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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

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

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

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

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

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

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

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

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

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

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

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

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

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

Regulatory elements in molecular networks.

Doane, A.S., and Elemento, O.

Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2017.

TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis.

Dominguez, P.M., Ghamlouch, H., Rosikiewicz, W., Kumar, P., Béguelin, W., Fontán, L., Rivas, M.A., Pawlikowska, P., Armand, M., Mouly, E., et al.

Cancer Discovery. 2018. 8, 1632–1653.  

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

bioRxiv

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.

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

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

Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology
Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda L.

Mol Cancer Res 1 February 2022; 20 (2): 202–206.

A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma

Ghantous Y,  Omar M, Broner EC, Agrawal N, Pearson AT, Rosenberg AJ, Mishra V, Singh A,  Abu El-naaj E, Savage PA, Sidransky D, Marchionni L, Izumchenko Y

Int. J. Cancer. 2022; 150( 3): 450- 460.

Biological Constraints Can Improve Prediction in Precision Oncology

Omar M, Mulder L, Coady T, Zanettini C, Imada EL, Dinalankara W, Younes L, Geman D, Marchionni L.

bioRxiv 2021.05.25.445604

2022

Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer

Martinez-Ordoñez A, Duran A, Ruiz-Martinez M, Cid-Diaz T, Zhang X, Han Q, Kinoshita H, Muta Y, Linares JF, Kasashima H, Nakanishi Y, Omar M, Nishimura S, Avila L, Yashiro M, Maeda K, Pannellini T, Pigazzi A, Inghirami G, Marchionni L, Sigal D, Diaz-Meco MT, Moscat J.

Cancer Cell, 2022, ISSN 1535-6108

Type 1 interferon remodels normal and neoplastic hematopoiesis in human

Lama C, Rosenberg S, Kubas-Meyer A, Xie XA, Moein S, Parghi N, Totwani M, Saurty-Seerunghen MS, Omar M, Dillard A, Omans ND, Dusaj N, Chamely P, Mimitou E, Smibert P, Kosiorek HE, Dueck AC, Weinberg R, Chaligne R, Marchionni L, Patel S, Simonson P, Landau DA, Hoffman R, Nam AS.

bioRxiv 2022.09.28.509751

2022

Using Attention-based Deep Learning to Predict ERG: TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images

Omar M, Xu Z, Rand SB, Mohammad M, Salles DC, Schaeffer EM, Robinson BD, Lotan TL, Loda M, Marchionni L.

bioRxiv 2022.11.18.517111

bioRxiv

Multi-omics biomarkers aid prostate cancer prognostication.

Xu Z, Omar M, Benedetti E, Rosenthal J, Umeton R, Krumsiek J, Pomerantz M, Loda M, Marchionni L.  bioRxiv. Sep 2022; doi:10.1101/2022.09.20.508244

Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology

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