Division of Bioinformatics and Computational Biology

Research Output

2019

Acute myeloid leukemia–induced T-cell suppression can be reversed by inhibition of the MAPK pathway

Moshofsky, K. B., Cho, H. J., Wu, G., Romine, K. A., Newman, M. T., Kosaka, Y., McWeeney, S. K. & Lind, E. F., Oct 22 2019, In : Blood Advances. 3, 20, p. 3038-3051 14 p.

Research output: Contribution to journalArticle

Open Access

Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms

Zhang, H., Savage, S., Schultz, A. R., Bottomly, D., White, L., Segerdell, E., Wilmot, B., McWeeney, S., Eide, C. A., Nechiporuk, T., Carlos, A., Henson, R., Lin, C., Searles, R., Ho, H., Lam, Y. L., Sweat, R., Follit, C., Jain, V., Lind, E. & 10 others, Borthakur, G., Garcia-Manero, G., Ravandi, F., Kantarjian, H. M., Cortes, J., Collins, R., Buelow, D. R., Baker, S. D., Druker, B. & Tyner, J., Dec 1 2019, In : Nature Communications. 10, 1, 244.

Research output: Contribution to journalArticle

15 Scopus citations

Controlling for contaminants in low-biomass 16S rRNA gene sequencing experiments

Karstens, L., Asquith, M., Davin, S., Fair, D., Gregory, W. T., Wolfe, A. J., Braun, J. & McWeeney, S., Jul 2019, In : mSystems. 4, 4, e00290-19.

Research output: Contribution to journalArticle

Open Access
12 Scopus citations

CSF1R inhibitors exhibit antitumor activity in acute myeloid leukemia by blocking paracrine signals from support cells

Edwards, D. K., Watanabe-Smith, K., Rofelty, A., Damnernsawad, A., Laderas, T., Lamble, A., Lind, E. F., Kaempf, A., Mori, M., Rosenberg, M., d’Almeida, A., Long, N., Agarwal, A., Sweeney, D. T., Loriaux, M., McWeeney, S. K. & Tyner, J. W., Feb 7 2019, In : Blood. 133, 6, p. 588-599 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

Illuminating biological pathways for drug targeting in head and neck squamous cell carcinoma

Choonoo, G., Blucher, A. S., Higgins, S., Boardman, M., Jeng, S., Zheng, C., Jacobs, J., Anderson, A., Chamberlin, S., Evans, N., Vigoda, M., Cordier, B., Tyner, J. W., Kulesz-Martin, M., McWeeney, S. K. & Laderas, T., Jan 1 2019, In : PloS one. 14, 10, e0223639.

Research output: Contribution to journalArticle

Open Access

Natural product target network reveals potential for cancer combination therapies

Chamberlin, S. R., Blucher, A., Wu, G., Shinto, L., Choonoo, G., Kulesz-Martin, M. & McWeeney, S., Jan 1 2019, In : Frontiers in Pharmacology. 10, MAY, 557.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Persistent Toll-like receptor 7 stimulation induces behavioral and molecular innate immune tolerance

Michaelis, K. A., Norgard, M. A., Levasseur, P. R., Olson, B., Burfeind, K. G., Buenafe, A. C., Zhu, X., Jeng, S., McWeeney, S. & Marks, D., Jan 1 2019, (Accepted/In press) In : Brain, Behavior, and Immunity.

Research output: Contribution to journalArticle

Open Access

Predicting response to BET inhibitors using computational modeling: A BEAT AML project study

Drusbosky, L. M., Vidva, R., Gera, S., Lakshminarayana, A. V., Shyamasundar, V. P., Agrawal, A. K., Talawdekar, A., Abbasi, T., Vali, S., Tognon, C. E., Kurtz, S. E., Tyner, J., McWeeney, S., Druker, B. & Cogle, C. R., Feb 1 2019, In : Leukemia Research. 77, p. 42-50 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Salt-sensitive transcriptome of isolated kidney distal tubule cells

Swanson, E. A., Nelson, J. W., Jeng, S., Erspamer, K. J., Yang, C. L., McWeeney, S. & Ellison, D. H., Apr 2019, In : Physiological genomics. 51, 4, p. 125-135 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

The TP53 apoptotic network is a primary mediator of resistance to BCL2 inhibition in AML cells

Nechiporuk, T., Kurtz, S. E., Nikolova, O., Liu, T., Jones, C. L., D’alessandro, A., Culp-Hill, R., D’almeida, A., Joshi, S. K., Rosenberg, M., Tognon, C. E., Danilov, A. V., Druker, B. J., Chang, B. H., McWeeney, S. K. & Tyner, J. W., Jul 2019, In : Cancer discovery. 9, 7, p. 910-925 16 p.

Research output: Contribution to journalArticle

14 Scopus citations

Visualization of drug target interactions in the contexts of pathways and networks with reactomefiviz

Blucher, A. S., McWeeney, S., Stein, L. & Wu, G., Jan 1 2019, In : F1000Research. 8, 908.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

What do functional genomics tell us about pathogenesis of AML?

Tyner, J. W., Bottomly, D., Wilmot, B. & McWeeney, S., Dec 2019, In : Best Practice and Research: Clinical Haematology. 32, 4, 101101.

Research output: Contribution to journalReview article

2018

A single-cell approach to the elusive latent human cytomegalovirus transcriptome

Goodrum, F. & McWeeney, S., May 1 2018, In : mBio. 9, 3, e01001-18.

Research output: Contribution to journalArticle

2 Scopus citations
13 Scopus citations

Cross-species molecular dissection across alcohol behavioral domains

Farris, S. P., Riley, B. P., Williams, R. W., Mulligan, M. K., Miles, M. F., Lopez, M. F., Hitzemann, R., Iancu, O., Colville, A., Walter, N. A. R., Darakjian, P., Oberbeck, D. L., Daunais, J. B., Zheng, C., Searles, R., McWeeney, S., Grant, K. K. & Mayfield, R. D., Nov 1 2018, In : Alcohol. 72, p. 19-31 13 p.

Research output: Contribution to journalReview article

3 Scopus citations

Functional genomic landscape of acute myeloid leukaemia

Tyner, J. W., Tognon, C. E., Bottomly, D., Wilmot, B., Kurtz, S. E., Savage, S. L., Long, N., Schultz, A. R., Traer, E., Abel, M., Agarwal, A., Blucher, A., Borate, U., Bryant, J., Burke, R., Carlos, A., Carpenter, R., Carroll, J., Chang, B. H., Coblentz, C. & 68 others, d’Almeida, A., Cook, R., Danilov, A., Dao, K. H. T., Degnin, M., Devine, D., Dibb, J., Edwards, D. K., Eide, C. A., English, I., Glover, J., Henson, R., Ho, H., Jemal, A., Johnson, K., Johnson, R., Junio, B., Kaempf, A., Leonard, J., Lin, C., Liu, S. Q., Lo, P., Loriaux, M. M., Luty, S., Macey, T., MacManiman, J., Martinez, J., Mori, M., Nelson, D., Nichols, C., Peters, J., Ramsdill, J., Rofelty, A., Schuff, R., Searles, R., Segerdell, E., Smith, R. L., Spurgeon, S. E., Sweeney, T., Thapa, A., Visser, C., Wagner, J., Watanabe-Smith, K., Werth, K., Wolf, J., White, L., Yates, A., Zhang, H., Cogle, C. R., Collins, R. H., Connolly, D. C., Deininger, M. W., Drusbosky, L., Hourigan, C. S., Jordan, C. T., Kropf, P., Lin, T. L., Martinez, M. E., Medeiros, B. C., Pallapati, R. R., Pollyea, D. A., Swords, R. T., Watts, J. M., Weir, S. J., Wiest, D. L., Winters, R. M., McWeeney, S. K. & Druker, B. J., Oct 25 2018, In : Nature. 562, 7728, p. 526-531 6 p.

Research output: Contribution to journalArticle

90 Scopus citations

Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs

Iancu, O., Colville, A. M., Wilmot, B., Searles, R., Darakjian, P., Zheng, C., McWeeney, S., Kawane, S., Crabbe, J. J., Metten, P., Oberbeck, D. & Hitzemann, R., Aug 1 2018, In : Alcoholism: Clinical and Experimental Research. 42, 8, p. 1454-1465 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Induction of anaplastic lymphoma kinase (ALK) as a novel mechanism of EGFR inhibitor resistance in head and neck squamous cell carcinoma patient-derived models

Ouyang, X., Barling, A., Lesch, A., Tyner, J., Choonoo, G., Zheng, C., Jeng, S., West, T. M., Clayburgh, D., Courtneidge, S., McWeeney, S. & Kulesz-Martin, M., Oct 3 2018, In : Cancer Biology and Therapy. 19, 10, p. 921-933 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

LSD1 activates a lethal prostate cancer gene network independently of its demethylase function

Sehrawat, A., Gao, L., Wang, Y., Bankhead, A., McWeeney, S., King, C. J., Schwartzman, J., Urrutia, J., Bisson, W. H., Coleman, D. J., Joshi, S. K., Kim, D. H., Sampson, D. A., Weinmann, S., Kallakury, B. V. S., Berry, D. L., Haque, R., Van Den Eeden, S. K., Sharma, S., Bearss, J. & 4 others, Beer, T. T., Thomas, G., Heiser, L. & Alumkal, J., May 1 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 18, p. E4179-E4188

Research output: Contribution to journalArticle

34 Scopus citations

Network-based predictors of progression in head and neck squamous cell carcinoma

Sanati, N., Iancu, O., Wu, G., Jacobs, J. E. & McWeeney, S., May 29 2018, In : Frontiers in Genetics. 9, MAY, 183.

Research output: Contribution to journalArticle

2 Scopus citations

Regional differences and similarities in the brain transcriptome for mice selected for ethanol preference from HS-CC founders

Colville, A. M., Iancu, O., Lockwood, D. R., Darakjian, P., McWeeney, S., Searles, R., Zheng, C. & Hitzemann, R., Aug 28 2018, In : Frontiers in Genetics. 9, AUG, 300.

Research output: Contribution to journalArticle

4 Scopus citations

Synthetic lethality of TNK2 inhibition in PTPN11-mutant leukemia

Jenkins, C., Luty, S. B., Maxson, J., Eide, C. A., Abel, M. L., Togiai, C., Nemecek, E., Bottomly, D., McWeeney, S., Wilmot, B., Loriaux, M., Chang, B. & Tyner, J., Jul 17 2018, In : Science Signaling. 11, 539, eaao5617.

Research output: Contribution to journalArticle

1 Scopus citations

Targeting of colony-stimulating factor 1 receptor (CSF1R) in the CLL microenvironment yields antineoplastic activity in primary patient samples

Edwards V, D. K., Sweeney, D. T., Ho, H., Eide, C. A., Rofelty, A., Agarwal, A., Liu, S. Q., Danilov, A., Lee, P., Chantry, D., McWeeney, S., Druker, B., Tyner, J., Spurgeon, S. & Loriaux, M., May 15 2018, In : Oncotarget. 9, 37, p. 24576-24589 14 p.

Research output: Contribution to journalArticle

10 Scopus citations
17 Scopus citations
2017

Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID)

Hitzemann, R., Oberbeck, D., Iancu, O., Darakjian, P., McWeeney, S., Spence, S., Schlumbohm, J., Metten, P. & Crabbe, J. J., May 1 2017, In : Alcohol. 60

Research output: Contribution to journalArticle

4 Scopus citations

A microRNA screen identifies the Wnt signaling pathway as a regulator of the interferon response during flavivirus infection

Smith, J. L., Jeng, S., McWeeney, S. & Hirsch, A., Apr 1 2017, In : Journal of Virology. 91, 8, e02388-16.

Research output: Contribution to journalArticle

43 Scopus citations

Characterization of the leukemogenic potential of distal cytoplasmic CSF3R truncation and missense mutations

Zhang, H., Reister Schultz, A., Luty, S., Rofelty, A., Su, Y., Means, S., Bottomly, D., Wilmot, B., McWeeney, S. & Tyner, J., Dec 1 2017, In : Leukemia. 31, 12, p. 2752-2760 9 p.

Research output: Contribution to journalArticle

9 Scopus citations

Comprehensive definition of human immunodominant CD8 antigens in tuberculosis

Lewinsohn, D., Swarbrick, G. M., Park, B., Cansler, M. E., Null, M. D., Toren, K. G., Baseke, J., Zalwango, S., Mayanja-Kizza, H., Malone, L. L., Nyendak, M., Wu, G., Guinn, K., McWeeney, S., Mori, M. T., Chervenak, K. A., Sherman, D. R., Boom, W. H. & Lewinsohn, D., Dec 1 2017, In : npj Vaccines. 2, 1, 8.

Research output: Contribution to journalArticle

14 Scopus citations

Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice

Colville, A. M., Iancu, O., Oberbeck, D. L., Darakjian, P., Zheng, C., Walter, N. A. R., Harrington, C. C., Searles, R., McWeeney, S. & Hitzemann, R., 2017, (Accepted/In press) In : Genes, Brain and Behavior.

Research output: Contribution to journalArticle

14 Scopus citations

Evidence-Based Precision Oncology with the Cancer Targetome

Blucher, A. S., Choonoo, G., Kulesz-Martin, M., Wu, G. & McWeeney, S., 2017, (Accepted/In press) In : Trends in Pharmacological Sciences.

Research output: Contribution to journalArticle

10 Scopus citations

Extensive Homeostatic T Cell Phenotypic Variation within the Collaborative Cross

Graham, J. B., Swarts, J. L., Mooney, M., Choonoo, G., Jeng, S., Miller, D. R., Ferris, M. T., McWeeney, S. & Lund, J. M., Nov 21 2017, In : Cell Reports. 21, 8, p. 2313-2325 13 p.

Research output: Contribution to journalArticle

14 Scopus citations

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics

for the Osteoporotic Fractures in Men (MrOS) Study Research Group, Jul 2017, In : Journal of Bone and Mineral Research. 32, 7, p. 1559-1567 9 p.

Research output: Contribution to journalArticle

6 Scopus citations

Identification of Interleukin-1 by Functional Screening as a Key Mediator of Cellular Expansion and Disease Progression in Acute Myeloid Leukemia

Carey, A., Edwards, D. K., Eide, C. A., Newell, L., Traer, E., Medeiros, B. C., Pollyea, D. A., Deininger, M. W., Collins, R. H., Tyner, J., Druker, B., Bagby, G. C., McWeeney, S. & Agarwal, A., Mar 28 2017, In : Cell Reports. 18, 13, p. 3204-3218 15 p.

Research output: Contribution to journalArticle

53 Scopus citations

Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia

Lamble, A. J., Dietz, M., Laderas, T., McWeeney, S. & Lind, E., Jan 1 2017, (Accepted/In press) In : Journal of Immunological Methods.

Research output: Contribution to journalArticle

6 Scopus citations

Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species

Davis, L., Jeng, S., Svalina, M. N., Huang, E., Pittsenbarger, J., Cantor, E. L., Berlow, N., Seguin, B., Mansoor, A., McWeeney, S. & Keller, C., 2017, In : Oncotarget. 8, 44, p. 76241-76256 16 p.

Research output: Contribution to journalArticle

2 Scopus citations

NFAT5 and SLC4A10 loci associate with plasma osmolality

Böger, C. A., Gorski, M., McMahon, G. M., Xu, H., Chang, Y. P. C., Van Der Most, P. J., Navis, G., Nolte, I. M., De Borst, M. H., Zhang, W., Lehne, B., Loh, M., Tan, S. T., Boerwinkle, E., Grams, M. E., Sekula, P., Li, M., Wilmot, B., Moon, J. G., Scheet, P. & 86 others, Cucca, F., Xiao, X., Lyytikäinen, L. P., Delgado, G., Grammer, T. B., Kleber, M. E., Sedaghat, S., Rivadeneira, F., Corre, T., Kutalik, Z., Bergmann, S., Nielson, C. M., Srikanth, P., Teumer, A., Müller-Nurasyid, M., Brockhaus, A. C., Pfeufer, A., Rathmann, W., Peters, A., Matsumoto, M., De Andrade, M., Atkinson, E. J., Robinson-Cohen, C., De Boer, I. H., Hwang, S. J., Heid, I. M., Gögele, M., Concas, M. P., Tanaka, T., Bandinelli, S., Nalls, M. A., Singleton, A., Tajuddin, S. M., Adeyemo, A., Zhou, J., Doumatey, A., McWeeney, S., Murabito, J., Franceschini, N., Flessner, M., Shlipak, M., Wilson, J. G., Chen, G., Rotimi, C. N., Zonderman, A. B., Evans, M. K., Ferrucci, L., Devuyst, O., Pirastu, M., Shuldiner, A., Hicks, A. A., Pramstaller, P. P., Kestenbaum, B., Kardia, S. L. R., Turner, S. T., Study, L. C., Briske, T. E., Gieger, C., Strauch, K., Meisinger, C., Meitinger, T., Völker, U., Nauck, M., Völzke, H., Vollenweider, P., Bochud, M., Waeber, G., Kähönen, M., Lehtimäki, T., März, W., Dehghan, A., Franco, O. H., Uitterlinden, A. G., Hofman, A., Taylor, H. A., Chambers, J. C., Kooner, J. S., Fox, C. S., Hitzemann, R., Orwoll, E. S., Pattaro, C., Schlessinger, D., Köttgen, A., Snieder, H., Parsa, A. & Cohen, D. M., Aug 2017, In : Journal of the American Society of Nephrology. 28, 8, p. 2311-2321 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Oas1b-dependent immune transcriptional profiles of west nile virus infection in the collaborative cross

Green, R., Wilkins, C., Thomas, S., Sekine, A., Hendrick, D. M., Voss, K., Ireton, R. C., Mooney, M., Go, J. T., Choonoo, G., Jeng, S., de Villena, F. P. M., Ferris, M. T., McWeeney, S. & Gale, M., Jun 1 2017, In : G3: Genes, Genomes, Genetics. 7, 6, p. 1665-1682 18 p.

Research output: Contribution to journalArticle

18 Scopus citations

On the relationships in rhesus macaques between chronic ethanol consumption and the brain transcriptome

Iancu, O., Colville, A., Walter, N. A. R., Darakjian, P., Oberbeck, D. L., Daunais, J. B., Zheng, C., Searles, R., McWeeney, S., Grant, K. K. & Hitzemann, R., 2017, (Accepted/In press) In : Addiction Biology.

Research output: Contribution to journalArticle

13 Scopus citations

Recurrent cyclin D2 mutations in myeloid neoplasms

Khanna, V., Eide, C. A., Tognon, C. E., Maxson, J., Wilmot, B., Bottomly, D., McWeeney, S., Edwards, V. D. K., Druker, B. & Tyner, J., Sep 1 2017, In : Leukemia. 31, 9, p. 2005-2008 4 p.

Research output: Contribution to journalLetter

3 Scopus citations

REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation- differentiation balance in the developing brain

Monaghan, C. E., Nechiporuk, T., Jeng, S., McWeeney, S., Wang, J., Rosenfeld, M. G. & Mandel, G., Jan 17 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 3, p. E406-E415

Research output: Contribution to journalArticle

14 Scopus citations

Unpaired extracellular cysteine mutations of CSF3R mediate gain or loss of function

Zhang, H., Means, S., Schultz, A. R., Watanabe-Smith, K., Medeiros, B. C., Bottomly, D., Wilmot, B., McWeeney, S., Kükenshöner, T., Hantschel, O. & Tyner, J., Aug 15 2017, In : Cancer Research. 77, 16, p. 4258-4267 10 p.

Research output: Contribution to journalArticle

6 Scopus citations
2016

A Mouse Model of Chronic West Nile Virus Disease

Graham, J. B., Swarts, J. L., Wilkins, C., Thomas, S., Green, R., Sekine, A., Voss, K. M., Ireton, R. C., Mooney, M., Choonoo, G., Miller, D. R., Treuting, P. M., Pardo Manuel de Villena, F., Ferris, M. T., McWeeney, S., Gale, M. & Lund, J. M., Nov 1 2016, In : PLoS pathogens. 12, 11, e1005996.

Research output: Contribution to journalArticle

25 Scopus citations

Combined targeting of SET and tyrosine kinases provides an effective therapeutic approach in human T-cell acute lymphoblastic leukemia

Richard, N. P., Pippa, R., Cleary, M. M., Puri, A., Tibbitts, D., Mahmood, S., Christensen, D. J., Jeng, S., McWeeney, S., Look, A. T., Chang, B., Tyner, J., Vitek, M. P., Odero, M. D., Sears, R. & Agarwal, A., 2016, In : Oncotarget. 7, 51, p. 84214-84227 14 p.

Research output: Contribution to journalArticle

12 Scopus citations

Cover Image, Volume 171B, Number 6, September 2016

IMAGE2 Consortium & German ADHD GWAS Group, Sep 1 2016, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 171, 6, p. 1 1 p.

Research output: Contribution to journalComment/debate

2 Scopus citations

Diversity outbred mice at 21: Maintaining allelic variation in the face of selection

Chesler, E. J., Gatti, D. M., Morgan, A. P., Strobel, M., Trepanier, L., Oberbeck, D., McWeeney, S., Hitzemann, R., Ferris, M., McMullan, R., Clayshultle, A., Bell, T. A., de Villena, F. P. M. & Churchill, G. A., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 12, p. 3893-3902 10 p.

Research output: Contribution to journalArticle

18 Scopus citations

Does the urinary microbiome play a role in urgency urinary incontinence and its severity?

Karstens, L., Asquith, M., Davin, S., Stauffer, P., Fair, D., Gregory, W. T., Rowsenbaum, J. T., McWeeney, S. K. & Nardos, R., Jul 27 2016, In : Frontiers in Cellular and Infection Microbiology. 6, JUL, 78.

Research output: Contribution to journalArticle

71 Scopus citations

HitWalker2: Visual analytics for precision medicine and beyond

Bottomly, D., McWeeney, S. & Wilmot, B., Apr 15 2016, In : Bioinformatics. 32, 8, p. 1253-1255 3 p.

Research output: Contribution to journalArticle

8 Scopus citations

Identification and characterization of tyrosine kinase nonreceptor 2 mutations in leukemia through integration of kinase inhibitor screening and genomic analysis

Maxson, J., Abel, M. L., Wang, J., Deng, X., Reckel, S., Luty, S. B., Sun, H., Gorenstein, J., Hughes, S. B., Bottomly, D., Wilmot, B., McWeeney, S., Radich, J., Hantschel, O., Middleton, R. E., Gray, N. S., Druker, B. & Tyner, J., Jan 1 2016, In : Cancer Research. 76, 1, p. 127-138 12 p.

Research output: Contribution to journalArticle

15 Scopus citations

IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Bornstein, S., Schmidt, M., Choonoo, G., Levin, T., Gray, J., Thomas, C., Wong, M. & McWeeney, S., Jan 8 2016, In : BMC Genomics. 17, 1, 38.

Research output: Contribution to journalArticle

25 Scopus citations

Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach

IMAGE2 Consortium & German ADHD GWAS Group, Sep 1 2016, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 171, 6, p. 815-826 12 p.

Research output: Contribution to journalArticle

20 Scopus citations