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Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia.

Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA.

Nature. 2019 May;569(7757):576-580. doi: 10.1038/s41586-019-1198-z. Epub 2019 May 15.


Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N.

Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.


Shank3 modulates sleep and expression of circadian transcription factors.

Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, Medina E, Risso D, Frank MG, Peixoto L.

Elife. 2019 Apr 11;8. pii: e42819. doi: 10.7554/eLife.42819.


Complementary networks of cortical somatostatin interneurons enforce layer specific control.

Naka A, Veit J, Shababo B, Chance RK, Risso D, Stafford D, Snyder B, Egladyous A, Chu D, Sridharan S, Mossing DP, Paninski L, Ngai J, Adesnik H.

Elife. 2019 Mar 18;8. pii: e43696. doi: 10.7554/eLife.43696.


An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking.

Kozlitina J, Risso D, Lansu K, Olsen RHJ, Sainz E, Luiselli D, Barik A, Frigerio-Domingues C, Pagani L, Wooding S, Kirchner T, Niaura R, Roth B, Drayna D.

PLoS Genet. 2019 Feb 15;15(2):e1007916. doi: 10.1371/journal.pgen.1007916. eCollection 2019 Feb.


Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data.

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2019 Feb 4;10(1):646. doi: 10.1038/s41467-019-08614-2.


Effective two-dimensional model for granular matter with phase separation.

Risso D, Soto R, Guzmán M.

Phys Rev E. 2018 Aug;98(2-1):022901. doi: 10.1103/PhysRevE.98.022901.


clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.

Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E.

PLoS Comput Biol. 2018 Sep 4;14(9):e1006378. doi: 10.1371/journal.pcbi.1006378. eCollection 2018 Sep. Erratum in: PLoS Comput Biol. 2019 Jan 11;15(1):e1006727.


Combinatorial Expression of Grp and Neurod6 Defines Dopamine Neuron Populations with Distinct Projection Patterns and Disease Vulnerability.

Kramer DJ, Risso D, Kosillo P, Ngai J, Bateup HS.

eNeuro. 2018 Jun 13;5(3). pii: ENEURO.0152-18.2018. doi: 10.1523/ENEURO.0152-18.2018. eCollection 2018 May-Jun.


Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S.

BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0.


Taste Perception of Antidesma bunius Fruit and Its Relationships to Bitter Taste Receptor Gene Haplotypes.

Risso D, Sainz E, Morini G, Tofanelli S, Drayna D.

Chem Senses. 2018 Aug 24;43(7):463-468. doi: 10.1093/chemse/bjy037.


Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L.

Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4.


A general and flexible method for signal extraction from single-cell RNA-seq data.

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2018 Jan 18;9(1):284. doi: 10.1038/s41467-017-02554-5. Erratum in: Nat Commun. 2019 Feb 4;10(1):646.


Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism.

Koberstein JN, Poplawski SG, Wimmer ME, Porcari G, Kao C, Gomes B, Risso D, Hakonarson H, Zhang NR, Schultz RT, Abel T, Peixoto L.

Sci Signal. 2018 Jan 16;11(513). pii: eaan6500. doi: 10.1126/scisignal.aan6500.


A Matter of Taste: Lineage-Specific Loss of Function of Taste Receptor Genes in Vertebrates.

Antinucci M, Risso D.

Front Mol Biosci. 2017 Nov 28;4:81. doi: 10.3389/fmolb.2017.00081. eCollection 2017. Review.


Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB.

Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22.


Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

Perraudeau F, Risso D, Street K, Purdom E, Dudoit S.

F1000Res. 2017 Jul 21;6:1158. doi: 10.12688/f1000research.12122.1. eCollection 2017.


Comparison of Central Corneal Thickness Measurements Using Ultrasonic Pachymetry, Anterior Segment OCT and Noncontact Specular Microscopy.

Scotto R, Bagnis A, Papadia M, Cutolo CA, Risso D, Traverso CE.

J Glaucoma. 2017 Oct;26(10):860-865. doi: 10.1097/IJG.0000000000000745.


A common SLC26A4-linked haplotype underlying non-syndromic hearing loss with enlargement of the vestibular aqueduct.

Chattaraj P, Munjal T, Honda K, Rendtorff ND, Ratay JS, Muskett JA, Risso DS, Roux I, Gertz EM, Schäffer AA, Friedman TB, Morell RJ, Tranebjærg L, Griffith AJ.

J Med Genet. 2017 Oct;54(10):665-673. doi: 10.1136/jmedgenet-2017-104721. Epub 2017 Aug 5. Erratum in: J Med Genet. 2018 Dec;55(12):846.


Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J.

Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11.


Normalizing single-cell RNA sequencing data: challenges and opportunities.

Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.

Nat Methods. 2017 Jun;14(6):565-571. doi: 10.1038/nmeth.4292. Epub 2017 May 15.


A bio-cultural approach to the study of food choice: The contribution of taste genetics, population and culture.

Risso DS, Giuliani C, Antinucci M, Morini G, Garagnani P, Tofanelli S, Luiselli D.

Appetite. 2017 Jul 1;114:240-247. doi: 10.1016/j.appet.2017.03.046. Epub 2017 Mar 31.


Probing the Evolutionary History of Human Bitter Taste Receptor Pseudogenes by Restoring Their Function.

Risso D, Behrens M, Sainz E, Meyerhof W, Drayna D.

Mol Biol Evol. 2017 Jul 1;34(7):1587-1595. doi: 10.1093/molbev/msx097.


Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.

Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd KC, Kim SY, Speed TP, He L.

Science. 2017 Feb 10;355(6325). pii: eaag1927. doi: 10.1126/science.aag1927. Epub 2017 Jan 12.


Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

Gerstner JR, Koberstein JN, Watson AJ, Zapero N, Risso D, Speed TP, Frank MG, Peixoto L.

BMC Genomics. 2016 Oct 25;17(Suppl 8):727.


Association of TAS2R38 Haplotypes and Menthol Cigarette Preference in an African American Cohort.

Risso D, Sainz E, Gutierrez J, Kirchner T, Niaura R, Drayna D.

Nicotine Tob Res. 2017 Apr 1;19(4):493-494. doi: 10.1093/ntr/ntw275. No abstract available.


Genetic Variation in the TAS2R38 Bitter Taste Receptor and Smoking Behaviors.

Risso DS, Kozlitina J, Sainz E, Gutierrez J, Wooding S, Getachew B, Luiselli D, Berg CJ, Drayna D.

PLoS One. 2016 Oct 6;11(10):e0164157. doi: 10.1371/journal.pone.0164157. eCollection 2016.


Contextual fear conditioning induces differential alternative splicing.

Poplawski SG, Peixoto L, Porcari GS, Wimmer ME, McNally AG, Mizuno K, Giese KP, Chatterjee S, Koberstein JN, Risso D, Speed TP, Abel T.

Neurobiol Learn Mem. 2016 Oct;134 Pt B:221-35. doi: 10.1016/j.nlm.2016.07.018. Epub 2016 Jul 20.


Corrigendum: Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal.

Risso DS, Mezzavilla M, Pagani L, Robino A, Morini G, Tofanelli S, Carrai M, Campa D, Barale R, Caradonna F, Gasparini P, Luiselli D, Wooding S, Drayna D.

Sci Rep. 2016 Jun 27;6:28406. doi: 10.1038/srep28406. No abstract available.


Copy Number Variation in TAS2R Bitter Taste Receptor Genes: Structure, Origin, and Population Genetics.

Roudnitzky N, Risso D, Drayna D, Behrens M, Meyerhof W, Wooding SP.

Chem Senses. 2016 Oct;41(8):649-59. doi: 10.1093/chemse/bjw067. Epub 2016 Jun 23.


Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal.

Risso DS, Mezzavilla M, Pagani L, Robino A, Morini G, Tofanelli S, Carrai M, Campa D, Barale R, Caradonna F, Gasparini P, Luiselli D, Wooding S, Drayna D.

Sci Rep. 2016 May 3;6:25506. doi: 10.1038/srep25506. Erratum in: Sci Rep. 2016 Jun 27;6:28406.


Comparison of computed tomography and magnetic resonance imaging in the discrimination of intraperitoneal and extraperitoneal rectal cancer: initial experience.

Revelli M, Paparo F, Bacigalupo L, Puppo C, Furnari M, Conforti C, Binda GA, Savarino E, Risso D, Rollandi GA.

Clin Imaging. 2016 Jan-Feb;40(1):57-62. doi: 10.1016/j.clinimag.2015.10.006. Epub 2015 Oct 21.


Effect of the vibration profile on shallow granular systems.

Cordero P, Risso D, Soto R.

Philos Trans A Math Phys Eng Sci. 2015 Dec 13;373(2056). pii: 20150116. doi: 10.1098/rsta.2015.0116.


A potential trigger for pine mouth: a case of a homozygous phenylthiocarbamide taster.

Risso DS, Howard L, VanWaes C, Drayna D.

Nutr Res. 2015 Dec;35(12):1122-5. doi: 10.1016/j.nutres.2015.09.011. Epub 2015 Oct 5.


Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach.

Risso D, Taglioli L, De Iasio S, Gueresi P, Alfani G, Nelli S, Rossi P, Paoli G, Tofanelli S.

PLoS One. 2015 Oct 9;10(10):e0140146. doi: 10.1371/journal.pone.0140146. eCollection 2015.


How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.

Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T.

Nucleic Acids Res. 2015 Sep 18;43(16):7664-74. doi: 10.1093/nar/gkv736. Epub 2015 Jul 21.


Shear viscosity of a model for confined granular media.

Soto R, Risso D, Brito R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Dec;90(6):062204. Epub 2014 Dec 18.


Genetic variation in taste receptor pseudogenes provides evidence for a dynamic role in human evolution.

Risso D, Tofanelli S, Morini G, Luiselli D, Drayna D.

BMC Evol Biol. 2014 Sep 13;14:198. doi: 10.1186/s12862-014-0198-8.


Normalization of RNA-seq data using factor analysis of control genes or samples.

Risso D, Ngai J, Speed TP, Dudoit S.

Nat Biotechnol. 2014 Sep;32(9):896-902. doi: 10.1038/nbt.2931. Epub 2014 Aug 24.


Genetic signature of differential sensitivity to stevioside in the Italian population.

Risso D, Morini G, Pagani L, Quagliariello A, Giuliani C, De Fanti S, Sazzini M, Luiselli D, Tofanelli S.

Genes Nutr. 2014 May;9(3):401. doi: 10.1007/s12263-014-0401-y. Epub 2014 Apr 6.


Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J.

Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001.


Hydrodynamic modes in a confined granular fluid.

Brito R, Risso D, Soto R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022209. Epub 2013 Feb 26.


Neuropathic pain in post-burn hypertrophic scars: a psychophysical and neurophysiological study.

Isoardo G, Stella M, Cocito D, Risso D, Migliaretti G, Cauda F, Palmitessa A, Faccani G, Ciaramitaro P.

Muscle Nerve. 2012 Jun;45(6):883-90. doi: 10.1002/mus.23259.


Acute meningoencephalomyelitis due to varicella-zoster virus in an AIDS patient: report of a case and review of the literature.

Corti M, Trione N, Villafañe MF, Risso D, Yampolsky C, Mamanna L.

Rev Soc Bras Med Trop. 2011 Nov-Dec;44(6):784-6. Review.


GC-content normalization for RNA-Seq data.

Risso D, Schwartz K, Sherlock G, Dudoit S.

BMC Bioinformatics. 2011 Dec 17;12:480. doi: 10.1186/1471-2105-12-480.


[Infection due to Strongyloides stercoralis: epidemiological, clinical, diagnosis findings and outcome in 30 patients].

Corti M, Villafañe MF, Trione N, Risso D, Abuín JC, Palmieri O.

Rev Chilena Infectol. 2011 Jun;28(3):217-22. doi: /S0716-10182011000300003. Epub 2011 Jul 14. Spanish.


Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies.

Martini P, Risso D, Sales G, Romualdi C, Lanfranchi G, Cagnin S.

BMC Bioinformatics. 2011 Apr 11;12:92. doi: 10.1186/1471-2105-12-92.


Role of advanced oxidation protein products and Thiol ratio in patients with acute coronary syndromes.

Barsotti A, Fabbi P, Fedele M, Garibaldi S, Balbi M, Bezante GP, Risso D, Indiveri F, Ghigliotti G, Brunelli C.

Clin Biochem. 2011 Jun;44(8-9):605-11. doi: 10.1016/j.clinbiochem.2011.03.134. Epub 2011 Mar 31.


Sudden chain energy transfer events in vibrated granular media.

Rivas N, Ponce S, Gallet B, Risso D, Soto R, Cordero P, Mujica N.

Phys Rev Lett. 2011 Feb 25;106(8):088001. Epub 2011 Feb 22.


A novel approach to the clustering of microarray data via nonparametric density estimation.

De Bin R, Risso D.

BMC Bioinformatics. 2011 Feb 8;12:49. doi: 10.1186/1471-2105-12-49.

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