We provide access to high-performance computing resources for research, and we support researchers in using these resources. This page shows a selection of papers in which SCU resources were utilized.
If you'd like us to include another paper, please let us know at scu@med.cornell.edu.
Acknowledging the SCU in your publications
To acknowledge use of SCU resources in your publications, please use the following text as a guideline:
The computations in this paper were run on HPC resources supported by the Scientific Computing Unit at Weill Cornell Medicine.
List of publications
...
Modern Methods for Delineating Metagenomic Complexity
Afshinnekoo E*, Meydan C*, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.
Cell Systems. 2015. doi:10.1016/j.cels.2015.07.007
...
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
Afshinnekoo E*, Meydan C*, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.
Cell Systems. 2015. doi:10.1016/j.cels.2015.01.001
...
Mutational Cooperativity Linked to Combinatorial Epigenetic Gain of Function in Acute Myeloid Leukemia
Shih A, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer S, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine R.
Cancer Cell. 2015 Apr 13;27(4):502-15. PMID: 25873173
...
An integrative computational approach for prioritization of genomic variants
Dubchak I, Balasubramanian S, Wang S, Meydan C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski A, Mirzaa G, Dave P, Agam G, Xu J, Al-Gazali L, Mason C, Ross E, Maltsev N, Gilliam T.
PLoS One. 2014 Dec 15;9(12):e114903. PMID: 25506935
...
Linder B, Grozhik A V., Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR.
Nature Methods. 2015. doi:10.1038/nmeth.3453
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Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis
Viny AD, Ott CJ, Spitzer B, Rivas M, Meydan C, Papalexi E, Yelin D, Shank K, Reyes J, Chiu A, Romin Y, Boyko V, Thota S, Maciejewski JP, Melnick A, Bradner JE, Levine RL.
Journal of Experimental Medicine. 2015. doi:10.1084/jem.20151317
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The metagenomics and metadesign of the subways and Urban biomes (MetaSUB) international consortium inaugural meeting report
The MetaSUB International Consortium
Microbiome. 2016. doi:10.1186/s40168-016-0168-z
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CREBBP inactivation promotes the development of HDAC3-dependent lymphomas
Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM.
Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-0975
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Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in hematopoietic stem/progenitor cells
Kunimoto H, McKenney AS, Meydan C, Shank K, Nazir A, Rapaport F, Durham B, Garrett-Bakelman FE, Pronier E, Shih AH, Melnick A, Chaudhuri J, Levine RL.
Blood. 2017. doi:10.1182/blood-2016-06-721977
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Combination targeted therapy to disrupt aberrant oncogenic signaling and reverse epigenetic dysfunction in IDH2- and TET2-mutant acute myeloid leukemia
Shih AH*, Meydan C*, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL.
Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-1049
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Epigenetic identity in AML depends on disruption of nonpromoter regulatory elements and is affected by antagonistic effects of mutations in epigenetic modifiers
Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME.
Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-1032
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rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline
Jain D, Meydan C, Lange J, Claeys Bouuaert C, Mason CE, Anderson K V., Keeney S.
PLoS Genetics. 2017. doi:10.1371/journal.pgen.1006964
...
Kunimoto H, Meydan C, Nazir A, Whitfield J, Shank K, Rapaport F, Maher R, Pronier E, Meyer SC, Garrett-Bakelman FE, Tallman M, Melnick A, Levine RL, Shih AH.
Cancer cell. 2018. doi:10.1016/j.ccell.2017.11.012
...
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S
eLife. 2018. doi:10.7554/eLife.30919.001
...
Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae
Topçuoğlu B, Meydan C, Orellana R, Holden JF
Environmental microbiology. 2018. doi:10.1111/1462-2920.14022
...
Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis
Hatzi K, Geng H, Doane AS, Meydan C, LaRiviere R, Cardenas M, Duy C, Shen H, Vidal MNC, Baslan T, Mohammad HP, Kruger RG, Shaknovich R, Haberman AM, Inghirami G, Lowe SW, Melnick A
Nature immunology. 2019. doi:10.1038/s41590-018-0273-1
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Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response
Agirre X*, Meydan C*, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A
Nature Communications. 2019. doi:10.1038/s41467-019-08679-z
...
The NASA Twins Study: A multi-dimensional analysis of a year-long human spaceflight
NASA Twins Investigators Group
Science. 12 Apr 2019. Vol. 364, Issue 6436, eaau8650, DOI: 10.1126/science.aau8650
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Augello, M.A., Liu, D., Deonarine, L.D., Robinson, B.D., Huang, D., Stelloo, S., Blattner, M., Doane, A.S., Wong, E.W.P., Chen, Y., et al.
Cancer Cell. 2019. doi:10.1016/j.ccell.2019.03.001
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Regulatory elements in molecular networks.
Doane, A.S., and Elemento, O.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2017.
...
Cancer Discovery. 2018. 8, 1632–1653.
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Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis.
Hatzi, K., Geng, H., Doane, A.S., Meydan, C., LaRiviere, R., Cardenas, M., Duy, C., Shen, H., Vidal, M.N.C., Baslan, T., et al.
Nat. Immunol. 2019. 20, 86–96.
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CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.
Jiang, Y., Ortega-Molina, A., Geng, H., Ying, H.-Y., Hatzi, K., Parsa, S., McNally, D., Wang, L., Doane, A.S., Agirre, X., et al.
Cancer Discov. 2017. 7, 38–53.
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Widespread mitotic bookmarking by histone marks and transcription factors in pluripotent stem cells.
Liu, Y., Pelham-Webb, B., Di Giammartino, D.C., Li, J., Kim, D., Kita, K., Saiz, N., Garg, V., Doane, A., Giannakakou, P., et al.
Cell Rep. 2017. 19, 1283–1293.
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Identification of cancer drivers at CTCF insulators in 1,962 whole-genomes.
Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong E, Chi P, Apostolou E, Sanjana NE, Khurana E
Cell Systems (In press). 2019.
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Comprehensive Characterization of Cancer Driver Genes and Mutations.
Bailey M, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl M, Kim J, Reardon B, Ng P, Jeong K, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortes-Ciriano I, Zhou D, Liang W, Hess J, Yellapantula V, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko J, Khurana E, Park P, Van Allen E, Liang H, The MC3 Working Group, The Cancer Genome Atlas Research Network, Lawrence M, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar A, Mills G, Karchin R, Ding L.
Cell. 2018.
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MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene.
Kim J, Geyer F, Martelotto L, Ng C, Lim R, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Kumar R, Forbes A, Khurana E, Mariani O, Badve S, Vincent-Saloman A, Norton L, Reis-Filho J, Weigelt B.
The Journal of Pathology. 2018.
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Identification of novel prostate cancer drivers using RegNetDriver: A framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.
Dhingra P, Martinez-Fundichely A, Berger A, Huang F, Forbes A, Liu M, Liu D, Sboner A, Tamayo P, Rickman D#, Rubin M, Khurana E.
Genome Biology. 2017.
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Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
Redmond D, Poran A, Elemento O
Genome Med. 2016. Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7.
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Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites.
Poran A, Nötzel C, Aly O, Mencia-Trinchant N, Harris CT, Guzman ML, Hassane DC, Elemento O, Kafsack BFC.
Nature. 2017. Nov 2;551(7678):95-99. doi: 10.1038/nature24280. Epub 2017 Sep 25.
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Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells.
Chen HJ, Poran A, Unni AM, Huang SX, Elemento O, Snoeck HW, Varmus H.
J Exp Med. 2019. Mar 4;216(3):674-687. doi: 10.1084/jem.20181155. Epub 2019 Feb 8.
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Chromosomal instability drives metastasis through a cytosolic DNA response.
Bakhoum, S. F., Ngo, B., Laughney, A. M., Cavallo, J.-A., Murphy, C. J., Ly, P., et al.
Nature. 2018. 376, 2109.
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Fenofibrate prevents skeletal muscle loss in mice with lung cancer.
Goncalves, M. D., Hwang, S.-K., Pauli, C., Murphy, C. J., Cheng, Z., Hopkins, B. D., et al.
Proceedings of the National Academy of Sciences of the United States of America. 2018. 115(4), E743–E752.
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High-fructose corn syrup enhances intestinal tumor growth in mice.
Goncalves, M. D., Lu, C., Tutnauer, J., Hartman, T. E., Hwang, S.-K., Murphy, C. J., et al.
Science. 2019. 363(6433), 1345–1349.
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R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine.
Han, T., Schatoff, E. M., Murphy, C., Zafra, M. P., Wilkinson, J. E., Elemento, O., & Dow, L. E..
Nature Communications. 2017. 8, 15945.
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Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer.
Liu, H., Murphy, C. J., Karreth, F. A., Emdal, K. B., Yang, K., White, F. M., et al.
Cancer Discovery. 2017. 8(3), 354–369.
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Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.
Palesch D, Bosinger SE, Tharp GK, Vanderford TH, Paiardini M, Chahroudi A, Johnson ZP, Kirchhoff F, Hahn BH, Norgren RB, Patel NB, Sodora DL, Dawoud RA, Stewart CB, Seepo SM, Harris RA, Liu Y, Raveendran M, Han Y, English A, Thomas GWC, Hahn MW, Pipes L, Mason CE, Muzny DM, Gibbs RA, Sauter D, Worley K, Rogers J, Silvestri G.
Nature. 2018. Jan 3;553(7686):77-81.
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ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2.
Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S.
Elife. 2018. Jan 23;7.
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The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics.
Shabaan H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE.
Gates Open Research 2018. Jan 5;2:3. doi: 10.12688/gatesopenres.12772.1.
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Characterization of Outer Space Radiation Induced Changes in Extremophiles Utilizing Deep Space Gateway Opportunities.
Venkateswaran K, Wang C, Smith D, Mason C, Landry K, Rettberg P.
LPI Contributions 2063. February 2018.
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Ontogeny and Biology of Human Small Airway Epithelial Club Cells.
Zuo WL, Shenoy SA, Li S, O'Beirne SL, Strulovici-Barel Y, Leopold PL, Wang G, Staudt MR, Walters MS, Mason C, Kaner RJ, Mezey JG, Crystal RG.
American Journal of Respiratory Critical Care Medicine. 2018. Jun 6.
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N6-Methyladenosine Modification of Hepatitis B Virus RNA Differentially Regulates the Viral Life Cycle.
Imama H, Khana M, Gokhale NS, McIntyrec ABR, Kim G, Jange JY, Kim S, Mason CE, Horner SM, Siddiquia A.
PNAS. 2018. Aug 28;115(35):8829-8834.
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Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.
Singh NK, Bezdan D, Checinska Sielaff A, Wheeler K, Mason CE, Venkateswaran K.
BMC Microbiology. 2018. Nov 23;18(1):175.
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Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, et. al.
Science. 2018. Dec 14;362(6420).
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Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics.
Danko DC, Meleshko D, Bezdan D, Mason CE, Hajirasouliha I.
Genome Research. 2019. Jan;29(1):116-124.
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Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.
McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE.
Nature Communications. 2019. Feb 4;10(1):579.
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Toward unrestricted use of public genomic data
Amann RI, Baichoo, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.
Science. 2019. Jan 25;363(6425):350-352.
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The comparative genomics and complex population history of Papio baboons.
Rogers JM, Raveendran RA, Harris T, Mailund K, Leppala G, et al.
Science Advances. Jan 30 2019; 5:eaau6947.
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Long non-coding RNAs discriminate the stages and gene regulatory states of the human humoral immune response.
Agirre X, Meydan C, JiangY, Garate L, Doane A, Li X, Verma A, Paiva B, Subero JM, Elemento O, Mason C*, Prosper F*, and Melnick A*.
Nature Communications. 2019. Feb 18;10(1):821. PMID: 30778059.
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City-wide metagenomics uncover antibiotic resistance reservoirs in urban beach and sewage waters.
Fresia P, Antelo V, Salazar C, Giménez M, D'Alessandro B, Afshinnekoo E, Mason C, Gonnet GH, Iraola G.
Microbiome. 2019. Feb 28;7(1):35. PMID: 30819245.
...
...
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes.
Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Labadibi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM.
Nature Biotechnology. 2019. Mar 11.
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Ligand discrimination and gating in CNG channels from apo and partial agonist-bound cryo-EM structures.
Rheinberger J., Gao X., Schmidpeter P.A.M., Nimigean C.M.
eLife. 2018. Jul 20;7. pii: e39775. doi: 10.7554/eLife.39775
...
We provide access to high-performance computing resources for research, and we support researchers in using these resources. This page shows a selection of papers in which SCU resources were utilized.
If you'd like us to include another paper, please let us know at scu@med.cornell.edu.
Acknowledging the SCU in your publications
To acknowledge use of SCU resources in your publications, please use the following text as a guideline:
The computations in this paper were run on HPC resources supported by the Scientific Computing Unit at Weill Cornell Medicine.
List of publications
| Citation | Year | Links |
|---|---|---|
Modern Methods for Delineating Metagenomic Complexity Afshinnekoo E*, Meydan C*, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Cell Systems. 2015. doi:10.1016/j.cels.2015.07.007 | 2015 | VIVO |
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Afshinnekoo E*, Meydan C*, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Cell Systems. 2015. doi:10.1016/j.cels.2015.01.001 | 2015 | VIVO |
Mutational Cooperativity Linked to Combinatorial Epigenetic Gain of Function in Acute Myeloid Leukemia Shih A, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer S, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine R. Cancer Cell. 2015 Apr 13;27(4):502-15. PMID: 25873173 | 2015 | VIVO |
An integrative computational approach for prioritization of genomic variants Dubchak I, Balasubramanian S, Wang S, Meydan C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski A, Mirzaa G, Dave P, Agam G, Xu J, Al-Gazali L, Mason C, Ross E, Maltsev N, Gilliam T. PLoS One. 2014 Dec 15;9(12):e114903. PMID: 25506935 | 2014 | VIVO |
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome Linder B, Grozhik A V., Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR. Nature Methods. 2015. doi:10.1038/nmeth.3453 | 2015 | VIVO |
Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis Viny AD, Ott CJ, Spitzer B, Rivas M, Meydan C, Papalexi E, Yelin D, Shank K, Reyes J, Chiu A, Romin Y, Boyko V, Thota S, Maciejewski JP, Melnick A, Bradner JE, Levine RL. Journal of Experimental Medicine. 2015. doi:10.1084/jem.20151317 | 2015 | VIVO |
The metagenomics and metadesign of the subways and Urban biomes (MetaSUB) international consortium inaugural meeting report The MetaSUB International Consortium Microbiome. 2016. doi:10.1186/s40168-016-0168-z | 2016 | VIVO |
CREBBP inactivation promotes the development of HDAC3-dependent lymphomas Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM. Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-0975 | 2017 | VIVO |
Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in hematopoietic stem/progenitor cells Kunimoto H, McKenney AS, Meydan C, Shank K, Nazir A, Rapaport F, Durham B, Garrett-Bakelman FE, Pronier E, Shih AH, Melnick A, Chaudhuri J, Levine RL. Blood. 2017. doi:10.1182/blood-2016-06-721977 | 2017 | VIVO |
Combination targeted therapy to disrupt aberrant oncogenic signaling and reverse epigenetic dysfunction in IDH2- and TET2-mutant acute myeloid leukemia Shih AH*, Meydan C*, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL. Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-1049 | 2017 | VIVO |
Epigenetic identity in AML depends on disruption of nonpromoter regulatory elements and is affected by antagonistic effects of mutations in epigenetic modifiers Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Cancer Discovery. 2017. doi:10.1158/2159-8290.CD-16-1032 | 2017 | VIVO |
rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline Jain D, Meydan C, Lange J, Claeys Bouuaert C, Mason CE, Anderson K V., Keeney S. PLoS Genetics. 2017. doi:10.1371/journal.pgen.1006964 | 2017 | VIVO |
Cooperative epigenetic remodeling by TET2 loss and NRAS mutation drives myeloid transformation and MEK inhibitor sensitivity Kunimoto H, Meydan C, Nazir A, Whitfield J, Shank K, Rapaport F, Maher R, Pronier E, Meyer SC, Garrett-Bakelman FE, Tallman M, Melnick A, Levine RL, Shih AH. Cancer cell. 2018. doi:10.1016/j.ccell.2017.11.012 | 2018 | Pubmed |
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2 Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S eLife. 2018. doi:10.7554/eLife.30919.001 | 2018 | VIVO |
Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae Topçuoğlu B, Meydan C, Orellana R, Holden JF Environmental microbiology. 2018. doi:10.1111/1462-2920.14022 | 2018 | Pubmed |
Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis Hatzi K, Geng H, Doane AS, Meydan C, LaRiviere R, Cardenas M, Duy C, Shen H, Vidal MNC, Baslan T, Mohammad HP, Kruger RG, Shaknovich R, Haberman AM, Inghirami G, Lowe SW, Melnick A Nature immunology. 2019. doi:10.1038/s41590-018-0273-1 | 2019 | VIVO |
Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response Agirre X*, Meydan C*, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A Nature Communications. 2019. doi:10.1038/s41467-019-08679-z | 2019 | VIVO |
The NASA Twins Study: A multi-dimensional analysis of a year-long human spaceflight NASA Twins Investigators Group Science. 12 Apr 2019. Vol. 364, Issue 6436, eaau8650, DOI: 10.1126/science.aau8650 | 2019 | Science |
Augello, M.A., Liu, D., Deonarine, L.D., Robinson, B.D., Huang, D., Stelloo, S., Blattner, M., Doane, A.S., Wong, E.W.P., Chen, Y., et al. Cancer Cell. 2019. doi:10.1016/j.ccell.2019.03.001 | 2019 | ScienceDirect |
Regulatory elements in molecular networks. Doane, A.S., and Elemento, O. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2017. | 2017 | VIVO |
Cancer Discovery. 2018. 8, 1632–1653. | 2018 | Pubmed |
Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis. Hatzi, K., Geng, H., Doane, A.S., Meydan, C., LaRiviere, R., Cardenas, M., Duy, C., Shen, H., Vidal, M.N.C., Baslan, T., et al. Nat. Immunol. 2019. 20, 86–96. | 2019 | VIVO |
CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas. Jiang, Y., Ortega-Molina, A., Geng, H., Ying, H.-Y., Hatzi, K., Parsa, S., McNally, D., Wang, L., Doane, A.S., Agirre, X., et al. Cancer Discov. 2017. 7, 38–53. | 2017 | VIVO |
Widespread mitotic bookmarking by histone marks and transcription factors in pluripotent stem cells. Liu, Y., Pelham-Webb, B., Di Giammartino, D.C., Li, J., Kim, D., Kita, K., Saiz, N., Garg, V., Doane, A., Giannakakou, P., et al. Cell Rep. 2017. 19, 1283–1293. | 2017 | VIVO |
Identification of cancer drivers at CTCF insulators in 1,962 whole-genomes. Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong E, Chi P, Apostolou E, Sanjana NE, Khurana E Cell Systems (In press). 2019. | 2019 | Khurana Lab |
Comprehensive Characterization of Cancer Driver Genes and Mutations. Bailey M, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl M, Kim J, Reardon B, Ng P, Jeong K, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortes-Ciriano I, Zhou D, Liang W, Hess J, Yellapantula V, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko J, Khurana E, Park P, Van Allen E, Liang H, The MC3 Working Group, The Cancer Genome Atlas Research Network, Lawrence M, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar A, Mills G, Karchin R, Ding L. Cell. 2018. | 2018 | VIVO |
MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene. Kim J, Geyer F, Martelotto L, Ng C, Lim R, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Kumar R, Forbes A, Khurana E, Mariani O, Badve S, Vincent-Saloman A, Norton L, Reis-Filho J, Weigelt B. The Journal of Pathology. 2018. | 2018 | VIVO |
Identification of novel prostate cancer drivers using RegNetDriver: A framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Dhingra P, Martinez-Fundichely A, Berger A, Huang F, Forbes A, Liu M, Liu D, Sboner A, Tamayo P, Rickman D#, Rubin M, Khurana E. Genome Biology. 2017. | 2017 | VIVO |
Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq Redmond D, Poran A, Elemento O Genome Med. 2016. Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7. | 2016 | Pubmed |
Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites. Poran A, Nötzel C, Aly O, Mencia-Trinchant N, Harris CT, Guzman ML, Hassane DC, Elemento O, Kafsack BFC. Nature. 2017. Nov 2;551(7678):95-99. doi: 10.1038/nature24280. Epub 2017 Sep 25. | 2017 | Pubmed |
Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells. Chen HJ, Poran A, Unni AM, Huang SX, Elemento O, Snoeck HW, Varmus H. J Exp Med. 2019. Mar 4;216(3):674-687. doi: 10.1084/jem.20181155. Epub 2019 Feb 8. | 2019 | Pubmed |
Chromosomal instability drives metastasis through a cytosolic DNA response. Bakhoum, S. F., Ngo, B., Laughney, A. M., Cavallo, J.-A., Murphy, C. J., Ly, P., et al. Nature. 2018. 376, 2109. | 2018 | Nature |
Fenofibrate prevents skeletal muscle loss in mice with lung cancer. Goncalves, M. D., Hwang, S.-K., Pauli, C., Murphy, C. J., Cheng, Z., Hopkins, B. D., et al. Proceedings of the National Academy of Sciences of the United States of America. 2018. 115(4), E743–E752. | 2018 | PNAS |
High-fructose corn syrup enhances intestinal tumor growth in mice. Goncalves, M. D., Lu, C., Tutnauer, J., Hartman, T. E., Hwang, S.-K., Murphy, C. J., et al. Science. 2019. 363(6433), 1345–1349. | 2019 | Science |
R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine. Han, T., Schatoff, E. M., Murphy, C., Zafra, M. P., Wilkinson, J. E., Elemento, O., & Dow, L. E.. Nature Communications. 2017. 8, 15945. | 2017 | Nature |
Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer. Liu, H., Murphy, C. J., Karreth, F. A., Emdal, K. B., Yang, K., White, F. M., et al. Cancer Discovery. 2017. 8(3), 354–369. | 2017 | Cancer Discovery |
Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host. Palesch D, Bosinger SE, Tharp GK, Vanderford TH, Paiardini M, Chahroudi A, Johnson ZP, Kirchhoff F, Hahn BH, Norgren RB, Patel NB, Sodora DL, Dawoud RA, Stewart CB, Seepo SM, Harris RA, Liu Y, Raveendran M, Han Y, English A, Thomas GWC, Hahn MW, Pipes L, Mason CE, Muzny DM, Gibbs RA, Sauter D, Worley K, Rogers J, Silvestri G. Nature. 2018. Jan 3;553(7686):77-81. | 2018 | VIVO |
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S. Elife. 2018. Jan 23;7. | 2018 | VIVO |
The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics. Shabaan H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE. Gates Open Research 2018. Jan 5;2:3. doi: 10.12688/gatesopenres.12772.1. | 2018 | Gates Open Research |
Characterization of Outer Space Radiation Induced Changes in Extremophiles Utilizing Deep Space Gateway Opportunities. Venkateswaran K, Wang C, Smith D, Mason C, Landry K, Rettberg P. LPI Contributions 2063. February 2018. | 2018 | ResearchGate |
Ontogeny and Biology of Human Small Airway Epithelial Club Cells. Zuo WL, Shenoy SA, Li S, O'Beirne SL, Strulovici-Barel Y, Leopold PL, Wang G, Staudt MR, Walters MS, Mason C, Kaner RJ, Mezey JG, Crystal RG. American Journal of Respiratory Critical Care Medicine. 2018. Jun 6. | 2018 | Pubmed |
N6-Methyladenosine Modification of Hepatitis B Virus RNA Differentially Regulates the Viral Life Cycle. Imama H, Khana M, Gokhale NS, McIntyrec ABR, Kim G, Jange JY, Kim S, Mason CE, Horner SM, Siddiquia A. PNAS. 2018. Aug 28;115(35):8829-8834. | 2018 | VIVO |
Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains. Singh NK, Bezdan D, Checinska Sielaff A, Wheeler K, Mason CE, Venkateswaran K. BMC Microbiology. 2018. Nov 23;18(1):175. | 2018 | Pubmed |
Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, et. al. Science. 2018. Dec 14;362(6420). | 2018 | Science |
Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics. Danko DC, Meleshko D, Bezdan D, Mason CE, Hajirasouliha I. Genome Research. 2019. Jan;29(1):116-124. | 2019 | VIVO |
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE. Nature Communications. 2019. Feb 4;10(1):579. | 2019 | VIVO |
Toward unrestricted use of public genomic data Amann RI, Baichoo, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Science. 2019. Jan 25;363(6425):350-352. | 2019 | Science |
The comparative genomics and complex population history of Papio baboons. Rogers JM, Raveendran RA, Harris T, Mailund K, Leppala G, et al. Science Advances. Jan 30 2019; 5:eaau6947. | 2019 | VIVO |
Long non-coding RNAs discriminate the stages and gene regulatory states of the human humoral immune response. Agirre X, Meydan C, JiangY, Garate L, Doane A, Li X, Verma A, Paiva B, Subero JM, Elemento O, Mason C*, Prosper F*, and Melnick A*. Nature Communications. 2019. Feb 18;10(1):821. PMID: 30778059. | 2019 | VIVO |
City-wide metagenomics uncover antibiotic resistance reservoirs in urban beach and sewage waters. Fresia P, Antelo V, Salazar C, Giménez M, D'Alessandro B, Afshinnekoo E, Mason C, Gonnet GH, Iraola G. Microbiome. 2019. Feb 28;7(1):35. PMID: 30819245. | 2019 | |
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes. Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Labadibi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM. Nature Biotechnology. 2019. Mar 11. | 2019 | VIVO |
Ligand discrimination and gating in CNG channels from apo and partial agonist-bound cryo-EM structures. Rheinberger J., Gao X., Schmidpeter P.A.M., Nimigean C.M. eLife. 2018. Jul 20;7. pii: e39775. doi: 10.7554/eLife.39775 | 2018 | Pubmed |
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. Jang JY, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk MJ, Wang Y, Lee Y, Lin HV, Huang X, Di Liberto M, Chen Z, Ballman KV, Cantley LC, Marchionni L, Inghirami G, Elemento O, Baiocchi RA, Chen-Kiang S, Belvedere S, Zheng H, Paik J. J Clin Invest. 2022 Dec 15;132(24):e160767. PMID: 36282572 | 2022 | JCI |
Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology Mol Cancer Res 1 February 2022; 20 (2): 202–206. | 2022 | aacrjournals |
A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma
Int. J. Cancer. 2022; 150( 3): 450- 460. | 2022 | Wiley |
Biological Constraints Can Improve Prediction in Precision Oncology
bioRxiv 2021.05.25.445604 | 2022 | bioRxiv |
Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer
Cancer Cell, 2022, ISSN 1535-6108 | 2022 | ScienceDirect |
Type 1 interferon remodels normal and neoplastic hematopoiesis in human
bioRxiv 2022.09.28.509751 | 2022 | bioRxiv |
Using Attention-based Deep Learning to Predict ERG: TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images
bioRxiv 2022.11.18.517111 | 2022 | |
Multi-omics biomarkers aid prostate cancer prognostication.
| 2022 | |