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Items: 1 to 50 of 93

1.

SafePredict: A Meta-Algorithm for Machine Learning That Uses Refusals to Guarantee Correctness.

Kocak MA, Ramirez D, Erkip E, Shasha D.

IEEE Trans Pattern Anal Mach Intell. 2019 Aug 1. doi: 10.1109/TPAMI.2019.2932415. [Epub ahead of print]

PMID:
31380747
2.

Quadrivalent versus trivalent influenza vaccine: clinical outcomes in two influenza seasons, historical cohort study.

Shasha D, Valinsky L, Hershkowitz Sikron F, Glatman-Freedman A, Mandelboim M, Toledano A, Paran Y, Ben-Ami R, Goldman D.

Clin Microbiol Infect. 2019 May 17. pii: S1198-743X(19)30216-2. doi: 10.1016/j.cmi.2019.05.003. [Epub ahead of print]

PMID:
31108229
3.

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions.

Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM.

Nat Commun. 2019 Apr 5;10(1):1569. doi: 10.1038/s41467-019-09522-1.

4.

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics.

Aparo A, Bonnici V, Micale G, Ferro A, Shasha D, Pulvirenti A, Giugno R.

Interdiscip Sci. 2019 Mar;11(1):21-32. doi: 10.1007/s12539-019-00323-0. Epub 2019 Feb 21.

PMID:
30790228
5.

An adaptive geometric search algorithm for macromolecular scaffold selection.

Jiang T, Renfrew PD, Drew K, Youngs N, Butterfoss GL, Bonneau R, Shasha DN.

Protein Eng Des Sel. 2018 Sep 1;31(9):345-354. doi: 10.1093/protein/gzy028.

6.

SuperNoder: a tool to discover over-represented modular structures in networks.

Dessì D, Cirrone J, Recupero DR, Shasha D.

BMC Bioinformatics. 2018 Sep 10;19(1):318. doi: 10.1186/s12859-018-2350-8.

7.

Delayed diagnosis of colorectal sexually transmitted diseases due to their resemblance to inflammatory bowel diseases.

Levy I, Gefen-Halevi S, Nissan I, Keller N, Pilo S, Wieder-Finesod A, Litchevski V, Shasha D, Kedem E, Rahav G.

Int J Infect Dis. 2018 Oct;75:34-38. doi: 10.1016/j.ijid.2018.08.004. Epub 2018 Aug 17.

8.

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.

Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499. doi: 10.1073/pnas.1721487115. Epub 2018 May 16.

9.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

10.

Elite controller CD8+ T cells exhibit comparable viral inhibition capacity, but better sustained effector properties compared to chronic progressors.

Shasha D, Karel D, Angiuli O, Greenblatt A, Ghebremichael M, Yu X, Porichis F, Walker BD.

J Leukoc Biol. 2016 Dec;100(6):1425-1433. Epub 2016 Jul 12.

11.

Management algorithm for HIV-associated parotid lymphoepithelial cysts.

Mourad WF, Patel S, Young R, Khorsandi AS, Concert C, Shourbaji RA, Ciarrocca K, Bakst RL, Shasha D, Guha C, Garg MK, Hu KS, Kalnicki S, Harrison LB.

Eur Arch Otorhinolaryngol. 2016 Oct;273(10):3355-62. doi: 10.1007/s00405-016-3926-4. Epub 2016 Feb 16.

PMID:
26879995
12.

NetMatchStar: an enhanced Cytoscape network querying app.

Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015.

13.

Fluoroquinolones or macrolides alone versus combined with β-lactams for adults with community-acquired pneumonia: Systematic review and meta-analysis.

Raz-Pasteur A, Shasha D, Paul M.

Int J Antimicrob Agents. 2015 Sep;46(3):242-8. doi: 10.1016/j.ijantimicag.2015.04.010. Epub 2015 Jun 3. Review.

PMID:
26092096
14.

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools.

Laganà A, Shasha D, Croce CM.

Front Bioeng Biotechnol. 2014 Dec 11;2:65. doi: 10.3389/fbioe.2014.00065. eCollection 2014. Review.

15.

β-glycosphingolipids ameliorated non-alcoholic steatohepatitis in the Psammomys obesus model.

Zigmond E, Tayer-Shifman O, Lalazar G, Ben Ya'acov A, Weksler-Zangen S, Shasha D, Sklair-Levy M, Zolotarov L, Shalev Z, Kalman R, Ziv E, Raz I, Ilan Y.

J Inflamm Res. 2014 Oct 8;7:151-8. doi: 10.2147/JIR.S50508. eCollection 2014.

16.

Postoperative radiation therapy for parotid pleomorphic adenoma with close or positive margins: treatment outcomes and toxicities.

Patel S, Mourad WF, Wang C, Dhanireddy B, Concert C, Ryniak M, Khorsandi AS, Shourbaji RA, Li Z, Culliney B, Patel R, Bakst RL, Tran T, Shasha D, Schantz S, Persky MS, Hu KS, Harrison LB.

Anticancer Res. 2014 Aug;34(8):4247-51.

PMID:
25075054
17.

Negative example selection for protein function prediction: the NoGO database.

Youngs N, Penfold-Brown D, Bonneau R, Shasha D.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003644. doi: 10.1371/journal.pcbi.1003644. eCollection 2014 Jun.

18.

miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs.

Laganà A, Acunzo M, Romano G, Pulvirenti A, Veneziano D, Cascione L, Giugno R, Gasparini P, Shasha D, Ferro A, Croce CM.

Nucleic Acids Res. 2014 May;42(9):5416-25. doi: 10.1093/nar/gku202. Epub 2014 Mar 13.

19.

Prophylactic sildenafil citrate improves select aspects of sexual function in men treated with radiotherapy for prostate cancer.

Zelefsky MJ, Shasha D, Branco RD, Kollmeier M, Baser RE, Pei X, Ennis R, Stock R, Bar-Chama N, Mulhall JP.

J Urol. 2014 Sep;192(3):868-74. doi: 10.1016/j.juro.2014.02.097. Epub 2014 Mar 3.

PMID:
24603102
20.

Visceral cat scratch disease with endocarditis in an immunocompetent adult: a case report and review of the literature.

Shasha D, Gilon D, Vernea F, Moses AE, Strahilevitz J.

Vector Borne Zoonotic Dis. 2014 Mar;14(3):175-81. doi: 10.1089/vbz.2012.1279. Epub 2014 Feb 27. Review.

PMID:
24575798
21.

Initial experience with oropharynx-targeted radiation therapy for metastatic squamous cell carcinoma of unknown primary of the head and neck.

Mourad WF, Hu KS, Shasha D, Concert C, Ishihara D, Lin W, Shourbaji RA, Ryniak M, Gamez ME, Lukens JN, Li Z, Culliney BE, Khorsandi AS, Tran T, Jacobson A, Manolidis S, Schantz S, Urken M, Persky MS, Harrison LB.

Anticancer Res. 2014 Jan;34(1):243-8.

PMID:
24403470
22.

Long-term outcome of seropositive HIV patients with head and neck squamous cell carcinoma treated with radiation therapy and chemotherapy.

Mourad WF, Hu KS, Shasha D, Concert C, Ishihara D, Lin W, Gamez ME, Lukens JN, Shourbaji RA, Ryniak M, Li Z, Culliney BE, Khorsandi AS, Tran T, Jacobson A, Manolidis S, Schantz S, Urken M, Persky MS, Harrison LB.

Anticancer Res. 2013 Dec;33(12):5511-6. Erratum in: Anticancer Res. 2014 May;34(5):2687. Lukens, John J [corrected to Lukens, John N].

PMID:
24324090
23.

[Elite controllers and the mechanisms behind spontaneous control of HIV].

Shasha D.

Harefuah. 2013 Aug;152(8):481-5, 498. Review. Hebrew.

PMID:
24167935
24.

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.

Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.

PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911. eCollection 2013.

25.

Comprehensive head and neck radiotherapy dose-volume constraints do not apply to smaller volumes.

Mourad WF, Shasha D, Blakaj DM, Khorsandi AS, Shourbaji RA, Glanzman J, Kabarriti R, Young R, Patel S, Katsoulakis E, Gámez M, Woode R, Lazarus C, Concert C, Hu KS, Harrison LB.

Anticancer Res. 2013 Oct;33(10):4483-9. Erratum in: Anticancer Res. 2013 Dec;33(12):5707. Concert, Catherine [added].

PMID:
24123019
26.

Exploration of the role of radiotherapy in the management of early glottic cancer with complete carotid artery occlusion.

Mourad WF, Hu KS, Shourbaji RA, Dolan J, Blakaj DM, Shasha D, Harrison LB.

Onkologie. 2013;36(7-8):433-5. doi: 10.1159/000353750. Epub 2013 Jul 8.

PMID:
23921763
27.

A subgraph isomorphism algorithm and its application to biochemical data.

Bonnici V, Giugno R, Pulvirenti A, Shasha D, Ferro A.

BMC Bioinformatics. 2013;14 Suppl 7:S13. doi: 10.1186/1471-2105-14-S7-S13. Epub 2013 Apr 22.

28.

Gene regulatory networks in plants: learning causality from time and perturbation.

Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D.

Genome Biol. 2013 Jun 27;14(6):123. doi: 10.1186/gb-2013-14-6-123.

29.

Lessons to be Learned from Natural Control of HIV - Future Directions, Therapeutic, and Preventive Implications.

Shasha D, Walker BD.

Front Immunol. 2013 Jun 25;4:162. doi: 10.3389/fimmu.2013.00162. eCollection 2013.

30.

Clinical validation and applications for CT-based atlas for contouring the lower cranial nerves for head and neck cancer radiation therapy.

Mourad WF, Young BM, Young R, Blakaj DM, Ohri N, Shourbaji RA, Manolidis S, Gámez M, Kumar M, Khorsandi A, Khan MA, Shasha D, Blakaj A, Glanzman J, Garg MK, Hu KS, Kalnicki S, Harrison LB.

Oral Oncol. 2013 Sep;49(9):956-963. doi: 10.1016/j.oraloncology.2013.03.449. Epub 2013 Apr 25.

PMID:
23623404
31.

Parametric Bayesian priors and better choice of negative examples improve protein function prediction.

Youngs N, Penfold-Brown D, Drew K, Shasha D, Bonneau R.

Bioinformatics. 2013 May 1;29(9):1190-8. doi: 10.1093/bioinformatics/btt110. Epub 2013 Mar 19.

32.

miR-EdiTar: a database of predicted A-to-I edited miRNA target sites.

Laganà A, Paone A, Veneziano D, Cascione L, Gasparini P, Carasi S, Russo F, Nigita G, Macca V, Giugno R, Pulvirenti A, Shasha D, Ferro A, Croce CM.

Bioinformatics. 2012 Dec 1;28(23):3166-8. doi: 10.1093/bioinformatics/bts589. Epub 2012 Oct 7.

33.

Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.

Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18524-9. doi: 10.1073/pnas.1108684108. Epub 2011 Oct 24.

34.

HIV/AIDS profile and realities at a regional antiretroviral therapy clinic in Jerusalem: 12 years analysis.

Elinav H, Pops KO, Shasha D, Korem M, Hauzi-Bashan M, Grossman Z, Maayan S.

Scand J Infect Dis. 2012 Jan;44(1):65-9. doi: 10.3109/00365548.2011.608713. Epub 2011 Sep 19.

PMID:
21923627
35.

Rational design of temperature-sensitive alleles using computational structure prediction.

Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R.

PLoS One. 2011;6(9):e23947. doi: 10.1371/journal.pone.0023947. Epub 2011 Sep 2.

36.

The Proteome Folding Project: proteome-scale prediction of structure and function.

Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R.

Genome Res. 2011 Nov;21(11):1981-94. doi: 10.1101/gr.121475.111. Epub 2011 Aug 8.

37.

[AIDS--past, present and future].

Levy I, Shasha D, Grossman Z.

Harefuah. 2011 Mar;150(3):246-50, 304, 303. Hebrew.

PMID:
21574358
38.

HIV/AIDS among Palestinians: detection, clinical presentation, prognosis and HIV testing patterns, 1994-2010.

Rosenthal A, Elinav H, Ramlawi A, Shasha D, Olshtain-Pops K, Korem M, Arafeh I, Maayan S.

Int J Infect Dis. 2011 Jun;15(6):e377-81. doi: 10.1016/j.ijid.2010.12.012. Epub 2011 Apr 3.

39.

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.

Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM.

Genome Biol. 2010;11(12):R123. doi: 10.1186/gb-2010-11-12-r123. Epub 2010 Dec 23.

40.

Contemporary management of localized penile cancer.

Shapiro D, Shasha D, Tareen M, Tareen B.

Expert Rev Anticancer Ther. 2011 Jan;11(1):29-36. doi: 10.1586/era.10.209. Review.

PMID:
21166509
41.

Predicting genome-wide redundancy using machine learning.

Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD.

BMC Evol Biol. 2010 Nov 18;10:357. doi: 10.1186/1471-2148-10-357.

42.

SING: subgraph search in non-homogeneous graphs.

Di Natale R, Ferro A, Giugno R, Mongiovì M, Pulvirenti A, Shasha D.

BMC Bioinformatics. 2010 Feb 19;11:96. doi: 10.1186/1471-2105-11-96.

43.

miRò: a miRNA knowledge base.

Laganà A, Forte S, Giudice A, Arena MR, Puglisi PL, Giugno R, Pulvirenti A, Shasha D, Ferro A.

Database (Oxford). 2009;2009:bap008. Epub 2009 Aug 4.

44.

VirtualPlant: a software platform to support systems biology research.

Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA.

Plant Physiol. 2010 Feb;152(2):500-15. doi: 10.1104/pp.109.147025. Epub 2009 Dec 9.

45.

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.

Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutiérrez RA.

PLoS Comput Biol. 2009 Mar;5(3):e1000326. doi: 10.1371/journal.pcbi.1000326. Epub 2009 Mar 20.

46.

GraphFind: enhancing graph searching by low support data mining techniques.

Ferro A, Giugno R, Mongiovì M, Pulvirenti A, Skripin D, Shasha D.

BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S10. doi: 10.1186/1471-2105-9-S4-S10.

47.

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.

Thum KE, Shin MJ, Gutiérrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM.

BMC Syst Biol. 2008 Apr 4;2:31. doi: 10.1186/1752-0509-2-31.

48.

Homology search for genes.

Cui X, Vinar T, Brejová B, Shasha D, Li M.

Bioinformatics. 2007 Jul 1;23(13):i97-103.

PMID:
17646351
49.

Insights into the genomic nitrate response using genetics and the Sungear Software System.

Gutiérrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM.

J Exp Bot. 2007;58(9):2359-67. Epub 2007 Apr 29. Review.

PMID:
17470441
50.

NetMatch: a Cytoscape plugin for searching biological networks.

Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.

Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.

PMID:
17277332

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