Lani Wu, PhD

Professor

Department of Pharmaceutical Chemistry

[email protected]

Phone: +1 415 502-3196

1700 4th Street, Rm 408D

UCSF Box 2540

San Francisco, CA 94158

United States

Links

Altschuler & Wu Laboratories UCSF Profiles

Affiliations

What I do

In my lab, I seek to understand design principles of biological systems and how biological networks rewire during disease progression. I bring to my biology research a blend of experimental science, engineering, and mathematics. Projects in my lab integrate advance technology, experiment, machine-learning based analysis and data-driven mathematical modeling.

Departmental research area

computational biology and chemistry

chemical biology and medicinal chemistry

protein and cellular engineering

My research expertise

systems biology, cell signaling, cell polarity, collective cell behaviors, Cancer Biology, Drug Discovery, computer vision, image analysis, mathematics

Professional background

Biography

Dr. Lani Wu is interested in discovering principles underlying cellular individuality, the emergence of collective cellular behaviors, and the evolution of drug resistance. She also applies the high-throughput technology developed by her laboratory to diverse applications, including mapping paths of signal transduction and accelerating drug discovery. Prior to arriving at UCSF, Dr. Wu has worked at the UT Southwestern, Harvard University, Rosetta Informatics, Microsoft, and Princeton University.

Research keywords

Neutrophils
Alprostadil
Cyclin-Dependent Kinase Inhibitor p21
cdc42 GTP-Binding Protein, Saccharomyces cerevisiae
Heterografts
Drug Discovery
doxorubicin
Biological Phenomena
Cell Polarity
Proto-Oncogene Proteins c-bcl-6
Protein Kinases
Ubiquitin-Protein Ligases
Fluorescence Microscopy
cell biology
Receptor Cross-Talk

News

Publications

Sun X, Wu LF, Altschuler SJ, Hata AN. Targeting therapy-persistent residual disease. Nat Cancer. 2024 Sep; 5(9):1298-1304.

Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun. 2024 Jun 19; 15(1):5230.

Kumbier K, Roth M, Li Z, Lazzari-Dean J, Waters C, Hammerlindl S, Rinaldi C, Huang P, Korobeynikov VA, New York Genome Center ALS Consortium, Phatnani H, Shneider N, Jacobson MP, Wu LF, Altschuler SJ. Identifying FUS amyotrophic lateral sclerosis disease signatures in patient dermal fibroblasts. Dev Cell. 2024 Aug 19; 59(16):2134-2142.e6.

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 10 31; 42(10):113260.

Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. Elife. 2023 07 26; 12.

Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. bioRxiv. 2023 May 30.

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 05 30; 42(5):112447.

Heinrich L, Kumbier K, Li L, Altschuler SJ, Wu LF. Selection of Optimal Cell Lines for High-Content Phenotypic Screening. ACS Chem Biol. 2023 04 21; 18(4):679-685.

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).

Heinrich L, Kumbier K, Li L, Altschuler SP, Wu LF. Selection of optimal cell lines for high-content phenotypic screening. bioRxiv. 2023 Jan 12.

Bao F, Deng Y, Wan S, Shen SQ, Wang B, Dai Q, Altschuler SJ, Wu LF. Publisher Correction: Integrative spatial analysis of cell morphologies and transcriptional states with MUSE. Nat Biotechnol. 2022 Aug; 40(8):1295.

Bao F, Deng Y, Wan S, Shen SQ, Wang B, Dai Q, Altschuler SJ, Wu LF. Integrative spatial analysis of cell morphologies and transcriptional states with MUSE. Nat Biotechnol. 2022 08; 40(8):1200-1209.

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. Sci Adv. 2022 01 28; 8(4):eabi7711.

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. Commun Biol. 2022 01 27; 5(1):99.

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 Genet. 2021 11; 17(11):e1009857.

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. Dev Cell. 2021 02 08; 56(3):356-365.e9.

Kochanowski K, Sander T, Link H, Chang J, Altschuler SJ, Wu LF. Systematic alteration of in vitro metabolic environments reveals empirical growth relationships in cancer cell phenotypes. Cell Rep. 2021 01 19; 34(3):108647.

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 Syst. 2020 07 22; 11(1):86-94.e5.

Sanman LE, Chen IW, Bieber JM, Thorne CA, Wu LF, Altschuler SJ. Generation and Quantitative Imaging of Enteroid Monolayers. Methods Mol Biol. 2020; 2171:99-113.

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. Sci Data. 2019 10 31; 6(1):253.

Hsu CH, Altschuler SJ, Wu LF. Patterns of Early p21 Dynamics Determine Proliferation-Senescence Cell Fate after Chemotherapy. Cell. 2019 07 11; 178(2):361-373.e12.

Deng Y, Bao F, Dai Q, Wu LF, Altschuler SJ. Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning. Nat Methods. 2019 04; 16(4):311-314.

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. 2018 08; 20(8):826-837.

Curtis A. Thorne, Ina W. Chen, Laura E. Sanman, Melanie H. Cobb, Lani F. Wu, Steven J. Altschuler. Planar Enteroids Reveal an Autonomous WNT And BMP Circuit Controlling Intestinal Epithelial Growth and Organization. The FASEB Journal. 2018 Apr 1; 32:659.14-659.14.

Kochanowski K, Morinishi L, Altschuler S, Wu L. Drug persistence - from antibiotics to cancer therapies. Curr Opin Syst Biol. 2018 Aug; 10:1-8.

Thurley K, Wu LF, Altschuler SJ. Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions. Cell Syst. 2018 Mar 28; 6(3):355-367.e5.

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. Dev Cell. 2018 03 12; 44(5):624-633.e4.

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 Oct; 14(10):967-970.

Dhruba Deb, Satwik Rajaram, Jill E. Larsen, Patrick P. Dospoy, Rossella Marullo, Longshan Li, Kimberley Avila, Leandro Cerchietti, John D. Minna, Lani F. Wu, Steven J. Altschuler. Abstract 3950: A novel combination therapy targeting BCL6 and phospho-STAT3 defeats intratumor heterogeneity in a subset of non-small cell lung cancers. Tumor Biology. 2017 Jul 1; 3950-3950.

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 Res. 2017 06 01; 77(11):3070-3081.

Zhang ER, Liu S, Wu LF, Altschuler SJ, Cobb MH. Chemoattractant concentration-dependent tuning of ERK signaling dynamics in migrating neutrophils. Sci Signal. 2016 12 13; 9(458):ra122.

Coster AD, Thorne CA, Wu LF, Altschuler SJ. Examining Crosstalk among Transforming Growth Factor β, Bone Morphogenetic Protein, and Wnt Pathways. J Biol Chem. 2017 Jan 06; 292(1):244-250.

Deng Y, Altschuler SJ, Wu LF. PHOCOS: inferring multi-feature phenotypic crosstalk networks. Bioinformatics. 2016 06 15; 32(12):i44-i51.

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 06; 14(6):e1002474.

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.

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. Nat Biotechnol. 2016 Jan; 34(1):70-77.

Julie Wu, Anne Pipathsouk, A Keizer-Gunnink, Wynand Alkema, Fabrizia Fusetti, Shanshan Liu, Steve Atschuler, Lani Wu, Arjan Kortholt, Orion Weiner. Abstract B48: Homer3 regulates the establishment of neutrophil polarity. Immunometabolism and Immunoregulation. 2015 Oct 1; b48-b48.

Langen M, Agi E, Altschuler DJ, Wu LF, Altschuler SJ, Hiesinger PR. The Developmental Rules of Neural Superposition in Drosophila. Cell. 2015 Jul 02; 162(1):120-33.

Wu J, Pipathsouk A, Keizer-Gunnink A, Fusetti F, Alkema W, Liu S, Altschuler S, Wu L, Kortholt A, Weiner OD. Homer3 regulates the establishment of neutrophil polarity. Mol Biol Cell. 2015 May 01; 26(9):1629-39.

Steininger RJ, Rajaram S, Girard L, Minna JD, Wu LF, Altschuler SJ. On comparing heterogeneity across biomarkers. Cytometry A. 2015 Jun; 87(6):558-67.

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. 2015 Jan; 11(1):58-63.

Agi E, Langen M, Altschuler SJ, Wu LF, Zimmermann T, Hiesinger PR. The evolution and development of neural superposition. J Neurogenet. 2014 Sep-Dec; 28(3-4):216-32.

Coster AD, Wichaidit C, Rajaram S, Altschuler SJ, Wu LF. A simple image correction method for high-throughput microscopy. Nat Methods. 2014 Jun; 11(6):602.

Benjamin Pavie, Satwik Rajaram, Austin Ouyang, Jason M. Altschuler, Robert J. Steininger III, Lani F. Wu, Steven J. Altschuler. Rapid Analysis and Exploration of Fluorescence Microscopy Images. Journal of Visualized Experiments. 2014 Mar 19; (85).

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 Mar 19; (85).

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.

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.

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.

Dylan J Altschuler, Steven J Altschuler, Sigurd B Angenent, Lani F Wu. The zoo of solitons for curve shortening in On the occasion of Richard Hamilton's nth birthday. Nonlinearity. 2013 May 1; 26(5):1189.

Dhruba Deb, Satwik Rajaram, Jill Larsen, John Minna, Lani Wu, Steven Altschuler. Abstract 5226: Understanding single cell variability in oncogene induced pathway aberration in lung cancer. Molecular and Cellular Biology. 2013 Apr 15; 5226-5226.

Rajaram S, Pavie B, Wu LF, Altschuler SJ. PhenoRipper: software for rapidly profiling microscopy images. Nat Methods. 2012 Jun 28; 9(7):635-7.

Rajaram S, Pavie B, Hac NE, Altschuler SJ, Wu LF. SimuCell: a flexible framework for creating synthetic microscopy images. Nat Methods. 2012 Jun 28; 9(7):634-5.

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.

Steven Altschuler, Sigurd Angenent, Sasha Jilkine, Lani Wu. Denial, acceptance, and loss of cell polarization for a stochastic model of positive feedback. The FASEB Journal. 2012 Apr 1; 26:468.2-468.2.

Lani Wu, Chin-Jen Ku, Yanqin Wang, Orion Weiner, Steven Altschuler. Dynamic information flow during neutrophil polarization. The FASEB Journal. 2012 Apr 1; 26:345.1-345.1.

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.

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.

Jilkine A, Angenent SB, Wu LF, Altschuler SJ. A density-dependent switch drives stochastic clustering and polarization of signaling molecules. PLoS Comput Biol. 2011 Nov; 7(11):e1002271.

Altschuler SJ, Wu LF. Cellular heterogeneity: do differences make a difference? Cell. 2010 May 14; 141(4):559-63.

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.

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 01; 14-17:1029-1032.

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 02; 187(3):375-84.

Loo LH, Lin HJ, Steininger RJ, Wang Y, Wu LF, Altschuler SJ. An approach for extensibly profiling the molecular states of cellular subpopulations. Nat Methods. 2009 Oct; 6(10):759-65.

Artyukhin AB, Wu LF, Altschuler SJ. Only two ways to achieve perfection. Cell. 2009 Aug 21; 138(4):619-21.

Slack MD, Martinez ED, Wu LF, Altschuler SJ. Characterizing heterogeneous cellular responses to perturbations. Proc Natl Acad Sci U S A. 2008 Dec 09; 105(49):19306-11.

Altschuler SJ, Angenent SB, Wang Y, Wu LF. On the spontaneous emergence of cell polarity. Nature. 2008 Aug 14; 454(7206):886-9.

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.

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.

Loo LH, Wu LF, Altschuler SJ. Image-based multivariate profiling of drug responses from single cells. Nat Methods. 2007 May; 4(5):445-53.

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.

Loo, L.H., Wu, L., Altschuler, S.J.. 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.

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.

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.

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.

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.

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.

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.

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

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

Acero, A., Altschuler S.J., Wu L.F . Proceedings of the ICSLP. Speech/Noise Separation Using Two Microphones and a VQ Model of Speech Signals. 2000.

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.. 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.

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

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.