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Items: 1 to 50 of 354

1.

Defining the Independence of the Liver Circadian Clock.

Koronowski KB, Kinouchi K, Welz PS, Smith JG, Zinna VM, Shi J, Samad M, Chen S, Magnan CN, Kinchen JM, Li W, Baldi P, Benitah SA, Sassone-Corsi P.

Cell. 2019 May 30;177(6):1448-1462.e14. doi: 10.1016/j.cell.2019.04.025.

PMID:
31150621
2.

The capacity of feedforward neural networks.

Baldi P, Vershynin R.

Neural Netw. 2019 Apr 22;116:288-311. doi: 10.1016/j.neunet.2019.04.009. [Epub ahead of print]

PMID:
31125915
3.

Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons.

Aras E, Ramadori G, Kinouchi K, Liu Y, Ioris RM, Brenachot X, Ljubicic S, Veyrat-Durebex C, Mannucci S, Galié M, Baldi P, Sassone-Corsi P, Coppari R.

Cell Rep. 2019 May 21;27(8):2385-2398.e3. doi: 10.1016/j.celrep.2019.04.093.

4.

Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives.

Sánchez A, Castro C, Flores DL, Gutiérrez E, Baldi P.

Int J Mol Sci. 2019 May 19;20(10). pii: E2476. doi: 10.3390/ijms20102476. Review.

5.

Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis.

Sato S, Basse AL, Schönke M, Chen S, Samad M, Altıntaş A, Laker RC, Dalbram E, Barrès R, Baldi P, Treebak JT, Zierath JR, Sassone-Corsi P.

Cell Metab. 2019 Apr 12. pii: S1550-4131(19)30183-4. doi: 10.1016/j.cmet.2019.03.013. [Epub ahead of print]

PMID:
31006592
6.

Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline.

Berchtold NC, Prieto GA, Phelan M, Gillen DL, Baldi P, Bennett DA, Buchman AS, Cotman CW.

Neurobiol Aging. 2019 Jun;78:142-154. doi: 10.1016/j.neurobiolaging.2019.02.012. Epub 2019 Feb 20.

PMID:
30927700
7.

The DNA modification N6-methyl-2'-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction.

Li X, Zhao Q, Wei W, Lin Q, Magnan C, Emami MR, Wearick-Silva LE, Viola TW, Marshall PR, Yin J, Madugalle SU, Wang Z, Nainar S, Vågbø CB, Leighton LJ, Zajaczkowski EL, Ke K, Grassi-Oliveira R, Bjørås M, Baldi PF, Spitale RC, Bredy TW.

Nat Neurosci. 2019 Apr;22(4):534-544. doi: 10.1038/s41593-019-0339-x. Epub 2019 Feb 18.

PMID:
30778148
8.

Population-wide analysis of differences in disease progression patterns in men and women.

Westergaard D, Moseley P, Sørup FKH, Baldi P, Brunak S.

Nat Commun. 2019 Feb 8;10(1):666. doi: 10.1038/s41467-019-08475-9.

9.

Looking for A Place for Dose-Dense TMZ Regimens in GBM Patients: An Experience with MGMT Exploratory Evaluation.

Napoleoni L, Cortellini A, Cannita K, Parisi A, Dal Mas A, Calvisi G, Venditti O, Baldi PL, Cocciolone V, Ricci A, Ficorella C.

Bioengineering (Basel). 2019 Jan 22;6(1). pii: E11. doi: 10.3390/bioengineering6010011.

10.

Protein malnutrition impairs the immune control of Trichinella spiralis infection.

Vila CC, Saracino MP, Falduto GH, Calcagno MA, Venturiello SM, Pallaro AN, Baldi PC.

Nutrition. 2019 Apr;60:161-169. doi: 10.1016/j.nut.2018.10.024. Epub 2018 Oct 24.

PMID:
30599460
11.

Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle.

Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P.

Cell Rep. 2018 Dec 18;25(12):3299-3314.e6. doi: 10.1016/j.celrep.2018.11.077.

12.

IL-1R and Inflammasomes Mediate Early Pulmonary Protective Mechanisms in Respiratory Brucella Abortus Infection.

Hielpos MS, Fernández AG, Falivene J, Alonso Paiva IM, Muñoz González F, Ferrero MC, Campos PC, Vieira AT, Oliveira SC, Baldi PC.

Front Cell Infect Microbiol. 2018 Nov 5;8:391. doi: 10.3389/fcimb.2018.00391. eCollection 2018.

13.

Learning in the machine: Recirculation is random backpropagation.

Baldi P, Sadowski P.

Neural Netw. 2018 Dec;108:479-494. doi: 10.1016/j.neunet.2018.09.006. Epub 2018 Sep 27.

PMID:
30317133
14.

Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming.

Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I.

iScience. 2018 Aug 31;6:232-246. doi: 10.1016/j.isci.2018.08.002. Epub 2018 Aug 8.

15.

Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks.

Dyar KA, Lutter D, Artati A, Ceglia NJ, Liu Y, Armenta D, Jastroch M, Schneider S, de Mateo S, Cervantes M, Abbondante S, Tognini P, Orozco-Solis R, Kinouchi K, Wang C, Swerdloff R, Nadeef S, Masri S, Magistretti P, Orlando V, Borrelli E, Uhlenhaut NH, Baldi P, Adamski J, Tschöp MH, Eckel-Mahan K, Sassone-Corsi P.

Cell. 2018 Sep 6;174(6):1571-1585.e11. doi: 10.1016/j.cell.2018.08.042.

PMID:
30193114
16.

Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory.

Kwapis JL, Alaghband Y, Kramár EA, López AJ, Vogel Ciernia A, White AO, Shu G, Rhee D, Michael CM, Montellier E, Liu Y, Magnan CN, Chen S, Sassone-Corsi P, Baldi P, Matheos DP, Wood MA.

Nat Commun. 2018 Aug 20;9(1):3323. doi: 10.1038/s41467-018-05868-0.

17.

Gene expression and metabolite accumulation during strawberry (Fragaria × ananassa) fruit development and ripening.

Baldi P, Orsucci S, Moser M, Brilli M, Giongo L, Si-Ammour A.

Planta. 2018 Nov;248(5):1143-1157. doi: 10.1007/s00425-018-2962-2. Epub 2018 Jul 31.

PMID:
30066220
18.

Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images.

Urban G, Bache KM, Phan D, Sobrino A, Shmakov AK, Hachey SJ, Hughes C, Baldi P.

IEEE/ACM Trans Comput Biol Bioinform. 2019 May-Jun;16(3):1029-1035. doi: 10.1109/TCBB.2018.2841396. Epub 2018 May 29.

PMID:
29993583
19.

Neoadjuvant chemotherapy in breast cancer: a dose-dense schedule in real life and putative role of PIK3CA mutations.

Cocciolone V, Cannita K, Tessitore A, Mastroiaco V, Rinaldi L, Paradisi S, Irelli A, Baldi PL, Sidoni T, Ricevuto E, Dal Mas A, Calvisi G, Coletti G, Ciccozzi A, Pizzorno L, Resta V, Bafile A, Alesse E, Ficorella C.

Oncotarget. 2018 Jun 8;9(44):27380-27396. doi: 10.18632/oncotarget.25270. eCollection 2018 Jun 8.

20.

Deep Learning Localizes and Identifies Polyps in Real Time With 96% Accuracy in Screening Colonoscopy.

Urban G, Tripathi P, Alkayali T, Mittal M, Jalali F, Karnes W, Baldi P.

Gastroenterology. 2018 Oct;155(4):1069-1078.e8. doi: 10.1053/j.gastro.2018.06.037. Epub 2018 Jun 18.

PMID:
29928897
21.

CircadiOmics: circadian omic web portal.

Ceglia N, Liu Y, Chen S, Agostinelli F, Eckel-Mahan K, Sassone-Corsi P, Baldi P.

Nucleic Acids Res. 2018 Jul 2;46(W1):W157-W162. doi: 10.1093/nar/gky441.

22.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas.

Chang P, Grinband J, Weinberg BD, Bardis M, Khy M, Cadena G, Su MY, Cha S, Filippi CG, Bota D, Baldi P, Poisson LM, Jain R, Chow D.

AJNR Am J Neuroradiol. 2018 Jul;39(7):1201-1207. doi: 10.3174/ajnr.A5667. Epub 2018 May 10.

PMID:
29748206
23.

Learning in the Machine: Random Backpropagation and the Deep Learning Channel.

Baldi P, Sadowski P, Lu Z.

Artif Intell. 2018 Jul;260:1-35. doi: 10.1016/j.artint.2018.03.003. Epub 2018 Apr 3.

PMID:
29731511
24.

Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-hospital Mortality.

Lee CK, Hofer I, Gabel E, Baldi P, Cannesson M.

Anesthesiology. 2018 Oct;129(4):649-662. doi: 10.1097/ALN.0000000000002186.

PMID:
29664888
25.

Longitudinal Monitoring of Biofilm Formation via Robust Surface-Enhanced Raman Scattering Quantification of Pseudomonas aeruginosa-Produced Metabolites.

Nguyen CQ, Thrift WJ, Bhattacharjee A, Ranjbar S, Gallagher T, Darvishzadeh-Varcheie M, Sanderson RN, Capolino F, Whiteson K, Baldi P, Hochbaum AI, Ragan R.

ACS Appl Mater Interfaces. 2018 Apr 18;10(15):12364-12373. doi: 10.1021/acsami.7b18592. Epub 2018 Apr 9.

PMID:
29589446
26.

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications.

Urban G, Subrahmanya N, Baldi P.

J Chem Inf Model. 2018 Feb 26;58(2):207-211. doi: 10.1021/acs.jcim.7b00384. Epub 2018 Jan 26.

PMID:
29320180
27.

Guidelines for Genome-Scale Analysis of Biological Rhythms.

Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.

28.

Prognostic significance of clinicopathological factors in early breast cancer: 20 years of follow-up in a single-center analysis.

Cocciolone V, Cannita K, Calandrella ML, Ricevuto E, Baldi PL, Sidoni T, Irelli A, Paradisi S, Pizzorno L, Resta V, Bafile A, Alesse E, Tessitore A, Ficorella C.

Oncotarget. 2017 Jun 16;8(42):72031-72043. doi: 10.18632/oncotarget.18526. eCollection 2017 Sep 22.

29.

Efficient second harmonic generation in low-loss planar GaN waveguides.

Gromovyi M, Brault J, Courville A, Rennesson S, Semond F, Feuillet G, Baldi P, Boucaud P, Duboz JY, De Micheli MP.

Opt Express. 2017 Sep 18;25(19):23035-23044. doi: 10.1364/OE.25.023035.

PMID:
29041607
30.

ClusterCAD: a computational platform for type I modular polyketide synthase design.

Eng CH, Backman TWH, Bailey CB, Magnan C, García Martín H, Katz L, Baldi P, Keasling JD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D509-D515. doi: 10.1093/nar/gkx893.

31.

Proinflammatory response of canine trophoblasts to Brucella canis infection.

Fernández AG, Hielpos MS, Ferrero MC, Fossati CA, Baldi PC.

PLoS One. 2017 Oct 16;12(10):e0186561. doi: 10.1371/journal.pone.0186561. eCollection 2017.

32.

Btp Proteins from Brucella abortus Modulate the Lung Innate Immune Response to Infection by the Respiratory Route.

Hielpos MS, Ferrero MC, Fernández AG, Falivene J, Vanzulli S, Comerci DJ, Baldi PC.

Front Immunol. 2017 Aug 24;8:1011. doi: 10.3389/fimmu.2017.01011. eCollection 2017.

33.

Learning in the machine: The symmetries of the deep learning channel.

Baldi P, Sadowski P, Lu Z.

Neural Netw. 2017 Nov;95:110-133. doi: 10.1016/j.neunet.2017.08.008. Epub 2017 Sep 5.

PMID:
28938130
34.

Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet.

Tognini P, Murakami M, Liu Y, Eckel-Mahan KL, Newman JC, Verdin E, Baldi P, Sassone-Corsi P.

Cell Metab. 2017 Sep 5;26(3):523-538.e5. doi: 10.1016/j.cmet.2017.08.015.

35.

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques.

Baldi P, La Porta N.

Front Plant Sci. 2017 Jun 8;8:944. doi: 10.3389/fpls.2017.00944. eCollection 2017. Review.

36.

Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception.

Mazziotti R, Baroncelli L, Ceglia N, Chelini G, Sala GD, Magnan C, Napoli D, Putignano E, Silingardi D, Tola J, Tognini P, Arthur JSC, Baldi P, Pizzorusso T.

Nat Commun. 2017 May 23;8:15488. doi: 10.1038/ncomms15488.

37.

Neutrophil Extracellular Traps Stimulate Proinflammatory Responses in Human Airway Epithelial Cells.

Sabbione F, Keitelman IA, Iula L, Ferrero M, Giordano MN, Baldi P, Rumbo M, Jancic C, Trevani AS.

J Innate Immun. 2017;9(4):387-402. doi: 10.1159/000460293. Epub 2017 May 4.

38.

Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling.

Vogel Ciernia A, Kramár EA, Matheos DP, Havekes R, Hemstedt TJ, Magnan CN, Sakata K, Tran A, Azzawi S, Lopez A, Dang R, Wang W, Trieu B, Tong J, Barrett RM, Post RJ, Baldi P, Abel T, Lynch G, Wood MA.

Learn Mem. 2017 Apr 17;24(5):199-209. doi: 10.1101/lm.044602.116. Print 2017 May.

39.

A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks.

Wang J, Fang Z, Lang N, Yuan H, Su MY, Baldi P.

Comput Biol Med. 2017 May 1;84:137-146. doi: 10.1016/j.compbiomed.2017.03.024. Epub 2017 Mar 27.

40.

MotifMap-RNA: a genome-wide map of RBP binding sites.

Liu Y, Sun S, Bredy T, Wood M, Spitale RC, Baldi P.

Bioinformatics. 2017 Jul 1;33(13):2029-2031. doi: 10.1093/bioinformatics/btx087.

PMID:
28334276
41.

SIRT6 Suppresses Cancer Stem-like Capacity in Tumors with PI3K Activation Independently of Its Deacetylase Activity.

Ioris RM, Galié M, Ramadori G, Anderson JG, Charollais A, Konstantinidou G, Brenachot X, Aras E, Goga A, Ceglia N, Sebastián C, Martinvalet D, Mostoslavsky R, Baldi P, Coppari R.

Cell Rep. 2017 Feb 21;18(8):1858-1868. doi: 10.1016/j.celrep.2017.01.065.

42.

Fine-tuning of the flavonoid and monolignol pathways during apple early fruit development.

Baldi P, Moser M, Brilli M, Vrhovsek U, Pindo M, Si-Ammour A.

Planta. 2017 May;245(5):1021-1035. doi: 10.1007/s00425-017-2660-5. Epub 2017 Feb 11.

PMID:
28188424
43.

Detecting Cardiovascular Disease from Mammograms With Deep Learning.

Wang J, Ding H, Bidgoli FA, Zhou B, Iribarren C, Molloi S, Baldi P.

IEEE Trans Med Imaging. 2017 May;36(5):1172-1181. doi: 10.1109/TMI.2017.2655486. Epub 2017 Jan 19.

44.

High Incidence of Respiratory Involvement in a Cluster of Brucella suis-Infected Workers from a Pork Processing Plant in Argentina.

Wallach JC, García JL, Cardinali PS, Seijo AP, Benchetrit AG, Echazarreta SE, Garro SL, Deodato B, Baldi PC.

Zoonoses Public Health. 2017 Nov;64(7):550-553. doi: 10.1111/zph.12339. Epub 2016 Dec 29.

PMID:
28032696
45.

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

Sadowski P, Fooshee D, Subrahmanya N, Baldi P.

J Chem Inf Model. 2016 Nov 28;56(11):2125-2128. Epub 2016 Oct 25.

PMID:
27749058
46.

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity.

Magnan C, Yu J, Chang I, Jahn E, Kanomata Y, Wu J, Zeller M, Oakes M, Baldi P, Sandmeyer S.

PLoS One. 2016 Sep 7;11(9):e0162363. doi: 10.1371/journal.pone.0162363. eCollection 2016.

47.

A theory of local learning, the learning channel, and the optimality of backpropagation.

Baldi P, Sadowski P.

Neural Netw. 2016 Nov;83:51-74. doi: 10.1016/j.neunet.2016.07.006. Epub 2016 Aug 5.

PMID:
27584574
48.

What time is it? Deep learning approaches for circadian rhythms.

Agostinelli F, Ceglia N, Shahbaba B, Sassone-Corsi P, Baldi P.

Bioinformatics. 2016 Oct 1;32(19):3051. doi: 10.1093/bioinformatics/btw504. Epub 2016 Aug 19. No abstract available.

49.

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge.

Murakami M, Tognini P, Liu Y, Eckel-Mahan KL, Baldi P, Sassone-Corsi P.

EMBO Rep. 2016 Sep;17(9):1292-303. doi: 10.15252/embr.201642463. Epub 2016 Jul 14.

50.

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone.

Gottardini E, Cristofori A, Pellegrini E, La Porta N, Nali C, Baldi P, Sablok G.

Front Plant Sci. 2016 Jun 1;7:713. doi: 10.3389/fpls.2016.00713. eCollection 2016.

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