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Items: 1 to 50 of 149

1.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT.

Nucleic Acids Res. 2018 Jun 1. doi: 10.1093/nar/gky437. [Epub ahead of print]

PMID:
29860520
2.

Publisher Correction: AKT-mTOR signaling modulates the dynamics of IRE1 RNAse activity by regulating ER-mitochondria contacts.

Sanchez-Alvarez M, Del Pozo MA, Bakal C.

Sci Rep. 2018 Apr 19;8(1):6476. doi: 10.1038/s41598-018-24796-z.

3.

A comprehensive model for the proliferation-quiescence decision in response to endogenous DNA damage in human cells.

Heldt FS, Barr AR, Cooper S, Bakal C, Novák B.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2532-2537. doi: 10.1073/pnas.1715345115. Epub 2018 Feb 20.

PMID:
29463760
4.

PERK links the clock and protein stress in cancer.

Sanchez-Alvarez M, Bakal C.

Nat Cell Biol. 2018 Jan;20(1):4-5. doi: 10.1038/s41556-017-0019-6. No abstract available.

PMID:
29269949
5.

AKT-mTOR signaling modulates the dynamics of IRE1 RNAse activity by regulating ER-mitochondria contacts.

Sanchez-Alvarez M, Del Pozo MA, Bakal C.

Sci Rep. 2017 Nov 28;7(1):16497. doi: 10.1038/s41598-017-16662-1. Erratum in: Sci Rep. 2018 Apr 19;8(1):6476.

6.

Usage of an Electronic Database and Checklist System for Improvement in Magnetic Resonance Imaging Acquisition.

Small JE, Semine L, Therrien J, Doyle P, Kelly L, Marquis R, Bakal CW.

Curr Probl Diagn Radiol. 2018 May - Jun;47(3):152-155. doi: 10.1067/j.cpradiol.2017.05.008. Epub 2017 May 20.

PMID:
28684054
7.

NucliTrack: an integrated nuclei tracking application.

Cooper S, Barr AR, Glen R, Bakal C.

Bioinformatics. 2017 Oct 15;33(20):3320-3322. doi: 10.1093/bioinformatics/btx404.

8.

Single-Cell Dynamics Determines Response to CDK4/6 Inhibition in Triple-Negative Breast Cancer.

Asghar US, Barr AR, Cutts R, Beaney M, Babina I, Sampath D, Giltnane J, Lacap JA, Crocker L, Young A, Pearson A, Herrera-Abreu MT, Bakal C, Turner NC.

Clin Cancer Res. 2017 Sep 15;23(18):5561-5572. doi: 10.1158/1078-0432.CCR-17-0369. Epub 2017 Jun 12.

PMID:
28606920
9.

DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression.

Barr AR, Cooper S, Heldt FS, Butera F, Stoy H, Mansfeld J, Novák B, Bakal C.

Nat Commun. 2017 Mar 20;8:14728. doi: 10.1038/ncomms14728.

10.

RNAi screens for Rho GTPase regulators of cell shape and YAP/TAZ localisation in triple negative breast cancer.

Pascual-Vargas P, Cooper S, Sero J, Bousgouni V, Arias-Garcia M, Bakal C.

Sci Data. 2017 Mar 1;4:170018. doi: 10.1038/sdata.2017.18.

11.

Society of Interventional Radiology: Resource and Environment Recommended Standards for IR.

Baerlocher MO, Kennedy SA, Ward TJ, Nikolic B, Bakal CW, Lewis CA, Winick AB, Niedzwiecki GA, Haskal ZJ, Matsumoto AH.

J Vasc Interv Radiol. 2017 Apr;28(4):513-516. doi: 10.1016/j.jvir.2016.12.1213. Epub 2017 Feb 6. No abstract available.

PMID:
28185771
12.

Accelerating Live Single-Cell Signalling Studies.

Cooper S, Bakal C.

Trends Biotechnol. 2017 May;35(5):422-433. doi: 10.1016/j.tibtech.2017.01.002. Epub 2017 Feb 2. Review.

PMID:
28161141
13.

Multiparametric Analysis of Cell Shape Demonstrates that β-PIX Directly Couples YAP Activation to Extracellular Matrix Adhesion.

Sero JE, Bakal C.

Cell Syst. 2017 Jan 25;4(1):84-96.e6. doi: 10.1016/j.cels.2016.11.015. Epub 2017 Jan 5.

14.

Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics.

Sailem HZ, Bakal C.

Genome Res. 2017 Feb;27(2):196-207. doi: 10.1101/gr.202028.115. Epub 2016 Nov 18.

15.

Proteomics profiling of interactome dynamics by colocalisation analysis (COLA).

Mardakheh FK, Sailem HZ, Kümper S, Tape CJ, McCully RR, Paul A, Anjomani-Virmouni S, Jørgensen C, Poulogiannis G, Marshall CJ, Bakal C.

Mol Biosyst. 2016 Dec 20;13(1):92-105.

16.

A Dynamical Framework for the All-or-None G1/S Transition.

Barr AR, Heldt FS, Zhang T, Bakal C, Novák B.

Cell Syst. 2016 Jan 27;2(1):27-37. doi: 10.1016/j.cels.2016.01.001. Epub 2016 Jan 27.

17.

Society of Interventional Radiology Position Statement: Staffing Guidelines for the Interventional Radiology Suite.

Baerlocher MO, Kennedy SA, Ward TJ, Nikolic B, Bakal CW, Lewis CA, Winick AB, Niedzwiecki GA, Haskal ZJ, Matsumoto AH.

J Vasc Interv Radiol. 2016 May;27(5):618-22. doi: 10.1016/j.jvir.2016.02.010. Epub 2016 Mar 4. No abstract available.

PMID:
26952124
18.

Visualizing quantitative microscopy data: History and challenges.

Sailem HZ, Cooper S, Bakal C.

Crit Rev Biochem Mol Biol. 2016;51(2):96-101. doi: 10.3109/10409238.2016.1146222. Epub 2016 Feb 24. Review.

19.

Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis.

Natrajan R, Sailem H, Mardakheh FK, Arias Garcia M, Tape CJ, Dowsett M, Bakal C, Yuan Y.

PLoS Med. 2016 Feb 16;13(2):e1001961. doi: 10.1371/journal.pmed.1001961. eCollection 2016 Feb.

20.

Cell cycle progression is an essential regulatory component of phospholipid metabolism and membrane homeostasis.

Sanchez-Alvarez M, Zhang Q, Finger F, Wakelam MJ, Bakal C.

Open Biol. 2015 Sep;5(9):150093. doi: 10.1098/rsob.150093.

21.

Apolar and polar transitions drive the conversion between amoeboid and mesenchymal shapes in melanoma cells.

Cooper S, Sadok A, Bousgouni V, Bakal C.

Mol Biol Cell. 2015 Nov 5;26(22):4163-70. doi: 10.1091/mbc.E15-06-0382. Epub 2015 Aug 26.

22.

Erratum: A sensitised RNAi screen reveals a ch-TOG genetic interaction network required for spindle assembly.

Barr AR, Bakal C.

Sci Rep. 2015 Jul 31;5:12384. doi: 10.1038/srep12384. No abstract available.

23.

Cell shape and the microenvironment regulate nuclear translocation of NF-κB in breast epithelial and tumor cells.

Sero JE, Sailem HZ, Ardy RC, Almuttaqi H, Zhang T, Bakal C.

Mol Syst Biol. 2015 Mar;11(3):790.

24.
25.

Visualizing cellular imaging data using PhenoPlot.

Sailem HZ, Sero JE, Bakal C.

Nat Commun. 2015 Jan 8;6:5825. doi: 10.1038/ncomms6825.

26.

How cells explore shape space: a quantitative statistical perspective of cellular morphogenesis.

Yin Z, Sailem H, Sero J, Ardy R, Wong ST, Bakal C.

Bioessays. 2014 Dec;36(12):1195-203. doi: 10.1002/bies.201400011. Epub 2014 Sep 12.

27.

Signaling networks converge on TORC1-SREBP activity to promote endoplasmic reticulum homeostasis.

Sanchez-Alvarez M, Finger F, Arias-Garcia Mdel M, Bousgouni V, Pascual-Vargas P, Bakal C.

PLoS One. 2014 Jul 9;9(7):e101164. doi: 10.1371/journal.pone.0101164. eCollection 2014.

28.

Cross-talk between Rho and Rac GTPases drives deterministic exploration of cellular shape space and morphological heterogeneity.

Sailem H, Bousgouni V, Cooper S, Bakal C.

Open Biol. 2014 Jan 22;4:130132. doi: 10.1098/rsob.130132.

29.

Chris Bakal: Look and learn. Interviewed by Caitlin Sedwick.

Bakal C.

J Cell Biol. 2013 Nov 11;203(3):378-9. doi: 10.1083/jcb.2033pi. No abstract available.

30.

Inferring signalling networks from images.

Evans L, Sailem H, Vargas PP, Bakal C.

J Microsc. 2013 Oct;252(1):1-7. doi: 10.1111/jmi.12062. Epub 2013 Jul 11. Review.

31.

A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes.

Yin Z, Sadok A, Sailem H, McCarthy A, Xia X, Li F, Garcia MA, Evans L, Barr AR, Perrimon N, Marshall CJ, Wong ST, Bakal C.

Nat Cell Biol. 2013 Jul;15(7):860-71. doi: 10.1038/ncb2764. Epub 2013 Jun 9.

32.

Differential RNAi screening provides insights into the rewiring of signalling networks during oxidative stress.

Garcia MA, Alvarez MS, Sailem H, Bousgouni V, Sero J, Bakal C.

Mol Biosyst. 2012 Oct;8(10):2605-13. doi: 10.1039/c2mb25092f.

PMID:
22790786
33.

A direct look at RNAi screens.

Barr AR, Bakal C.

Mol Syst Biol. 2012 Apr 24;8:580. doi: 10.1038/msb.2012.14. No abstract available.

34.

Mechanistic insight into the microtubule and actin cytoskeleton coupling through dynein-dependent RhoGEF inhibition.

Meiri D, Marshall CB, Greeve MA, Kim B, Balan M, Suarez F, Bakal C, Wu C, Larose J, Fine N, Ikura M, Rottapel R.

Mol Cell. 2012 Mar 9;45(5):642-55. doi: 10.1016/j.molcel.2012.01.027. Erratum in: Mol Cell. 2012 Mar 30;45(6):844. Bakal, Chris [added].

35.

Dynamic systems.

Bakal C.

Genome Biol. 2012 Jan 30;13(1):312. doi: 10.1186/gb-2012-13-1-312.

36.

Paxillin mediates sensing of physical cues and regulates directional cell motility by controlling lamellipodia positioning.

Sero JE, Thodeti CK, Mammoto A, Bakal C, Thomas S, Ingber DE.

PLoS One. 2011;6(12):e28303. doi: 10.1371/journal.pone.0028303. Epub 2011 Dec 14.

37.

Drosophila RNAi screening in a postgenomic world.

Bakal C.

Brief Funct Genomics. 2011 Jul;10(4):197-205. doi: 10.1093/bfgp/elr015. Epub 2011 Jul 12. Review.

38.

Realizing the promise of RNAi high throughput screening.

Bakal C, Perrimon N.

Dev Cell. 2010 Apr 20;18(4):506-7. doi: 10.1016/j.devcel.2010.04.005.

39.

Genomic screening with RNAi: results and challenges.

Mohr S, Bakal C, Perrimon N.

Annu Rev Biochem. 2010;79:37-64. doi: 10.1146/annurev-biochem-060408-092949. Review.

40.

Quality improvement guidelines for percutaneous drainage/aspiration of abscess and fluid collections.

Wallace MJ, Chin KW, Fletcher TB, Bakal CW, Cardella JF, Grassi CJ, Grizzard JD, Kaye AD, Kushner DC, Larson PA, Liebscher LA, Luers PR, Mauro MA, Kundu S; Society of Interventional Radiology (SIR).

J Vasc Interv Radiol. 2010 Apr;21(4):431-5. doi: 10.1016/j.jvir.2009.12.398. No abstract available.

PMID:
20346880
41.

Endovascular temporary vessel occlusion with a reverse-thermosensitive polymer for bloodless minimally invasive renal surgery.

Flacke S, Moinzadeh A, Libertino JA, Merhige J, Vogel JM, Lyall K, Khettry U, Bakal CW, Madras PN.

J Vasc Interv Radiol. 2010 May;21(5):711-8. doi: 10.1016/j.jvir.2010.01.027. Epub 2010 Mar 21.

42.

Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen.

Nir O, Bakal C, Perrimon N, Berger B.

Genome Res. 2010 Mar;20(3):372-80. doi: 10.1101/gr.100248.109. Epub 2010 Feb 9.

43.

Temporary segmental renal artery occlusion using reverse phase polymer for bloodless robotic partial nephrectomy.

Moinzadeh A, Flacke S, Libertino JA, Merhige J, Vogel JM, Lyall K, Bakal CW, Madras PN.

J Urol. 2009 Oct;182(4):1582-7. doi: 10.1016/j.juro.2009.06.009. Epub 2009 Aug 15.

44.

The twin spot generator for differential Drosophila lineage analysis.

Griffin R, Sustar A, Bonvin M, Binari R, del Valle Rodriguez A, Hohl AM, Bateman JR, Villalta C, Heffern E, Grunwald D, Bakal C, Desplan C, Schubiger G, Wu CT, Perrimon N.

Nat Methods. 2009 Aug;6(8):600-2. doi: 10.1038/nmeth.1349. Epub 2009 Jul 26.

45.

Quality improvement guidelines for transhepatic arterial chemoembolization, embolization, and chemotherapeutic infusion for hepatic malignancy.

Brown DB, Cardella JF, Sacks D, Goldberg SN, Gervais DA, Rajan DK, Vedantham S, Miller DL, Brountzos EN, Grassi CJ, Towbin RB; SIR Standards of Practice Committee, Angle JF, Balter S, Clark TW, Cole PE, Drescher P, Freeman NJ, Georgia JD, Haskal Z, Hovsepian DM, Kilnani NM, Kundu S, Malloy PC, Martin LG, McGraw JK, Meranze SG, Meyers PM, Millward SF, Murphy K, Neithamer CD Jr, Omary RA, Patel NH, Roberts AC, Schwartzberg MS, Siskin GP, Smouse HR, Swan TL, Thorpe PE, Vesely TM, Wagner LK, Wiechmann BN, Bakal CW, Lewis CA, Nemcek AA Jr, Rholl KS.

J Vasc Interv Radiol. 2009 Jul;20(7 Suppl):S219-S226, S226.e1-10. doi: 10.1016/j.jvir.2009.04.033. No abstract available.

PMID:
19560002
46.

RNAiCut: automated detection of significant genes from functional genomic screens.

Kaplow IM, Singh R, Friedman A, Bakal C, Perrimon N, Berger B.

Nat Methods. 2009 Jul;6(7):476-7. doi: 10.1038/nmeth0709-476. No abstract available.

PMID:
19564846
47.

Phosphorylation networks regulating JNK activity in diverse genetic backgrounds.

Bakal C, Linding R, Llense F, Heffern E, Martin-Blanco E, Pawson T, Perrimon N.

Science. 2008 Oct 17;322(5900):453-6. doi: 10.1126/science.1158739.

48.

Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens.

Yin Z, Zhou X, Bakal C, Li F, Sun Y, Perrimon N, Wong ST.

BMC Bioinformatics. 2008 Jun 5;9:264. doi: 10.1186/1471-2105-9-264.

49.

Quantitative morphological signatures define local signaling networks regulating cell morphology.

Bakal C, Aach J, Church G, Perrimon N.

Science. 2007 Jun 22;316(5832):1753-6.

50.

ACC/AHA Guidelines for the Management of Patients with Peripheral Arterial Disease (lower extremity, renal, mesenteric, and abdominal aortic): a collaborative report from the American Associations for Vascular Surgery/Society for Vascular Surgery, Society for Cardiovascular Angiography and Interventions, Society for Vascular Medicine and Biology, Society of Interventional Radiology, and the ACC/AHA Task Force on Practice Guidelines (writing committee to develop guidelines for the management of patients with peripheral arterial disease)--summary of recommendations.

Hirsch AT, Haskal ZJ, Hertzer NR, Bakal CW, Creager MA, Halperin JL, Hiratzka LF, Murphy WR, Olin JW, Puschett JB, Rosenfield KA, Sacks D, Stanley JC, Taylor LM Jr, White CJ, White J, White RA, Antman EM, Smith SC Jr, Adams CD, Anderson JL, Faxon DP, Fuster V, Gibbons RJ, Hunt SA, Jacobs AK, Nishimura R, Ornato JP, Page RL, Riegel B; American Association for Vascular Surgery/Society for Vascular Surgery; Society for Cardiovascular Angiography and Interventions; Society for Vascular Medicine and Biology; Society of Interventional Radiology; ACC/AHA Task Force on Practice Guidelines.

J Vasc Interv Radiol. 2006 Sep;17(9):1383-97; quiz 1398. No abstract available.

PMID:
16990459

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