, J., Agarwal, B., Pradhan, K., Banerjee, D., Nagrath, D., Maitra, A. & Verma, A., Oct 2019, In : eLife. 8, e50663.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

MicroRNAs in Skeletal Muscle Aging: Current Issues and Perspectives

Jung, H. J., Lee, K. P., Kwon, K. S. & Suh, Y., Jun 18 2019, In : Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 74, 7, p. 1008-1014 7 p.

Research output: Contribution to journalReview article

Open Access
8 Scopus citations

Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions

Bowler, T. G., Pradhan, K., Kong, Y., Bartenstein, M., Morrone, K. A., Shridharan, A., Kessel, R. M., Shastri, A., Giricz, O., Bhagat, T. D., Gordon-Mitchell, S., Rohanizadegan, M., Hooda, L., Datt, I., Przychodzen, B. P., Parmar, S., Maqbool, S., Maciejewski, J. P., Steidl, U., Greally, J. M. & 1 others, Verma, A., Jan 1 2019, In : Leukemia and Lymphoma.

Research output: Contribution to journalArticle

mTOR inhibitors may benefit kidney transplant recipients with mitochondrial diseases

Johnson, S. C., Martinez, F., Bitto, A., Gonzalez, B., Tazaerslan, C., Cohen, C., Delaval, L., Timsit, J., Knebelmann, B., Terzi, F., Mahal, T., Zhu, Y., Morgan, P. G., Sedensky, M. M., Kaeberlein, M., Legendre, C., Suh, Y. & Canaud, G., Feb 2019, In : Kidney international. 95, 2, p. 455-466 12 p.

Research output: Contribution to journalArticle

6 Scopus citations

Myelodysplastic syndrome progression to acute myeloid leukemia at the stem cell level

Chen, J., Kao, Y. R., Sun, D., Todorova, T. I., Reynolds, D., Narayanagari, S. R., Montagna, C., Will, B., Verma, A. & Steidl, U., Jan 1 2019, In : Nature Medicine. 25, 1, p. 103-110 8 p.

Research output: Contribution to journalLetter

24 Scopus citations

New Insights into Bioactive Compounds of Traditional Chinese Medicines for Insulin Resistance Based on Signaling Pathways

He, J., Wang, H. & Vijg, J., Sep 1 2019, In : Chemistry and Biodiversity. 16, 9, e1900176.

Research output: Contribution to journalReview article

1 Scopus citations

Non-catalytic Roles of Tet2 Are Essential to Regulate Hematopoietic Stem and Progenitor Cell Homeostasis

Ito, K., Lee, J., Chrysanthou, S., Zhao, Y., Josephs, K., Sato, H., Teruya-Feldstein, J., Zheng, D., Dawlaty, M. M. & Ito, K., Sep 3 2019, In : Cell Reports. 28, 10, p. 2480-2490.e4

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

Sato, H., Wu, B., Delahaye, F., Singer, R. H. & Greally, J. M., Jun 3 2019, In : Journal of Cell Biology. 218, 6, p. 1810-1823 14 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Rinf Regulates Pluripotency Network Genes and Tet Enzymes in Embryonic Stem Cells

Ravichandran, M., Lei, R., Tang, Q., Zhao, Y., Lee, J., Ma, L., Chrysanthou, S., Lorton, B. M., Cvekl, A., Shechter, D., Zheng, D. & Dawlaty, M. M., Aug 20 2019, In : Cell Reports. 28, 8, p. 1993-2003.e5

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access

Septin 9 isoforms promote tumorigenesis in mammary epithelial cells by increasing migration and ECM degradation through metalloproteinase secretion at focal adhesions

Marcus, J., Bejerano-Sagie, M., Patterson, N., Bagchi, S., Verkhusha, V. V., Connolly, D., Goldberg, G. L., Golden, A., Sharma, V. P., Condeelis, J. & Montagna, C., Jul 25 2019, In : Oncogene. 38, 30, p. 5839-5859 21 p.

Research output: Contribution to journalArticle

1 Scopus citations

Signal transduction, ageing and disease

Zhang, L., Yousefzadeh, M. J., Suh, Y., Niedernhofer, L. J. & Robbins, P. D., Jan 1 2019, Subcellular Biochemistry. Springer New York, p. 227-247 21 p. (Subcellular Biochemistry; vol. 91).

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Scopus citations
Open Access
20 Scopus citations

SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species

Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., Goldfarb, A., Tam, J., Zheng, K., Cornwell, A., Johnson, A., Yang, J. N., Mao, Z., Manta, B., Dang, W., Zhang, Z. & 8 others, Vijg, J., Wolfe, A., Moody, K., Kennedy, B. K., Bohmann, D., Gladyshev, V. N., Seluanov, A. & Gorbunova, V., Apr 18 2019, In : Cell. 177, 3, p. 622-638.e22

Research output: Contribution to journalArticle

19 Scopus citations

Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis

Liu, Y., Lu, P., Wang, Y., Morrow, B. E., Zhou, B. & Zheng, D., Aug 6 2019, In : Journal of the American Heart Association. 8, 15, e012941.

Research output: Contribution to journalArticle

Open Access