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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

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

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

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

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

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

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 : The 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
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

Superoxide anions mediate the effects of angiotensin (1-7) analog, alamandine, on blood pressure and sympathetic activity in the paraventricular nucleus

Gong, J., Shen, Y., Li, P., Zhao, K., Chen, X., Li, Y., Sheng, Y., Zhou, B. & Kong, X., Aug 2019, In : Peptides. 118, 170101.

Research output: Contribution to journalArticle

2 Scopus citations

Targeted sequencing to discover germline variants in the BRCA1 and BRCA2 genes in a Russian population and their association with breast cancer risk

Solodskikh, S. A., Panevina, A. V., Gryaznova, M. V., Gureev, A. P., Serzhantova, O. V., Mikhailov, A. A., Maslov, A. Y. & Popov, V. N., Jan 2019, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 813, p. 51-57 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

The 22q11 low copy repeats are characterized by unprecedented size and structural variability

Demaerel, W., Mostovoy, Y., Yilmaz, F., Vervoort, L., Pastor, S., Hestand, M. S., Swillen, A., Vergaelen, E., Geiger, E. A., Coughlin, C. R., Chow, S. K., McDonald-McGinn, D., Morrow, B., Kwok, P. Y., Xiao, M., Emanuel, B. S., Shaikh, T. H. & Vermeesch, J. R., Jan 1 2019, In : Genome research. 29, 9, p. 1389-1401 13 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The histone demethylase KDM5 controls developmental timing in Drosophila by promoting prothoracic gland endocycles

Drelon, C., Rogers, M. F., Belalcazar, H. M. & Secombe, J., Jan 1 2019, In : Development (Cambridge). 146, 24, dev182568.

Research output: Contribution to journalArticle

Open Access

The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis

Li, W., Zimmerman, S. E., Peregrina, K., Houston, M., Mayoral, J., Zhang, J., Maqbool, S., Zhang, Z., Cai, Y., Ye, K. & Augenlicht, L. H., Aug 22 2019, In : Carcinogenesis. 40, 8, p. 937-946 10 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

TIAM-1/GEF can shape somatosensory dendrites independently of its GEF activity by regulating F-actin localization

Tang, L. T., Diaz-Balzac, C. A., Rahman, M., Ramirez-Suarez, N. J., Salzberg, Y., Lázaro-Peña, M. I. & Bülow, H. E., Jan 29 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
6 Scopus citations
1 Scopus citations

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

Kong, Y., Rose, C. M., Cass, A. A., Williams, A. G., Darwish, M., Lianoglou, S., Haverty, P. M., Tong, A. J., Blanchette, C., Albert, M. L., Mellman, I., Bourgon, R., Greally, J., Jhunjhunwala, S. & Chen-Harris, H., Dec 1 2019, In : Nature communications. 10, 1, 5228.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Whole-animal connectomes of both Caenorhabditis elegans sexes

Cook, S. J., Jarrell, T. A., Brittin, C. A., Wang, Y., Bloniarz, A. E., Yakovlev, M. A., Nguyen, K. C. Q., Tang, L. T. H., Bayer, E. A., Duerr, J. S., Bülow, H. E., Hobert, O., Hall, D. H. & Emmons, S. W., Jul 4 2019, In : Nature. 571, 7763, p. 63-71 9 p.

Research output: Contribution to journalArticle

28 Scopus citations