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Items: 1 to 50 of 295

1.

DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to Mutational Signatures.

Wojtowicz D, Leiserson MDM, Sharan R, Przytycka TM.

Pac Symp Biocomput. 2020;25:262-273.

2.

A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits.

Bruner A, Sharan R.

J Comput Biol. 2019 Nov 26. doi: 10.1089/cmb.2019.0290. [Epub ahead of print]

PMID:
31770006
3.

Novel Technique to Increase the PMMC Flap Pedicle Length by Coplanar Rotation Along the Pedicle Axis.

Sharan R, Attakkil A, Manikantan K, Arun P.

J Maxillofac Oral Surg. 2019 Dec;18(4):637-639. doi: 10.1007/s12663-019-01184-2. Epub 2019 Jan 23.

PMID:
31624450
4.

Unusual loco-regional presentation in papillary carcinoma of thyroid: A case series.

Jain PV, Sharan R, Manikantan K, Biswas G, Ray S, Arun P.

Indian J Cancer. 2019 Oct-Dec;56(4):325-329. doi: 10.4103/ijc.IJC_368_18.

5.

The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.

Song W, Sharan R, Ovcharenko I.

Genome Biol. 2019 Sep 12;20(1):197. doi: 10.1186/s13059-019-1808-y.

6.

Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.

Puddu F, Herzog M, Selivanova A, Wang S, Zhu J, Klein-Lavi S, Gordon M, Meirman R, Millan-Zambrano G, Ayestaran I, Salguero I, Sharan R, Li R, Kupiec M, Jackson SP.

Nature. 2019 Sep;573(7774):416-420. doi: 10.1038/s41586-019-1549-9. Epub 2019 Sep 11.

PMID:
31511699
7.

Modeling clinical and molecular covariates of mutational process activity in cancer.

Robinson W, Sharan R, Leiserson MDM.

Bioinformatics. 2019 Jul 15;35(14):i492-i500. doi: 10.1093/bioinformatics/btz340.

PMID:
31510643
8.

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer.

Wojtowicz D, Sason I, Huang X, Kim YA, Leiserson MDM, Przytycka TM, Sharan R.

Genome Med. 2019 Jul 26;11(1):49. doi: 10.1186/s13073-019-0659-1.

9.

A systematic approach to orient the human protein-protein interaction network.

Silverbush D, Sharan R.

Nat Commun. 2019 Jul 9;10(1):3015. doi: 10.1038/s41467-019-10887-6.

10.

A prospective multicentre study testing the diagnostic accuracy of an automated cough sound centred analytic system for the identification of common respiratory disorders in children.

Porter P, Abeyratne U, Swarnkar V, Tan J, Ng TW, Brisbane JM, Speldewinde D, Choveaux J, Sharan R, Kosasih K, Della P.

Respir Res. 2019 Jun 6;20(1):81. doi: 10.1186/s12931-019-1046-6.

11.

To Embed or Not: Network Embedding as a Paradigm in Computational Biology.

Nelson W, Zitnik M, Wang B, Leskovec J, Goldenberg A, Sharan R.

Front Genet. 2019 May 1;10:381. doi: 10.3389/fgene.2019.00381. eCollection 2019. Review.

12.

Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules.

Silverbush D, Cristea S, Yanovich-Arad G, Geiger T, Beerenwinkel N, Sharan R.

Cell Syst. 2019 May 22;8(5):456-466.e5. doi: 10.1016/j.cels.2019.04.005. Epub 2019 May 15.

PMID:
31103572
13.

The EXPANDER Integrated Platform for Transcriptome Analysis.

Hait TA, Maron-Katz A, Sagir D, Amar D, Ulitsky I, Linhart C, Tanay A, Sharan R, Shiloh Y, Elkon R, Shamir R.

J Mol Biol. 2019 Jun 14;431(13):2398-2406. doi: 10.1016/j.jmb.2019.05.013. Epub 2019 May 14.

14.

Corrections to "Automatic Croup Diagnosis Using Cough Sound Recognition".

Sharan RV, Abeyratne UR, Swarnkar VR, Porter P.

IEEE Trans Biomed Eng. 2019 May;66(5):1491. doi: 10.1109/TBME.2019.2907427.

PMID:
31021746
15.

Corrigendum: Predicting spirometry readings using cough sound features and regression (2018 Physiol. Meas. 39 095001).

Sharan RV, Abeyratne UR, Swarnkar VR, Claxton S, Hukins C, Porter P.

Physiol Meas. 2019 Feb 13. doi: 10.1088/1361-6579/ab06ce. [Epub ahead of print]

PMID:
30759425
16.

Comparative Analysis of Normalization Methods for Network Propagation.

Biran H, Kupiec M, Sharan R.

Front Genet. 2019 Jan 22;10:4. doi: 10.3389/fgene.2019.00004. eCollection 2019.

17.

Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans.

Segal ES, Gritsenko V, Levitan A, Yadav B, Dror N, Steenwyk JL, Silberberg Y, Mielich K, Rokas A, Gow NAR, Kunze R, Sharan R, Berman J.

MBio. 2018 Oct 30;9(5). pii: e02048-18. doi: 10.1128/mBio.02048-18.

18.

A subtype of cancer-associated fibroblasts with lower expression of alpha-smooth muscle actin suppresses stemness through BMP4 in oral carcinoma.

Patel AK, Vipparthi K, Thatikonda V, Arun I, Bhattacharjee S, Sharan R, Arun P, Singh S.

Oncogenesis. 2018 Oct 5;7(10):78. doi: 10.1038/s41389-018-0087-x.

19.

Principles of Systems Biology, No. 31.

Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, Vandin F, Silverbush D, Cristea S, Yanovich G, Geiger T, Beerenwinkel N, Sharan R, Zhou Z, Luhmann N, Alikhan NF, Achtman M.

Cell Syst. 2018 Aug 22;7(2):133-135. doi: 10.1016/j.cels.2018.08.005.

20.

Vicenin-2: a potential radiosensitizer of non-small cell lung cancer cells.

Baruah TJ, Sharan RN, Kma L.

Mol Biol Rep. 2018 Oct;45(5):1219-1225. doi: 10.1007/s11033-018-4275-8. Epub 2018 Aug 11.

PMID:
30099686
21.

Predicting spirometry readings using cough sound features and regression.

Sharan RV, Abeyratne UR, Swarnkar VR, Claxton S, Hukins C, Porter P.

Physiol Meas. 2018 Sep 5;39(9):095001. doi: 10.1088/1361-6579/aad948.

PMID:
30091716
22.

Comparative studies of mineralization and detoxification of Mordant Black 17 in aqueous solution by UV light induced Mn+/H2O2 and Mn+/S2O82- systems.

Sahoo MK, Kumar JE, Sinha B, Marbaniang M, Sharan RN.

Water Sci Technol. 2018 Jul;77(11-12):2917-2928. doi: 10.2166/wst.2018.290.

PMID:
30065144
23.

Automatic Croup Diagnosis Using Cough Sound Recognition.

Sharan RV, Abeyratne UR, Swarnkar VR, Porter P.

IEEE Trans Biomed Eng. 2019 Feb;66(2):485-495. doi: 10.1109/TBME.2018.2849502. Epub 2018 Jun 21. Erratum in: IEEE Trans Biomed Eng. 2019 May;66(5):1491.

PMID:
29993458
24.

Intraperitoneal Instillation of Bupivacaine and Ropivacaine for Postoperative Analgesia in Laparoscopic Cholecystectomy.

Sharan R, Singh M, Kataria AP, Jyoti K, Jarewal V, Kadian R.

Anesth Essays Res. 2018 Apr-Jun;12(2):377-380. doi: 10.4103/aer.AER_6_18.

25.

An optimization framework for network annotation.

Patkar S, Sharan R.

Bioinformatics. 2018 Jul 1;34(13):i502-i508. doi: 10.1093/bioinformatics/bty236.

26.

Gp78 involvement in cellular proliferation: Can act as a promising modulator for cell cycle regulatory proteins?

Joshi V, Upadhyay A, Chhangani D, Amanullah A, Sharan RN, Mishra A.

J Cell Physiol. 2018 Oct;233(10):6352-6368. doi: 10.1002/jcp.26618. Epub 2018 May 9.

PMID:
29741771
27.

Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas.

Atak A, Khurana S, Gollapalli K, Reddy PJ, Levy R, Ben-Salmon S, Hollander D, Donyo M, Heit A, Hotz-Wagenblatt A, Biran H, Sharan R, Rane S, Shelar A, Ast G, Srivastava S.

Oncotarget. 2018 Feb 5;9(17):13530-13544. doi: 10.18632/oncotarget.24418. eCollection 2018 Mar 2.

28.

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence.

Sharan R, Yang HJ, Sule P, Cirillo JD.

J Vis Exp. 2018 Feb 26;(132). doi: 10.3791/56801.

29.

WebPropagate: A Web Server for Network Propagation.

Biran H, Almozlino T, Kupiec M, Sharan R.

J Mol Biol. 2018 Jul 20;430(15):2231-2236. doi: 10.1016/j.jmb.2018.02.025. Epub 2018 Mar 7.

PMID:
29524510
30.

Using deep learning to model the hierarchical structure and function of a cell.

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T.

Nat Methods. 2018 Apr;15(4):290-298. doi: 10.1038/nmeth.4627. Epub 2018 Mar 5.

31.

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer.

Patkar S, Magen A, Sharan R, Hannenhalli S.

PLoS Comput Biol. 2017 Nov 30;13(11):e1005793. doi: 10.1371/journal.pcbi.1005793. eCollection 2017 Nov.

32.

ANAT 2.0: reconstructing functional protein subnetworks.

Almozlino Y, Atias N, Silverbush D, Sharan R.

BMC Bioinformatics. 2017 Nov 16;18(1):495. doi: 10.1186/s12859-017-1932-1.

33.

Myosin 2-Induced Mitotic Rounding Enables Columnar Epithelial Cells to Interpret Cortical Spindle Positioning Cues.

Chanet S, Sharan R, Khan Z, Martin AC.

Curr Biol. 2017 Nov 6;27(21):3350-3358.e3. doi: 10.1016/j.cub.2017.09.039. Epub 2017 Oct 26.

34.

A comparison of dexmedetomidine with propofol versus esmolol with propofol to attenuate the hemodynamic stress responses after electroconvulsive therapy.

Sharan R, Bala N, Attri JP, Garg K.

Indian J Psychiatry. 2017 Jul-Sep;59(3):366-369. doi: 10.4103/psychiatry.IndianJPsychiatry_373_16.

35.

High Dose Ofloxacin-induced Bimodal Hallucinations in a 4 Years Old Child.

Bhattacharya A, Sharan R, Praharaj SK.

Clin Psychopharmacol Neurosci. 2017 Nov 30;15(4):416-417. doi: 10.9758/cpn.2017.15.4.416.

36.

Cough sound analysis for diagnosing croup in pediatric patients using biologically inspired features.

Sharan RV, Abeyratne UR, Swarnkar VR, Porter P.

Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:4578-4581. doi: 10.1109/EMBC.2017.8037875.

PMID:
29060916
37.

Automatic picking of snore events from overnight breath sound recordings.

Swarnkar VR, Abeyratne UR, Sharan RV.

Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:2822-2825. doi: 10.1109/EMBC.2017.8037444.

PMID:
29060485
38.

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.

Dao P, Kim YA, Wojtowicz D, Madan S, Sharan R, Przytycka TM.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005695. doi: 10.1371/journal.pcbi.1005695. eCollection 2017 Oct.

39.

Pratap Narain Srivastava (1927-2017).

Sharan RN, Asotra K.

Int J Radiat Biol. 2017 Dec;93(12):1289-1290. doi: 10.1080/09553002.2017.1385873. No abstract available.

PMID:
28967289
40.

Spectrum of prenatally detected central nervous system malformations: Neural tube defects continue to be the leading foetal malformation.

Siddesh A, Gupta G, Sharan R, Agarwal M, Phadke SR.

Indian J Med Res. 2017 Apr;145(4):471-478. doi: 10.4103/ijmr.IJMR_1882_14.

41.

Therapeutic Neck Dissection in Oral Squamous Cell Carcinoma: Is Selective Neck Dissection the Way Ahead?

Manikantan K, Bang B, Sharan R, Mallick I, Chatterjee S, Arun P.

Kathmandu Univ Med J (KUMJ). 2016 Jul-Sept.;14(55):221-225.

PMID:
28814682
42.

Computational Generation of RNA Nanorings.

Sharan R, Bindewald E, Kasprzak WK, Shapiro BA.

Methods Mol Biol. 2017;1632:19-32. doi: 10.1007/978-1-4939-7138-1_2.

PMID:
28730430
43.

Conscious Sedation: Emerging Trends in Pediatric Dentistry.

Attri JP, Sharan R, Makkar V, Gupta KK, Khetarpal R, Kataria AP.

Anesth Essays Res. 2017 Apr-Jun;11(2):277-281. doi: 10.4103/0259-1162.171458. Review.

44.

Network propagation: a universal amplifier of genetic associations.

Cowen L, Ideker T, Raphael BJ, Sharan R.

Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. Review.

PMID:
28607512
45.

Genome Rearrangement with ILP.

Hartmann T, Wieseke N, Sharan R, Middendorf M, Bernt M.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1585-1593. doi: 10.1109/TCBB.2017.2708121. Epub 2017 May 25.

PMID:
28574364
46.

GLADIATOR: a global approach for elucidating disease modules.

Silberberg Y, Kupiec M, Sharan R.

Genome Med. 2017 May 26;9(1):48. doi: 10.1186/s13073-017-0435-z.

47.

Complexity and algorithms for copy-number evolution problems.

El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R.

Algorithms Mol Biol. 2017 May 16;12:13. doi: 10.1186/s13015-017-0103-2. eCollection 2017.

48.

Identification and Preliminary Validation of Radiation Response Protein(s) in Human Blood for a High-throughput Molecular Biodosimetry Technology for the Future.

Nongrum S, Vaiphei ST, Keppen J, Ksoo M, Kashyap E, Sharan RN.

Genome Integr. 2017 Jan 23;8:5. doi: 10.4103/2041-9414.198910. eCollection 2017.

49.

Strengthening Biological Dosimetry in Member States of the International Atomic Energy Agency.

Hande P, Sharan R, Belyakov O.

Genome Integr. 2016 Dec 30;7:1. doi: 10.4103/2041-9414.197170. eCollection 2016. No abstract available.

50.

Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks.

Rudolph JD, de Graauw M, van de Water B, Geiger T, Sharan R.

Cell Syst. 2016 Dec 21;3(6):585-593.e3. doi: 10.1016/j.cels.2016.11.005.

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