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Benchmarking of computational error-correction methods for next-generation sequencing data.

Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S.

Genome Biol. 2020 Mar 17;21(1):71. doi: 10.1186/s13059-020-01988-3.


Physically Crosslinked Poly (Vinyl Alcohol)/Kappa-Carrageenan Hydrogels: Structure and Applications.

Croitoru C, Pop MA, Bedo T, Cosnita M, Roata IC, Hulka I.

Polymers (Basel). 2020 Mar 3;12(3). pii: E560. doi: 10.3390/polym12030560.


Probiotic Bacillus Spores Protect Against Acetaminophen Induced Acute Liver Injury in Rats.

Neag MA, Catinean A, Muntean DM, Pop MR, Bocsan CI, Botan EC, Buzoianu AD.

Nutrients. 2020 Feb 27;12(3). pii: E632. doi: 10.3390/nu12030632.


Multi-contrast volumetric imaging with isotropic resolution for assessing infarct heterogeneity: Initial clinical experience.

Zhang L, Lai P, Roifman I, Pop M, Wright GA.

NMR Biomed. 2020 Feb 5:e4253. doi: 10.1002/nbm.4253. [Epub ahead of print]


Evaluation of Heat-Treated AISI 316 Stainless Steel in Solar Furnaces to Be Used as Possible Implant Material.

Milosan I, Florescu M, Cristea D, Voiculescu I, Pop MA, Cañadas I, Rodriguez J, Bogatu CA, Bedo T.

Materials (Basel). 2020 Jan 26;13(3). pii: E581. doi: 10.3390/ma13030581.


Ketoconazole-p-aminobenzoic Acid Cocrystal: Revival of an Old Drug by Crystal Engineering.

Martin F, Pop M, Kacso I, Grosu IG, Miclăuş M, Vodnar D, Lung I, Filip GA, Olteanu ED, Moldovan R, Nagy A, Filip X, Bâldea I.

Mol Pharm. 2020 Mar 2;17(3):919-932. doi: 10.1021/acs.molpharmaceut.9b01178. Epub 2020 Feb 7.


Pathological fractures of humerus in children. Therapeutic and pathological considerations.

Trăilescu MD, Pavel AI, Pop MA, Zurbău-Anghel N, Stoica GA, Fruntelată RF, Singer CE, Stoica M, Constantin C.

Rom J Morphol Embryol. 2019;60(3):831-840.


Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics.

Chopyk J, Nasko DJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR.

Sci Total Environ. 2020 Mar 1;706:135395. doi: 10.1016/j.scitotenv.2019.135395. Epub 2019 Nov 25.


Novel atlas of fiber directions built from ex-vivo diffusion tensor images of porcine hearts.

Mojica M, Pop M, Sermesant M, Ebrahimi M.

Comput Methods Programs Biomed. 2020 Apr;187:105200. doi: 10.1016/j.cmpb.2019.105200. Epub 2019 Nov 14.


Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications.

Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR.

Water Res. 2020 Feb 1;169:115250. doi: 10.1016/j.watres.2019.115250. Epub 2019 Oct 31.


Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data.

Shah N, Meisel JS, Pop M.

Front Genet. 2019 Oct 17;10:1022. doi: 10.3389/fgene.2019.01022. eCollection 2019.


Detection of epithelial specific cell adhesion molecules in colon cancer and the correlation with clinical and pathological characteristics EpCAM expression in colon cancer.

Pop MG, Bartoș DM, Fiț AM, Vesa ȘC, Bartoș A, Corpădean AG, Nadim AH, Cosmin PI, Cornel I.

Ann Ital Chir. 2019;90:318-323.


Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP.

mSystems. 2019 Oct 8;4(5). pii: e00392-19. doi: 10.1128/mSystems.00392-19.


Near infrared light examination as part of the management of sporadic pancreatic head insulinoma: Case report.

Constantinescu DP, Constantinescu MI, Ciocan RA, Chiorescu S, Pop MG, Pintea DS, Muntean V.

Int J Surg Case Rep. 2019;64:35-40. doi: 10.1016/j.ijscr.2019.09.024. Epub 2019 Sep 24.


MetaCarvel: linking assembly graph motifs to biological variants.

Ghurye J, Treangen T, Fedarko M, Hervey WJ 4th, Pop M.

Genome Biol. 2019 Aug 26;20(1):174. doi: 10.1186/s13059-019-1791-3.


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. eCollection 2019 Aug.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


[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.


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.


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.


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.


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.


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.


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.


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.


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. 2019 Jul 19;20(4):1140-1150. doi: 10.1093/bib/bbx098.


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.


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.


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.


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.


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.


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.

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