SOFTWARE

Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - an Organism Independent Strategy for Natural Product Discovery. bioRxiv 2023.03.02.530684; doi: https://doi.org/10.1101/2023.03.02.530684
View in: BioRxiv.
 

Kumbier K, Roth M, Li Z, Lazzari-Dean J, Waters C, Huang P, Korobeynikov V, New York Genome Center ALS Consortium, Phatnani H, Shneider N, Jacobson MP, Wu LF, Altschuler SJ. Profiling ALS patient-derived fibroblasts reveals a phenotypic spectrum between FUS-ALS and health.
View in: BioRxiv.
 

Waters CS, Angenent SB, Altschuler SJ, Wu LF. A PINK1 input threshold arises from positive feedback in the PINK1/Parkin mitophagy decision circuit. Cell Rep. 2023 Oct 17;42(10):113260. doi: 10.1016/j.celrep.2023.113260. Epub ahead of print. PMID: 37851575.
View in: PubMed. 
 

Rinaldi C, Waters CS, Li Z, Kumbier K, Rao L, Nichols RJ, Jacobson MP, Wu LF, Altschuler SJ. Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity. Cell Rep. 2023 May 30;42(5):112447. doi: 10.1016/j.celrep.2023.112447. Epub 2023 May 3. PMID: 37141099.
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Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. eLife 12:e87705, 2023 July 23, doi: https://doi.org/10.7554/eLife.87705.View in: PubMed.
 

Heinrich L, Kumbier K, Li L, Altschuler SP, Wu LF. Selection of optimal cell lines for high-content phenotypic screening. ACS Chemical Biology. 2023 March 15 https://doi.org/10.1021/acschembio.2c00878.
See also: Science, Derek Lowe blog In the pipeline
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Stölzel F, Fordham SE, Nandana D, Lin WY, Blair H, Elstob C, Bell HL, Mohr B, Ruhnke L, Kunadt D, Dill C, Allsop D, Piddock R, Soura EN, Park C, Fadly M, Rahman T, Alharbi A, Wobus M, Altmann H, Röllig C, Wagenführ L, Jones GL, Menne T, Jackson GH, Marr HJ, Fitzgibbon J, Onel K, Meggendorfer M, Robinson A, Bziuk Z, Bowes E, Heidenreich O, Haferlach T, Villar S, Ariceta B, Diaz RA, Altschuler SJ, Wu LF, Prosper F, Montesinos P, Martinez-Lopez J, Bornhäuser M, Allan JM. Biallelic TET2 mutations confer sensitivity to 5'-azacitidine in acute myeloid leukemia. JCI Insight. 2023 Jan 24;8(2):e150368. doi: 10.1172/jci.insight.150368. PMID: 36480300.
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Bao F, Deng Y, Wan S, Shen SQ, Wang B, Dai Q, Altschuler SJ, Wu LF. Characterizing tissue composition through combined analysis of single-cell morphologies and transcriptional states. Nature Biotechnology. 2022 Mar 28, doi: 10.1038/s41587-022-01251-z
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Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Science Advances. 2022 Jan 28;8(4):eabi7711. doi: 10.1126/sciadv.abi7711. Epub 2022 Jan 28.
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Bieber JM, Sanman LE, Sun X, Hammerlindl H, Bao F, Roth MA, Koleske ML, Huang L, Aweeka F, Wu LF, Altschuler SJ. Differential toxicity to murine small and large intestinal epithelium induced by oncology drugs. Communications Biology. 2022 Jan 27;5(1):99. doi: 10.1038/s42003-022-03048-x.
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Ji W, Wu LF, Altschuler SJ. Analysis of growth cone extension in standardized coordinates highlights self-organization rules during wiring of the Drosophila visual system. PLoS Genetics. 2021 November 3, 2021. doi:https://doi.org/10.1371/journal.pgen.1009857.
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Sanman LE, Chen IW, Bieber JM, Steri V, Trentesaux C, Hann B, Klein OD,  Wu LF, Altschuler SJ. Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition. Developmental Cell. 2021 Jan 22.  doi:https://doi.org/10.1016/j.devcel.2020.12.020.
View in: Pubmed.
 

Kochanowski K, Sander T, Link H, Chang J, Altschuler SJ, Wu LF. Dissecting the impact of metabolic environment on three common cancer cell phenotypes. Cell Reports. 2021 Jan 19;34(3):108647. doi:https://doi.org/10.1016/j.celrep.2020.108647.
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Morinishi L, Kochanowski K, Levine RL,Wu LF, Altschuler SJ. Loss of TET2 Affects Proliferation and Drug Sensitivity through Altered Dynamics of Cell-State Transitions. Cell Systems. 2020 July;16(4):311-314. DOI:https://doi.org/10.1016/j.cels.2020.06.003.
See also: Science Translational Medicine, Editor's Choice.
View in: PubMed.
 

Sanman LE, Chen IW, Bieber JM, Thorne CA, Wu LF, Altschuler SJ. Generation and Quantitative Imaging of Enteroid Monolayers. Methods in Molecular Biology, volume 2171: Intestinal Stem Cells Methods and Protocols. 2020;2171:99-113. doi: 10.1007/978-1-0716-0747-3_6; PMID: 32705637.
View in: Pubmed.
Full Book: Intestinal Stem Cells, Methods and Protocols.
 

Rajaram S, Roth MA, Malato J, VandenBerg S, Hann B, Atreya CE, Altschuler SJ, Wu LF. A multi-modal data resource for investigating topographic heterogeneity in patient-derived xenograft tumors. Scientific Data. 2019 October 31. ;6(1):253. doi: 10.1038/s41597-019-0225-0.

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Hsu CH, Altschuler SJ, Wu LF. Patterns of Early p21 Dynamics Determine Proliferation-Senescence Cell Fate after Chemotherapy. Cell. 2019 Jun 7. pii: S0092-8674(19)30612-9. doi: 10.1016/j.cell.2019.05.041.
See also: Cell, Preview;  Science Translational Medicine, Editor's Choice;  Nature, News & Views.
View in: PubMed.
 

Deng Y., Bao F., Dai Q., Wu LF, Altschuler SJ. Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning. Nature Methods. 2019 Apr;16(4):311-314. doi: 10.1038/s41592-019-0353-7. Epub 2019 Mar 18.
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Sebag AS, Heinrich L, Schoenauer M, Sebag M, Wu LF, Altschuler SJ. Multi-domain adversarial learning. ICLR’19 - Seventh annual International Conference on Learning Representations, May 2019, New Orleans, United States. 2019, Proc. ICLR. 2019.
View in: Preprint 
Code: GitHub
 

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. Telomerase-Mediated Strategy for Overcoming Non-Small Cell Lung Cancer Targeted Therapy and Chemotherapy Resistance. Neoplasia. Jul 6;20(8):826-837. doi: 10.1016/j.neo.2018.06.002.
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Kochanowski K, Morinishi L, Altschuler SJ, Wu LF. Drug persistence - From antibiotics to cancer therapies. Current Opinion in Systems Biology. 2018 Aug; 10:1-8.
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Thurley K, Wu LF, Altschuler SJ. Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions. Cell Systems. 2018 March 7. DOI: https://doi.org/10.1016/j.cels.2018.01.016.
View in: bioRxiv and PubMed
 

Thorne CA, Chen IW, Sanman LE, Cobb MH, Wu LF, Altschuler SJ; Enteroid Monolayers Reveal an Autonomous WNT and BMP Circuit Controlling Intestinal Epithelial Growth and Organization. Developmental Cell. 2018 Feb 26. pii: S1534-5807(18)30059-5. doi: 10.1016/j.devcel.2018.01.024.
Accompanying Preview. 
View in: PubMed
 

Rajaram S, Heinrich LE, Gordan JD, Avva J, Bonness KM, Witkiewicz AK, Malter JS, Atreya CE, Warren RS, Wu LF, Altschuler SJ. Sampling strategies to capture single-cell heterogeneity. Nat Methods. 2017 Sep 4. doi: 10.1038/nmeth.4427. PMID: 28869755. 
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Deb D, Rajaram S, Larsen JE, Dospoy PD, Marullo R, Li LS, Avila K, Xue F, Cerchietti L, Minna JD, Altschuler SJ, Wu LF.  Combination Therapy Targeting BCL6 and Phospho-STAT3 Defeats Intratumor Heterogeneity in a Subset of Non-Small Cell Lung Cancers. Cancer Research. 2017 Jun 1;77(11):3070-3081. PMID: 28377453
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Zhang ER, Liu S, Wu LF, Altschuler SJ, Cobb MH. Chemoattractant concentration-dependent tuning of ERK signaling dynamics in migrating neutrophils. J Sci Signal. 2016 Dec 13;9(458):ra122
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Coster AD, Thorne CA, Wu LF, Altschuler SJ.  Examining crosstalk among Transforming Growth Factor β, Bone Morphogen Protein, and Wnt pathways. J Biol Chem. 2016 Nov 28. pii: jbc.M116.759654
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Deng Y, Altschuler SJ, Wu LF.  PHOCOS: inferring multi-feature phenotypic crosstalk networks.Bioinformatics (special issue in ISMB 2016 proceedings). 2016 Jun 15;32(12):i44-i51. doi: 10.1093/bioinformatics/btw251. PMID: 27307643
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Diz-Muñoz A, Thurley K, Chintamen S, Altschuler SJ, Wu LF, Fletcher DA, Weiner OD. Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration. PLoS Biol. 2016 Jun 9;14(6):e1002474. doi: 10.1371/journal.pbio.1002474. eCollection 2016 Jun. 
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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. Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells. Nat Commun. 2016 Feb 19;7:10690. doi: 10.1038/ncomms10690. PMCID: PMC4762880.
Accompanying news and views. 
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Kang J, Hsu CH, Wu Q, Liu S, Coster AD, Posner BA, Altschuler SJ, Wu LF. Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines. Nature Biotechnology. 2015 Dec 14;doi: 10.1038/nbt.3419. 
Accompanying article in the news.
View in: PubMed
 

Langen M, Agi E, Altschuler DJ, Wu LF, Altschuler SJ, Hiesinger PR. The Developmental Rules of Neural Superposition in Drosophila. Cell. 2015 Jul 2;162(1):120-133. doi: 10.1016/j.cell.2015.05.055. Epub 2015 Jun 25. 
Accompanying Cell preview article and in the news. 
View in: PubMed
 

Wu J, Pipathsouk A, Keizer-Gunnink A, Fusetti F, Alkema W, Liu S, Altschuler SJ, Wu LF, Kortholt A, Weiner OD.  Homer3 regulates the establishment of neutrophil polarity. Mol Biol Cell. 2015 May 1;26(9):1629-39. doi: 10.1091/mbc.E14-07-1197. Epub 2015 Mar 4. 
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Steininger RJ 3rd, Rajaram S, Girard L, Minna JD, Wu LF, Altschuler SJ.  On comparing heterogeneity across biomarkers. Cytometry part A (special issue on systems microscopy). 2014 Nov 25. doi: 10.1002/cyto.a.22599.
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Thorne CA, Wichaidit C, Coster AD, Posner BA, Wu LF, Altschuler SJ.  GSK-3 modulates cellular responses to a broad spectrum of kinase inhibitors. Nat Chem Biol. 2014 Nov 17. doi: 10.1038/nchembio.1690. 
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Agi E, Langen M, Altschuler SJ, Wu LF, Zimmermann T, Hiesinger PR. The Evolution and Development of Neural Superposition. J Neurogenet. 2014 Jul 8; 1-17. 
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Coster AD, Wichaidit C, Rajaram S, Altschuler SJ, Wu LF. A simple image correction method for high-throughput microscopy. Nature Methods. 2014 May 29; 11(6):602. 
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Pavie B, Rajaram S, Ouyang A, Altschuler JM, Steininger RJ, Wu LF, Altschuler SJ. Rapid analysis and exploration of fluorescence microscopy images. J Vis Exp. 2014; (85). 
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Wang Y, Ku CJ, Zhang ER, Artyukhin AB, Weiner OD, Wu LF, Altschuler SJ. Identifying network motifs that buffer front-to-back signaling in polarized neutrophils. Cell Rep. 2013 May 30; 3(5):1607-16. 
View in: PubMed
 

Zhang ER, Wu LF, Altschuler SJ. Envisioning migration: mathematics in both experimental analysis and modeling of cell behavior. Curr Opin Cell Biol. 2013 Oct; 25(5):538-42. 
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Altschuler D.J., Altschuler S.J., Angenent S.B., Wu L.F. The Zoo of Solitons for Curve Shortening in ℝn. Nonlinearity. 2013; 26(5):1189-1226. 
Videos.
 

Rajaram S, Pavie B, Hac NE, Altschuler SJ, Wu LF. SimuCell: a flexible framework for creating synthetic microscopy images. Nature Methods. 2012 Jul; 9(7):634-5. 
View in: PubMed
 

Rajaram S, Pavie B, Wu LF, Altschuler SJ. PhenoRipper: software for rapidly profiling microscopy images.  Nature Methods. 2012 Jul; 9(7):635-7. 
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Ku CJ, Wang Y, Weiner OD, Altschuler SJ, Wu LF. Network crosstalk dynamically changes during neutrophil polarization. Cell. 2012 May 25; 149(5):1073-83. 
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Orchard RC, Kittisopikul M, Altschuler SJ, Wu LF, Süel GM, Alto NM. Identification of F-actin as the dynamic hub in a microbial-induced GTPase polarity circuit. Cell. 2012 Feb 17; 148(4):803-15.
View in: PubMed
 

Houk AR, Jilkine A, Mejean CO, Boltyanskiy R, Dufresne ER, Angenent SB, Altschuler SJ, Wu LF, Weiner OD. Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration. Cell. 2012 Jan 20; 148(1-2):175-88. 
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Jilkine A, Angenent SB, Wu LF,
Altschuler SJ. A density-dependent switch drives stochastic clustering and polarization of signaling molecules. PLoS Computational Biol. 2011 Nov; 7(11):e1002271. 
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Altschuler SJ, Wu LF. Cellular heterogeneity: do differences make a difference? Cell. 2010 May 14; 141(4):559-63. 
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Singh DK, Ku CJ, Wichaidit C, Steininger RJ, Wu LF, Altschuler SJ. Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Mol Syst Biol. 2010 May 11; 6:369. 
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Ku CJ, Wang Y, Pavie B, Altschuler SJ, Wu LF. On identifying information from image-based spatial polarity phenotypes in neutrophils. Proc IEEE Int Symp Biomed Imaging. 2010 Apr 1; 14-17:1029-1032. 
View in: PubMed
 

Loo LH, Lin HJ, Singh DK, Lyons KM, Altschuler SJ, Wu LF. Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes. J Cell Biol. 2009 Nov 2; 187(3):375-84. 
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Loo LH, Lin HJ, Steininger RJ, Wang Y, Wu LF, Altschuler SJ. An approach for extensibly profiling the molecular states of cellular subpopulations. Nature Methods. 2009 Oct; 6(10):759-65. 
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Artyukhin AB, Wu LF, Altschuler SJ. Only two ways to achieve perfection. Cell. 2009 Aug 21; 138(4):619-21. 
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Slack MD, Martinez ED, Wu LF, Altschuler SJ. Characterizing heterogeneous cellular responses to perturbations. Proc Natl Acad Sci U S A. 2008 Dec 9; 105(49):19306-11. 
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Altschuler SJ, Angenent SB, Wang Y, Wu LF. On the spontaneous emergence of cell polarity. Nature. 2008 Aug 14; 454(7206):886-9.
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Weiner OD, Marganski WA, Wu LF, Altschuler SJ, Kirschner MW. An actin-based wave generator organizes cell motility. PLoS Biol. 2007 Sep; 5(9):e221. 
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Marco E, Wedlich-Soldner R, Li R, Altschuler SJ, Wu LF. Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity. Cell. 2007 Apr 20; 129(2):411-22. 
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Loo LH, Wu LF, Altschuler SJ. Image-based multivariate profiling of drug responses from single cells. Nature Methods. 2007 May; 4(5):445-53. 
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Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol. 2006; 2:2006.0003. 
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Loo, L.H., Wu, L., Altschuler, S.J., 2006; 251-54. Automated Multivariate Profiling of Drug Effects from Fluorescence Microscopy Images. IEEE International Symposium on Biomedical Imaging. 2006; 251-254.
 

Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae. Science. 2005 Jul 22; 309(5734):626-30. 
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Dion MF, Altschuler SJ, Wu LF, Rando OJ. Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci U S A. 2005 Apr 12; 102(15):5501-6. 
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Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ. Multidimensional drug profiling by automated microscopy. Science. 2004 Nov 12; 306(5699):1194-8. 
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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. A panoramic view of yeast noncoding RNA processing. Cell. 2003 Jun 27; 113(7):919-33. 
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Wedlich-Soldner R, Altschuler S, Wu L, Li R. Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase. Science. 2003 Feb 21; 299(5610):1231-5. 
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Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002 Jul; 31(3):255-65. 
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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. Experimental annotation of the human genome using microarray technology. Nature. 2001 Feb 15; 409(6822):922-7. 
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Acero, A., Altschuler S.J., Wu L.F. Speech/Noise Separation Using Two Microphones and a VQ Model of Speech Signals. Proceedings of the ICSLP. 2000.
 

Altschuler, S.J., Wu, L.F. On deforming confoliations. Journal of Differential Geometry. 2000; 54(1):75-97.
 

Ridgeway, G., Altschuler, S.J. Clustering finite discrete markov chains. Proceedings of the Section on Physical and Engineering Sciences. 1998; 228-229.
 

Altschuler, S.J., Kim, W. Generating Signal Processing Software. Proceedings of the ICSR5. 1998.
 

Altschuler, S.J., Angenet, S., Giga, Y. Mean curvature flow through singularities for surfaces of rotation. Journal of Geometric Analysis. 1995; 5(3):293-358.
 

Altschuler, S.J. A geometric heat flow for one-forms on three dimensional manifolds. Illinois Journal of Mathematics. 1995; 39(1):98-118.
 

Altschuler, S.J., Wu, L.F. Translating surfaces of the non-parametric mean curvature flow with prescribed contact angle. Calc. Var. Partial Diff. Eq. 1994; 2(1):101-111.
 

Wu, L.F. The Ricci Flow on complete R2. Comm. in Analysis and Geometry. 1993; 1:439-472.
 

Wu, L.F. A new result for the porous medium equation on R2 derived from the Ricci flow. Bulletin of the American Mathematical Society. 1993; 28:90-94.
 

Altschuler, S.J., Wu, L.F. Convergence to translating solitons for a class of quasilinear parabolic boundary problems. Math. Annalen. 1993; 295:761-765.
 

Altschuler, S.J., Grayson, M. Shortening space curves and flow through singularities. Journal of Differential Geometry. 1992; 35(2):283-298.
 

Altschuler, S.J. Singularities for the curve shortening flow for space curves. Journal of Differential Geometry. 1991; 34(2):491-514.
 

Wu, L.F. The Ricci Flow on 2-orbifolds with positive curvature. Journal of Differential Geometry. 1991; 33:575-596.
 

Chow, B., Wu, L.F. The Ricci Flow on compact 2-orbifolds with curvature negative somewhere. Communications on Pure and Applied Mathematics. 1991; 44:275-286.