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Items: 45

1.

Patterns of Early p21 Dynamics Determine Proliferation-Senescence Cell Fate after Chemotherapy.

Hsu CH, Altschuler SJ, Wu LF.

Cell. 2019 Jun 7. pii: S0092-8674(19)30612-9. doi: 10.1016/j.cell.2019.05.041. [Epub ahead of print]

PMID:
31204100
2.

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.

Deng Y, Bao F, Dai Q, Wu LF, Altschuler SJ.

Nat Methods. 2019 Apr;16(4):311-314. doi: 10.1038/s41592-019-0353-7. Epub 2019 Mar 18.

PMID:
30886411
3.

Telomerase-Mediated Strategy for Overcoming Non-Small Cell Lung Cancer Targeted Therapy and Chemotherapy Resistance.

Mender I, LaRanger R, Luitel K, Peyton M, Girard L, Lai TP, Batten K, Cornelius C, Dalvi MP, Ramirez M, Du W, Wu LF, Altschuler SJ, Brekken R, Martinez ED, Minna JD, Wright WE, Shay JW.

Neoplasia. 2018 Aug;20(8):826-837. doi: 10.1016/j.neo.2018.06.002. Epub 2018 Jul 6.

4.

Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions.

Thurley K, Wu LF, Altschuler SJ.

Cell Syst. 2018 Mar 28;6(3):355-367.e5. doi: 10.1016/j.cels.2018.01.016. Epub 2018 Mar 7.

5.

Enteroid Monolayers Reveal an Autonomous WNT and BMP Circuit Controlling Intestinal Epithelial Growth and Organization.

Thorne CA, Chen IW, Sanman LE, Cobb MH, Wu LF, Altschuler SJ.

Dev Cell. 2018 Mar 12;44(5):624-633.e4. doi: 10.1016/j.devcel.2018.01.024. Epub 2018 Mar 1.

6.

Sampling strategies to capture single-cell heterogeneity.

Rajaram S, Heinrich LE, Gordan JD, Avva J, Bonness KM, Witkiewicz AK, Malter JS, Atreya CE, Warren RS, Wu LF, Altschuler SJ.

Nat Methods. 2017 Oct;14(10):967-970. doi: 10.1038/nmeth.4427. Epub 2017 Sep 4.

7.

Combination Therapy Targeting BCL6 and Phospho-STAT3 Defeats Intratumor Heterogeneity in a Subset of Non-Small Cell Lung Cancers.

Deb D, Rajaram S, Larsen JE, Dospoy PD, Marullo R, Li LS, Avila K, Xue F, Cerchietti L, Minna JD, Altschuler SJ, Wu LF.

Cancer Res. 2017 Jun 1;77(11):3070-3081. doi: 10.1158/0008-5472.CAN-15-3052. Epub 2017 Apr 4.

8.

Chemoattractant concentration-dependent tuning of ERK signaling dynamics in migrating neutrophils.

Zhang ER, Liu S, Wu LF, Altschuler SJ, Cobb MH.

Sci Signal. 2016 Dec 13;9(458):ra122.

9.

Examining Crosstalk among Transforming Growth Factor β, Bone Morphogenetic Protein, and Wnt Pathways.

Coster AD, Thorne CA, Wu LF, Altschuler SJ.

J Biol Chem. 2017 Jan 6;292(1):244-250. doi: 10.1074/jbc.M116.759654. Epub 2016 Nov 28.

10.

PHOCOS: inferring multi-feature phenotypic crosstalk networks.

Deng Y, Altschuler SJ, Wu LF.

Bioinformatics. 2016 Jun 15;32(12):i44-i51. doi: 10.1093/bioinformatics/btw251.

11.

Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration.

Diz-Muñoz A, Thurley K, Chintamen S, Altschuler SJ, Wu LF, Fletcher DA, Weiner OD.

PLoS Biol. 2016 Jun 9;14(6):e1002474. doi: 10.1371/journal.pbio.1002474. eCollection 2016 Jun.

12.

Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells.

Ramirez M, Rajaram S, Steininger RJ, Osipchuk D, Roth MA, Morinishi LS, Evans L, Ji W, Hsu CH, Thurley K, Wei S, Zhou A, Koduru PR, Posner BA, Wu LF, Altschuler SJ.

Nat Commun. 2016 Feb 19;7:10690. doi: 10.1038/ncomms10690.

13.

Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines.

Kang J, Hsu CH, Wu Q, Liu S, Coster AD, Posner BA, Altschuler SJ, Wu LF.

Nat Biotechnol. 2016 Jan;34(1):70-77. doi: 10.1038/nbt.3419. Epub 2015 Dec 14.

14.

The Developmental Rules of Neural Superposition in Drosophila.

Langen M, Agi E, Altschuler DJ, Wu LF, Altschuler SJ, Hiesinger PR.

Cell. 2015 Jul 2;162(1):120-33. doi: 10.1016/j.cell.2015.05.055. Epub 2015 Jun 25.

15.

On comparing heterogeneity across biomarkers.

Steininger RJ 3rd, Rajaram S, Girard L, Minna JD, Wu LF, Altschuler SJ.

Cytometry A. 2015 Jun;87(6):558-67. doi: 10.1002/cyto.a.22599. Epub 2014 Nov 25.

16.

GSK-3 modulates cellular responses to a broad spectrum of kinase inhibitors.

Thorne CA, Wichaidit C, Coster AD, Posner BA, Wu LF, Altschuler SJ.

Nat Chem Biol. 2015 Jan;11(1):58-63. doi: 10.1038/nchembio.1690. Epub 2014 Nov 17.

17.

The evolution and development of neural superposition.

Agi E, Langen M, Altschuler SJ, Wu LF, Zimmermann T, Hiesinger PR.

J Neurogenet. 2014 Sep-Dec;28(3-4):216-32. doi: 10.3109/01677063.2014.922557. Epub 2014 Jul 8. Review.

18.

A simple image correction method for high-throughput microscopy.

Coster AD, Wichaidit C, Rajaram S, Altschuler SJ, Wu LF.

Nat Methods. 2014 Jun;11(6):602. doi: 10.1038/nmeth.2971. No abstract available.

19.

Rapid analysis and exploration of fluorescence microscopy images.

Pavie B, Rajaram S, Ouyang A, Altschuler JM, Steininger RJ 3rd, Wu LF, Altschuler SJ.

J Vis Exp. 2014 Mar 19;(85). doi: 10.3791/51280.

20.

Identifying network motifs that buffer front-to-back signaling in polarized neutrophils.

Wang Y, Ku CJ, Zhang ER, Artyukhin AB, Weiner OD, Wu LF, Altschuler SJ.

Cell Rep. 2013 May 30;3(5):1607-16. doi: 10.1016/j.celrep.2013.04.009. Epub 2013 May 9.

21.

Envisioning migration: mathematics in both experimental analysis and modeling of cell behavior.

Zhang ER, Wu LF, Altschuler SJ.

Curr Opin Cell Biol. 2013 Oct;25(5):538-42. doi: 10.1016/j.ceb.2013.04.004. Epub 2013 May 6. Review.

22.

PhenoRipper: software for rapidly profiling microscopy images.

Rajaram S, Pavie B, Wu LF, Altschuler SJ.

Nat Methods. 2012 Jun 28;9(7):635-7. doi: 10.1038/nmeth.2097. No abstract available.

23.

SimuCell: a flexible framework for creating synthetic microscopy images.

Rajaram S, Pavie B, Hac NE, Altschuler SJ, Wu LF.

Nat Methods. 2012 Jun 28;9(7):634-5. doi: 10.1038/nmeth.2096. No abstract available.

24.

Network crosstalk dynamically changes during neutrophil polarization.

Ku CJ, Wang Y, Weiner OD, Altschuler SJ, Wu LF.

Cell. 2012 May 25;149(5):1073-83. doi: 10.1016/j.cell.2012.03.044.

25.

Identification of F-actin as the dynamic hub in a microbial-induced GTPase polarity circuit.

Orchard RC, Kittisopikul M, Altschuler SJ, Wu LF, Süel GM, Alto NM.

Cell. 2012 Feb 17;148(4):803-15. doi: 10.1016/j.cell.2011.11.063.

26.

Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration.

Houk AR, Jilkine A, Mejean CO, Boltyanskiy R, Dufresne ER, Angenent SB, Altschuler SJ, Wu LF, Weiner OD.

Cell. 2012 Jan 20;148(1-2):175-88. doi: 10.1016/j.cell.2011.10.050.

27.

A density-dependent switch drives stochastic clustering and polarization of signaling molecules.

Jilkine A, Angenent SB, Wu LF, Altschuler SJ.

PLoS Comput Biol. 2011 Nov;7(11):e1002271. doi: 10.1371/journal.pcbi.1002271. Epub 2011 Nov 10.

28.

ON IDENTIFYING INFORMATION FROM IMAGE-BASED SPATIAL POLARITY PHENOTYPES IN NEUTROPHILS.

Ku CJ, Wang Y, Pavie B, Altschuler SJ, Wu LF.

Proc IEEE Int Symp Biomed Imaging. 2010 Apr 1;14-17:1029-1032.

29.

Cellular heterogeneity: do differences make a difference?

Altschuler SJ, Wu LF.

Cell. 2010 May 14;141(4):559-63. doi: 10.1016/j.cell.2010.04.033.

30.

Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities.

Singh DK, Ku CJ, Wichaidit C, Steininger RJ 3rd, Wu LF, Altschuler SJ.

Mol Syst Biol. 2010 May 11;6:369. doi: 10.1038/msb.2010.22.

31.

Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes.

Loo LH, Lin HJ, Singh DK, Lyons KM, Altschuler SJ, Wu LF.

J Cell Biol. 2009 Nov 2;187(3):375-84. doi: 10.1083/jcb.200904140. Epub 2009 Oct 26.

32.

An approach for extensibly profiling the molecular states of cellular subpopulations.

Loo LH, Lin HJ, Steininger RJ 3rd, Wang Y, Wu LF, Altschuler SJ.

Nat Methods. 2009 Oct;6(10):759-65. doi: 10.1038/nmeth.1375. Epub 2009 Sep 20.

33.

Only two ways to achieve perfection.

Artyukhin AB, Wu LF, Altschuler SJ.

Cell. 2009 Aug 21;138(4):619-21. doi: 10.1016/j.cell.2009.08.010.

34.

Characterizing heterogeneous cellular responses to perturbations.

Slack MD, Martinez ED, Wu LF, Altschuler SJ.

Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19306-11. doi: 10.1073/pnas.0807038105. Epub 2008 Dec 3.

35.

On the spontaneous emergence of cell polarity.

Altschuler SJ, Angenent SB, Wang Y, Wu LF.

Nature. 2008 Aug 14;454(7206):886-9. doi: 10.1038/nature07119.

36.

An actin-based wave generator organizes cell motility.

Weiner OD, Marganski WA, Wu LF, Altschuler SJ, Kirschner MW.

PLoS Biol. 2007 Sep;5(9):e221.

37.

Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity.

Marco E, Wedlich-Soldner R, Li R, Altschuler SJ, Wu LF.

Cell. 2007 Apr 20;129(2):411-22.

38.

Image-based multivariate profiling of drug responses from single cells.

Loo LH, Wu LF, Altschuler SJ.

Nat Methods. 2007 May;4(5):445-53. Epub 2007 Apr 1.

PMID:
17401369
39.

Systems-level analyses identify extensive coupling among gene expression machines.

Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF.

Mol Syst Biol. 2006;2:2006.0003. Epub 2006 Jan 17.

40.

Genome-scale identification of nucleosome positions in S. cerevisiae.

Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ.

Science. 2005 Jul 22;309(5734):626-30. Epub 2005 Jun 16.

41.

Genomic characterization reveals a simple histone H4 acetylation code.

Dion MF, Altschuler SJ, Wu LF, Rando OJ.

Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5501-6. Epub 2005 Mar 28.

42.

Multidimensional drug profiling by automated microscopy.

Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ.

Science. 2004 Nov 12;306(5699):1194-8.

43.

A panoramic view of yeast noncoding RNA processing.

Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR.

Cell. 2003 Jun 27;113(7):919-33.

44.

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters.

Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ.

Nat Genet. 2002 Jul;31(3):255-65. Epub 2002 Jun 24.

PMID:
12089522
45.

Experimental annotation of the human genome using microarray technology.

Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS.

Nature. 2001 Feb 15;409(6822):922-7.

PMID:
11237012

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