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Items: 1 to 50 of 341

1.

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S.

PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. doi: 10.1371/journal.pcbi.1007273. [Epub ahead of print]

2.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL.

Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x.

3.

Romanian carnivores at a crossroads.

Popescu V, Pop M, Chiriac S, Rozylowicz L.

Science. 2019 Jun 14;364(6445):1041. doi: 10.1126/science.aax6742. No abstract available.

PMID:
31197005
4.

Modern technologies and algorithms for scaffolding assembled genomes.

Ghurye J, Pop M.

PLoS Comput Biol. 2019 Jun 5;15(6):e1006994. doi: 10.1371/journal.pcbi.1006994. eCollection 2019 Jun. Review.

5.

Ti-Zr-Si-Nb Nanocrystalline Alloys and Metallic Glasses: Assessment on the Structural Development, Thermal Stability, Corrosion and Mechanical Properties.

Gabor C, Cristea D, Velicu IL, Bedo T, Gatto A, Bassoli E, Varga B, Pop MA, Geanta V, Stefanoiu R, Codescu MM, Manta E, Patroi D, Florescu M, Munteanu SI, Ghiuta I, Lupu N, Munteanu D.

Materials (Basel). 2019 May 12;12(9). pii: E1551. doi: 10.3390/ma12091551.

6.

Pharmaceuticals, herbicides, and disinfectants in agricultural water sources.

Panthi S, Sapkota AR, Raspanti G, Allard SM, Bui A, Craddock HA, Murray R, Zhu L, East C, Handy E, Callahan MT, Haymaker J, Kulkarni P, Anderson B, Craighead S, Gartley S, Vanore A, Betancourt WQ, Duncan R, Foust D, Sharma M, Micallef SA, Gerba C, Parveen S, Hashem F, May E, Kniel K, Pop M, Ravishankar S, Sapkota A.

Environ Res. 2019 Jul;174:1-8. doi: 10.1016/j.envres.2019.04.011. Epub 2019 Apr 17.

PMID:
31015109
7.

Microbiota of the Hickey Run Tributary of the Anacostia River.

Cagle R, Ramachandran P, Reed E, Commichaux S, Mammel MK, Lacher DW, Miller D, Lindley S, Pop M, Bazaco MC, Wolpert B, Strain EA, Aker S, Feely J, Ottesen A.

Microbiol Resour Announc. 2019 Mar 21;8(12). pii: e00123-19. doi: 10.1128/MRA.00123-19.

8.
9.

DBC1 Regulates p53 Stability via Inhibition of CBP-Dependent p53 Polyubiquitination.

Akande OE, Damle PK, Pop M, Sherman NE, Szomju BB, Litovchick LV, Grossman SR.

Cell Rep. 2019 Mar 19;26(12):3323-3335.e4. doi: 10.1016/j.celrep.2019.02.076.

10.

Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription.

Struntz NB, Chen A, Deutzmann A, Wilson RM, Stefan E, Evans HL, Ramirez MA, Liang T, Caballero F, Wildschut MHE, Neel DV, Freeman DB, Pop MS, McConkey M, Muller S, Curtin BH, Tseng H, Frombach KR, Butty VL, Levine SS, Feau C, Elmiligy S, Hong JA, Lewis TA, Vetere A, Clemons PA, Malstrom SE, Ebert BL, Lin CY, Felsher DW, Koehler AN.

Cell Chem Biol. 2019 May 16;26(5):711-723.e14. doi: 10.1016/j.chembiol.2019.02.009. Epub 2019 Mar 14.

PMID:
30880155
11.

Predictors of 1-year postoperative mortality in radical colon cancer surgery.

Pop MG, Fit AM, Vesa SC, Bartos A, Bartos DM, Corpadean AG, Puia C, Al-Hajjar N, Cornel I.

Ann Ital Chir. 2018;89:507-512.

PMID:
30665223
12.

Incidence of fecal indicator and pathogenic bacteria in reclaimed and return flow waters in Arizona, USA.

Zhu L, Torres M, Betancourt WQ, Sharma M, Micallef SA, Gerba C, Sapkota AR, Sapkota A, Parveen S, Hashem F, May E, Kniel K, Pop M, Ravishankar S.

Environ Res. 2019 Mar;170:122-127. doi: 10.1016/j.envres.2018.11.048. Epub 2018 Dec 1.

PMID:
30579985
13.

You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details.

Treangen TJ, Pop M.

EMBO Rep. 2018 Dec;19(12). pii: e47036. doi: 10.15252/embr.201847036. Epub 2018 Nov 21. No abstract available.

PMID:
30467235
14.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ.

Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

15.

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.

Shah N, Nute MG, Warnow T, Pop M.

Bioinformatics. 2019 May 1;35(9):1613-1614. doi: 10.1093/bioinformatics/bty833. No abstract available.

PMID:
30247621
16.

Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.

Sandoval GJ, Pulice JL, Pakula H, Schenone M, Takeda DY, Pop M, Boulay G, Williamson KE, McBride MJ, Pan J, St Pierre R, Hartman E, Garraway LA, Carr SA, Rivera MN, Li Z, Ronco L, Hahn WC, Kadoch C.

Mol Cell. 2018 Aug 16;71(4):554-566.e7. doi: 10.1016/j.molcel.2018.06.040. Epub 2018 Aug 2.

17.

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water.

Kulkarni P, Olson ND, Paulson JN, Pop M, Maddox C, Claye E, Rosenberg Goldstein RE, Sharma M, Gibbs SG, Mongodin EF, Sapkota AR.

Sci Total Environ. 2018 Oct 15;639:1126-1137. doi: 10.1016/j.scitotenv.2018.05.178. Epub 2018 May 26.

PMID:
29929281
18.

Obtaining adequate surgical margin status in breast-conservation therapy: intraoperative ultrasound-guided resection versus specimen mammography.

Pop MM, Cristian S, Hanko-Bauer O, Ghiga DV, Georgescu R.

Clujul Med. 2018;91(2):197-202. doi: 10.15386/cjmed-891. Epub 2018 Apr 25.

19.

Evaluation of Richmond Agitation Sedation Scale (RASS) in Mechanically Ventilated in the Emergency Department.

Pop MK, Dervay KR, Dansby M, Jones C.

Adv Emerg Nurs J. 2018 Apr/Jun;40(2):131-137. doi: 10.1097/TME.0000000000000184.

PMID:
29715257
20.

[Radiotherapy of bone metastases in France: A descriptive monocentric retrospective study].

Le Fèvre C, Antoni D, Thiéry A, Keller A, Truntzer P, Vigneron C, Clavier JB, Guihard S, Pop M, Schumacher C, Salze P, Noël G.

Cancer Radiother. 2018 Apr;22(2):148-162. doi: 10.1016/j.canrad.2017.09.006. Epub 2018 Mar 27. French.

PMID:
29602695
21.

Outlier detection in BLAST hits.

Shah N, Altschul SF, Pop M.

Algorithms Mol Biol. 2018 Mar 22;13:7. doi: 10.1186/s13015-018-0126-3. eCollection 2018.

22.

Cardiovascular magnetic resonance guided ablation and intra-procedural visualization of evolving radiofrequency lesions in the left ventricle.

Krahn PRP, Singh SM, Ramanan V, Biswas L, Yak N, Anderson KJT, Barry J, Pop M, Wright GA.

J Cardiovasc Magn Reson. 2018 Mar 15;20(1):20. doi: 10.1186/s12968-018-0437-z.

23.

Rectal cancer: factors predicting short outcomes after radical anterior resection.

Ciorogar G, Bartos A, Bartos D, Vesa SC, Pop M, Herdean A, Betea I, Ciorogar A, Mois E, Zaharie F, Iancu C.

Ann Ital Chir. 2017;88:505-513.

PMID:
29339590
24.

Drug-induced thrombocytopenia after anticoagulation with rivaroxaban.

Pop MK, Farokhi F, Iduna L.

Am J Emerg Med. 2018 Mar;36(3):531.e1-531.e2. doi: 10.1016/j.ajem.2017.12.052. Epub 2017 Dec 24.

PMID:
29306643
25.

Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139.

Ceccarelli D, Garriss G, Choi SY, Hasan NA, Stepanauskas R, Pop M, Huq A, Colwell RR.

Front Microbiol. 2017 Nov 23;8:2283. doi: 10.3389/fmicb.2017.02283. eCollection 2017.

26.

Sequence Alignment.

Altschul SF, Pop M.

In: Rosen KH, Shier DR, Goddard W, editors. Handbook of Discrete and Combinatorial Mathematics. 2nd edition. Boca Raton (FL): CRC Press/Taylor & Francis; 2017 Nov. 20.1.

27.
28.

Identification of microbiota dynamics using robust parameter estimation methods.

Chung M, Krueger J, Pop M.

Math Biosci. 2017 Dec;294:71-84. doi: 10.1016/j.mbs.2017.09.009. Epub 2017 Oct 10.

29.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M.

Brief Bioinform. 2017 Aug 7. doi: 10.1093/bib/bbx098. [Epub ahead of print]

PMID:
28968737
30.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

31.

Integrating sign surveys and telemetry data for estimating brown bear (Ursus arctos) density in the Romanian Carpathians.

Popescu VD, Iosif R, Pop MI, Chiriac S, Bouroș G, Furnas BJ.

Ecol Evol. 2017 Aug 1;7(18):7134-7144. doi: 10.1002/ece3.3177. eCollection 2017 Sep.

32.

Scaffolding of long read assemblies using long range contact information.

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.

BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z.

33.

Hemorrhage promotes inflammation and myocardial damage following acute myocardial infarction: insights from a novel preclinical model and cardiovascular magnetic resonance.

Ghugre NR, Pop M, Thomas R, Newbigging S, Qi X, Barry J, Strauss BH, Wright GA.

J Cardiovasc Magn Reson. 2017 Jul 4;19(1):50. doi: 10.1186/s12968-017-0361-7.

34.

Predictive factors of maternal hypothermia during Cesarean delivery: a prospective cohort study.

Desgranges FP, Bapteste L, Riffard C, Pop M, Cogniat B, Gagey AC, Boucher P, Bonnard C, Paturel B, Mullet C, Chassard D, Bouvet L.

Can J Anaesth. 2017 Sep;64(9):919-927. doi: 10.1007/s12630-017-0912-2. Epub 2017 Jun 15.

PMID:
28620807
35.

Real-time MRI guidance of cardiac interventions.

Campbell-Washburn AE, Tavallaei MA, Pop M, Grant EK, Chubb H, Rhode K, Wright GA.

J Magn Reson Imaging. 2017 Oct;46(4):935-950. doi: 10.1002/jmri.25749. Epub 2017 May 11. Review.

36.

Polarization image segmentation of radiofrequency ablated porcine myocardial tissue.

Ahmad I, Gribble A, Murtza I, Ikram M, Pop M, Vitkin A.

PLoS One. 2017 Apr 5;12(4):e0175173. doi: 10.1371/journal.pone.0175173. eCollection 2017.

37.

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions.

Chopyk J, Chattopadhyay S, Kulkarni P, Smyth EM, Hittle LE, Paulson JN, Pop M, Buehler SS, Clark PI, Mongodin EF, Sapkota AR.

Front Microbiol. 2017 Mar 7;8:358. doi: 10.3389/fmicb.2017.00358. eCollection 2017.

38.

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.

Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF.

Microbiome. 2017 Feb 15;5(1):22. doi: 10.1186/s40168-017-0235-0.

39.

Prenatal diagnoses of an uncommon isolated obstructed supracardiac total anomalous pulmonary venous connection: Case report and review of the literature (CARE compliant).

Muntean I, Mărginean C, Stanca R, Togănel R, Pop M, Gozar L.

Medicine (Baltimore). 2017 Feb;96(5):e6061. doi: 10.1097/MD.0000000000006061. Review.

40.

Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli.

Del Canto F, O'Ryan M, Pardo M, Torres A, Gutiérrez D, Cádiz L, Valdés R, Mansilla A, Martínez R, Hernández D, Caro B, Levine MM, Rasko DA, Hill CM, Pop M, Stine OC, Vidal R.

Front Cell Infect Microbiol. 2017 Jan 6;6:200. doi: 10.3389/fcimb.2016.00200. eCollection 2016.

41.

Biomaterials: A potential pathway to healing chronic wounds?

Pop MA, Almquist BD.

Exp Dermatol. 2017 Sep;26(9):760-763. doi: 10.1111/exd.13290. Epub 2017 Feb 14.

42.

Comparison of 360-Degree Circumferential Trabeculotomy and Conventional Trabeculotomy in Primary Pediatric Glaucoma Surgery: Part 1.

Celea C, Dragosloveanu S, Pop M, Celea C.

J Pediatr Ophthalmol Strabismus. 2016 Nov 1;53(6):357-364. doi: 10.3928/01913913-20160809-01.

PMID:
27858948
43.

Assessment of the longitudinal changes in infarct heterogeneity post myocardial infarction.

Roifman I, Ghugre NR, Vira T, Zia MI, Zavodni A, Pop M, Connelly KA, Wright GA.

BMC Cardiovasc Disord. 2016 Oct 14;16(1):198.

44.

Metagenomic Assembly: Overview, Challenges and Applications.

Ghurye JS, Cepeda-Espinoza V, Pop M.

Yale J Biol Med. 2016 Sep 30;89(3):353-362. eCollection 2016 Sep. Review.

45.

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

Davison M, Treangen TJ, Koren S, Pop M, Bhaya D.

PLoS One. 2016 Sep 9;11(9):e0160574. doi: 10.1371/journal.pone.0160574. eCollection 2016.

46.

Multicontrast reconstruction using compressed sensing with low rank and spatially varying edge-preserving constraints for high-resolution MR characterization of myocardial infarction.

Zhang L, Athavale P, Pop M, Wright GA.

Magn Reson Med. 2017 Aug;78(2):598-610. doi: 10.1002/mrm.26402. Epub 2016 Sep 8.

PMID:
27604855
47.

Changes in qualitative and quantitative ultrasound assessment of the gastric antrum before and after elective caesarean section in term pregnant women: a prospective cohort study.

Rouget C, Chassard D, Bonnard C, Pop M, Desgranges FP, Bouvet L.

Anaesthesia. 2016 Nov;71(11):1284-1290. doi: 10.1111/anae.13605. Epub 2016 Aug 26.

48.

Chronic impalement- Case report of a knitting needle 33 years' ascension.

Pop M, Suciu BA.

J Cardiothorac Surg. 2016 Jul 29;11(1):112. doi: 10.1186/s13019-016-0511-2.

49.

New clinical application of amniotic membrane transplant for ocular surface disease.

Gheorghe A, Pop M, Burcea M, Serban M.

J Med Life. 2016 Apr-Jun;9(2):177-9.

50.

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection.

Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E.

Microbiome. 2016 Jul 8;4(1):38. doi: 10.1186/s40168-016-0183-0.

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