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Items: 1 to 50 of 105

1.

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice.

Du B, Zielinski DC, Monk JM, Palsson BO.

Proc Natl Acad Sci U S A. 2018 Oct 11. pii: 201805367. doi: 10.1073/pnas.1805367115. [Epub ahead of print]

PMID:
30309961
2.

FGFR3 mRNA overexpression defines a subset of oligometastatic colorectal cancers with worse prognosis.

Fromme JE, Schmitz K, Wachter A, Grzelinski M, Zielinski D, Koppel C, Conradi LC, Homayounfar K, Hugo T, Hugo S, Lukat L, Rüschoff J, Ströbel P, Ghadimi M, Beißbarth T, Reuter-Jessen K, Bleckmann A, Schildhaus HU.

Oncotarget. 2018 Aug 14;9(63):32204-32218. doi: 10.18632/oncotarget.25941. eCollection 2018 Aug 14.

3.

Safety and Side Effects of Rifampin versus Isoniazid in Children.

Diallo T, Adjobimey M, Ruslami R, Trajman A, Sow O, Obeng Baah J, Marks GB, Long R, Elwood K, Zielinski D, Gninafon M, Wulandari DA, Apriani L, Valiquette C, Fregonese F, Hornby K, Li PZ, Hill PC, Schwartzman K, Benedetti A, Menzies D.

N Engl J Med. 2018 Aug 2;379(5):454-463. doi: 10.1056/NEJMoa1714284.

4.

Optimization and validation of PD-L1 immunohistochemistry staining protocols using the antibody clone 28-8 on different staining platforms.

Koppel C, Schwellenbach H, Zielinski D, Eckstein S, Martin-Ortega M, D'Arrigo C, Schildhaus HU, Rüschoff J, Jasani B.

Mod Pathol. 2018 Jun 26. doi: 10.1038/s41379-018-0071-1. [Epub ahead of print]

PMID:
29946185
5.

Measuring visual search and distraction in immersive virtual reality.

Olk B, Dinu A, Zielinski DJ, Kopper R.

R Soc Open Sci. 2018 May 2;5(5):172331. doi: 10.1098/rsos.172331. eCollection 2018 May.

6.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC.

Biophys J. 2018 Jun 5;114(11):2691-2702. doi: 10.1016/j.bpj.2018.04.030.

PMID:
29874618
7.

Impact of environmental diversity of hunting complexes in the Lublin region on ontogenetic quality indicators in roe deer (Capreolus capreolus).

Czyżowski P, Drozd L, Karpiński M, Tajchman K, Goleman M, Wojtaś J, Zieliński D.

Biologia (Bratisl). 2018;73(2):185-189. doi: 10.2478/s11756-018-0025-6. Epub 2018 Mar 15.

8.

Sensorimotor Learning during a Marksmanship Task in Immersive Virtual Reality.

Rao HM, Khanna R, Zielinski DJ, Lu Y, Clements JM, Potter ND, Sommer MA, Kopper R, Appelbaum LG.

Front Psychol. 2018 Feb 6;9:58. doi: 10.3389/fpsyg.2018.00058. eCollection 2018.

9.

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.

10.

DNA.Land is a framework to collect genomes and phenomes in the era of abundant genetic information.

Yuan J, Gordon A, Speyer D, Aufrichtig R, Zielinski D, Pickrell J, Erlich Y.

Nat Genet. 2018 Feb;50(2):160-165. doi: 10.1038/s41588-017-0021-8. No abstract available.

PMID:
29374253
11.

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism.

Du B, Zielinski DC, Palsson BO.

PLoS One. 2017 Dec 21;12(12):e0189880. doi: 10.1371/journal.pone.0189880. eCollection 2017.

12.

Methacholine challenge test: Comparison of tidal breathing and dosimeter methods in children.

Mazi A, Lands LC, Zielinski D.

Pediatr Pulmonol. 2018 Feb;53(2):174-180. doi: 10.1002/ppul.23890. Epub 2017 Nov 27.

PMID:
29178471
13.

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.

Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO.

J Biol Chem. 2017 Dec 1;292(48):19556-19564. doi: 10.1074/jbc.M117.804914. Epub 2017 Oct 13.

PMID:
29030425
14.

Silver, bighead, and common carp orient to acoustic particle motion when avoiding a complex sound.

Zielinski DP, Sorensen PW.

PLoS One. 2017 Jun 27;12(6):e0180110. doi: 10.1371/journal.pone.0180110. eCollection 2017.

15.

Genome-wide profiling of heritable and de novo STR variations.

Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y.

Nat Methods. 2017 Jun;14(6):590-592. doi: 10.1038/nmeth.4267. Epub 2017 Apr 24.

16.

Predictors of false-positive stroke thrombectomy transfers.

Yi J, Zielinski D, Ouyang B, Conners J, Dafer R, Chen M.

J Neurointerv Surg. 2017 Sep;9(9):834-836. doi: 10.1136/neurintsurg-2017-013043. Epub 2017 Mar 30.

PMID:
28360354
17.

DNA Fountain enables a robust and efficient storage architecture.

Erlich Y, Zielinski D.

Science. 2017 Mar 3;355(6328):950-954. doi: 10.1126/science.aaj2038.

PMID:
28254941
18.

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models.

Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE.

Cell Syst. 2017 Mar 22;4(3):318-329.e6. doi: 10.1016/j.cels.2017.01.010. Epub 2017 Feb 15.

19.

Wireless, Web-Based Interactive Control of Optical Coherence Tomography with Mobile Devices.

Mehta R, Nankivil D, Zielinski DJ, Waterman G, Keller B, Limkakeng AT Jr, Kopper R, Izatt JA, Kuo AN.

Transl Vis Sci Technol. 2017 Jan 20;6(1):5. doi: 10.1167/tvst.6.1.5. eCollection 2017 Jan.

20.

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.

Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO.

Sci Rep. 2017 Jan 25;7:41241. doi: 10.1038/srep41241.

21.

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE.

Cell Syst. 2016 Nov 23;3(5):434-443.e8. doi: 10.1016/j.cels.2016.10.020.

22.

Transapical off-pump mitral valve repair. First experience with the NeoChord system in Poland (report of two cases).

Wróbel K, Kurnicka K, Zygier M, Dyk W, Wojdyga R, Zieliński D, Jarzębska M, Juraszyński Z, Lichodziejewska B, Pruszczyk P, Biederman A, Speziali G, Kasten U.

Kardiol Pol. 2017;75(1):7-12. doi: 10.5603/KP.a2016.0149. Epub 2016 Oct 7.

23.

Physician driven variation in the care of children with spinal muscular atrophy type 1.

Oskoui M, Ng P, Liben S, Zielinski D.

Pediatr Pulmonol. 2017 May;52(5):662-668. doi: 10.1002/ppul.23616. Epub 2016 Sep 29.

PMID:
27685758
24.

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K.

Plant Physiol. 2016 Sep;172(1):589-602. doi: 10.1104/pp.16.00593. Epub 2016 Jul 2.

25.

Recon 2.2: from reconstruction to model of human metabolism.

Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, Orellana CA, Quek LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P.

Metabolomics. 2016;12:109. Epub 2016 Jun 7.

26.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.

BMC Syst Biol. 2016 Jun 6;10(1):40. doi: 10.1186/s12918-016-0283-2.

27.

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO.

Cell Syst. 2015 Oct 28;1(4):283-92. doi: 10.1016/j.cels.2015.10.003. Epub 2015 Oct 28.

28.

Jack-of-all-trades effects drive biodiversity-ecosystem multifunctionality relationships in European forests.

van der Plas F, Manning P, Allan E, Scherer-Lorenzen M, Verheyen K, Wirth C, Zavala MA, Hector A, Ampoorter E, Baeten L, Barbaro L, Bauhus J, Benavides R, Benneter A, Berthold F, Bonal D, Bouriaud O, Bruelheide H, Bussotti F, Carnol M, Castagneyrol B, Charbonnier Y, Coomes D, Coppi A, Bastias CC, Muhie Dawud S, De Wandeler H, Domisch T, Finér L, Gessler A, Granier A, Grossiord C, Guyot V, Hättenschwiler S, Jactel H, Jaroszewicz B, Joly FX, Jucker T, Koricheva J, Milligan H, Müller S, Muys B, Nguyen D, Pollastrini M, Raulund-Rasmussen K, Selvi F, Stenlid J, Valladares F, Vesterdal L, Zielínski D, Fischer M.

Nat Commun. 2016 Mar 24;7:11109. doi: 10.1038/ncomms11109.

29.

Biotic homogenization can decrease landscape-scale forest multifunctionality.

van der Plas F, Manning P, Soliveres S, Allan E, Scherer-Lorenzen M, Verheyen K, Wirth C, Zavala MA, Ampoorter E, Baeten L, Barbaro L, Bauhus J, Benavides R, Benneter A, Bonal D, Bouriaud O, Bruelheide H, Bussotti F, Carnol M, Castagneyrol B, Charbonnier Y, Coomes DA, Coppi A, Bastias CC, Dawud SM, De Wandeler H, Domisch T, Finér L, Gessler A, Granier A, Grossiord C, Guyot V, Hättenschwiler S, Jactel H, Jaroszewicz B, Joly FX, Jucker T, Koricheva J, Milligan H, Mueller S, Muys B, Nguyen D, Pollastrini M, Ratcliffe S, Raulund-Rasmussen K, Selvi F, Stenlid J, Valladares F, Vesterdal L, Zielínski D, Fischer M.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3557-62. doi: 10.1073/pnas.1517903113. Epub 2016 Mar 15. Erratum in: Proc Natl Acad Sci U S A. 2016 May 2;:.

30.

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach.

Nida H, Blum S, Zielinski D, Srivastava DA, Elbaum R, Xin Z, Erlich Y, Fridman E, Shental N.

Plant J. 2016 May;86(4):349-59. doi: 10.1111/tpj.13161.

31.

Cerebral Aneurysm Size before and after Rupture: Case Series and Literature Review.

Yi J, Zielinski D, Chen M.

J Stroke Cerebrovasc Dis. 2016 May;25(5):1244-1248. doi: 10.1016/j.jstrokecerebrovasdis.2016.01.031. Epub 2016 Feb 27. Review.

PMID:
26935121
32.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients.

Schlick B, Massoner P, Lueking A, Charoentong P, Blattner M, Schaefer G, Marquart K, Theek C, Amersdorfer P, Zielinski D, Kirchner M, Trajanoski Z, Rubin MA, Müllner S, Schulz-Knappe P, Klocker H.

PLoS One. 2016 Feb 10;11(2):e0147739. doi: 10.1371/journal.pone.0147739. eCollection 2016.

33.

Inspired by Nature: The Use of Plant-derived Substrate/Enzyme Combinations to Generate Antimicrobial Activity in situ.

Estevam EC, Griffin S, Nasim MJ, Zieliński D, Aszyk J, Osowicka M, Dawidowska N, Idroes R, Bartoszek A, Jacob C.

Nat Prod Commun. 2015 Oct;10(10):1733-8.

PMID:
26669114
34.

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.

35.

Medial prefrontal pathways for the contextual regulation of extinguished fear in humans.

Åhs F, Kragel PA, Zielinski DJ, Brady R, LaBar KS.

Neuroimage. 2015 Nov 15;122:262-71. doi: 10.1016/j.neuroimage.2015.07.051. Epub 2015 Jul 26.

36.

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.

Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO.

Nat Commun. 2015 Jun 9;6:7101. doi: 10.1038/ncomms8101.

37.

An unusual cause of stridor after thoracotomy.

Zielinski DM, Weber F.

JAAPA. 2015 Mar;28(3):38-40. doi: 10.1097/01.JAA.0000459812.72641.1a.

PMID:
25710402
38.

Spatial proximity amplifies valence in emotional memory and defensive approach-avoidance.

Åhs F, Dunsmoor JE, Zielinski D, LaBar KS.

Neuropsychologia. 2015 Apr;70:476-85. doi: 10.1016/j.neuropsychologia.2014.12.018. Epub 2014 Dec 23.

39.

Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R.

Microbiology. 2014 Dec;160(Pt 12):2780-93. doi: 10.1099/mic.0.082180-0. Epub 2014 Sep 22.

PMID:
25246670
40.

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO.

PLoS Comput Biol. 2014 Sep 18;10(9):e1003837. doi: 10.1371/journal.pcbi.1003837. eCollection 2014 Sep.

41.

iPipet: sample handling using a tablet.

Zielinski D, Gordon A, Zaks BL, Erlich Y.

Nat Methods. 2014 Aug;11(8):784-5. doi: 10.1038/nmeth.3028. No abstract available.

PMID:
25075904
42.

OTX2 duplication is implicated in hemifacial microsomia.

Zielinski D, Markus B, Sheikh M, Gymrek M, Chu C, Zaks M, Srinivasan B, Hoffman JD, Aizenbud D, Erlich Y.

PLoS One. 2014 May 9;9(5):e96788. doi: 10.1371/journal.pone.0096788. eCollection 2014.

43.

Extinction in multiple virtual reality contexts diminishes fear reinstatement in humans.

Dunsmoor JE, Ahs F, Zielinski DJ, LaBar KS.

Neurobiol Learn Mem. 2014 Sep;113:157-64. doi: 10.1016/j.nlm.2014.02.010. Epub 2014 Feb 28.

44.

Effects of virtual environment platforms on emotional responses.

Kim K, Rosenthal MZ, Zielinski DJ, Brady R.

Comput Methods Programs Biomed. 2014 Mar;113(3):882-93. doi: 10.1016/j.cmpb.2013.12.024. Epub 2014 Jan 7.

PMID:
24440136
45.

[New development lines in immunology. Perspective of pathology].

Rüschoff J, Zielinski D, Heinmöller E.

Pathologe. 2013 Nov;34 Suppl 2:226-9. doi: 10.1007/s00292-013-1811-0. Review. German. No abstract available.

PMID:
24196618
46.

HER2 staining intensity in HER2-positive disease: relationship with FISH amplification and clinical outcome in the HERA trial of adjuvant trastuzumab.

Zabaglo L, Stoss O, Rüschoff J, Zielinski D, Salter J, Arfi M, Bradbury I, Dafni U, Piccart-Gebhart M, Procter M, Dowsett M; HERA Trial Study Team.

Ann Oncol. 2013 Nov;24(11):2761-6. doi: 10.1093/annonc/mdt275. Epub 2013 Jul 25.

PMID:
23894039
47.

Back to the family: a renewed approach to rare variant studies.

Zielinski D, Gymrek M, Erlich Y.

Genome Med. 2012 Dec 19;4(12):97. doi: 10.1186/gm398. eCollection 2012.

48.

Atypical presentations of achalasia in the pediatric population.

Roskies M, Zielinski D, Levesque D, Daniel SJ.

J Otolaryngol Head Neck Surg. 2012 Oct;41(5):E44-6. No abstract available.

PMID:
23092842
49.

Evaluating display fidelity and interaction fidelity in a virtual reality game.

McMahan RP, Bowman DA, Zielinski DJ, Brady RB.

IEEE Trans Vis Comput Graph. 2012 Apr;18(4):626-33. doi: 10.1109/TVCG.2012.43.

PMID:
22402690
50.

Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.

Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B.

BMC Syst Biol. 2012 Jan 30;6:9. doi: 10.1186/1752-0509-6-9.

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