Publication

Published Articles - Invited Book Chapters - Google Scholar Publications

PUBLISHED ARTICLES 

* indicates joint first authorship

152. Fang Z, Monteiro VS, Renauer PA, Shang X, Suzuki K, Ling X, Bai M, Xiang Y, Levchenko A, Booth CJ, Lucas C, Chen S. Polyvalent mRNA vaccination elicited potent immune response to monkeypox virus surface antigens. Cell Research. May 2023; 33(5): 407-410; DOI: 10.1038/s41422-023-00792-5

151. Vanaja K, Apostolidi M, Levchenko A, Rinehart J. Non-metabolic regulatory functions of nuclear pyruvate kinase M2 induce a MAPK mediated phenotypic switch in invasive cancers. Cancer Research. April 4 2023; 83(7_Supplement): 293; DOI: 10.1158/1538-7445.AM2023-293

150. Levchenko A. Genetic diseases: How the noise fits in. Current Biology. March 27 2023; 33(6): R228-R230; DOI: 10.1016/j.cub.2023.02.052

149. Greaney AM, Raredon MSBR, Kochugaeva MP, Niklason LE, Levchenko A. SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection. Iscience. March 17 2023; 26(3): 106175; DOI: 10.1016/j.isci.2023.106175

148. Feinberg AP*, Levchenko A*. Epigenetics as a mediator of plasticity in cancer. Science. Feburary 10 2023; 379(6632): eaaw3835; DOI: 10.1126/science.aaw3835

147. Afzal J, Suhail Y, Chang H, Hubbi ME, Hamidzadeh A, Goyal R, Liu Y, Sun P, Nicoli S, Dang CV, Levchenko A. Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells. Cell Systems. December 21 2022; 13(12): 1048-1064; DOI: 10.1016/j.cels.2022.11.003

146. Li X, Shim S, Hardin KR, Vanaja KG, Song H, Levchenko A, Ming G, Zheng JQ. Signal amplification in growth cone gradient sensing by a double negative feedback loop among PTEN, PI(3,4,5)P3 and actomyosin. Molecular and Cellular Neuroscience. December 1 2022; 123: 103772; DOI: 10.1016/j.mcn.2022.103772

145. Scanlon VM, Thompson EN, Lawton BR, Kochugaeva M, Ta K, Mayday MY, Xavier-Ferrucio J, Kang E, Eskow NM, Lu YC, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel ST, Reed FE, Pena-Carmona G, Ubbelohde A, Lee JP, Boobalan S, Oppong Y, Anderson R, Maynard C, Sahirul Km Lajeune C, Ivathraya V, Addy R, Sanchez P, Holbrrok C, Ho ATV, Duncan JS, Blau HM, Levchenko A, Krause DS. Multiparameter analysis of timelapse imaging reveals kinetics of megakaryocytic erythroid progenitor clonal expansion and differentiation. Scientific Reports. September 28 2022; 12: 16218; DOI: 10.1038/s41598-022-19013-x

144. Lee SH, Hou JC, Hamidzadeh A, Yousafzai MS, Ajeti V, Chang H, Odde DJ, Murrell M, Levchenko A. A molecular clock controls periodically driven cell migration in confined spaces. Cell Systems. June 8 2022; 13(7): 514-529; DOI: 10.1016/j.cels.2022.05.005

143. Scanlon V, Thompson E, Lawton BR, Kochugaeva M, Ta K, Mayday MY, Xavier-Ferrucio J, Kang E, Eskow N, Lu YC, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel S, Reed F, Carmona GP, Ubbelohde Am Lee JP, Boobalan S, Oppong Y, Aderson R, Maynard C, Sahirul K, Lajeune C, Ivathraya V, Addy T, Sanchez P, Holbrook C, Ho ATV, Duncan JS, Blau H, Levchenko A, Krause DS. Time-lapse imaging reveals kinetics of megakaryocytic-erythroid progenitor self-renewal and differentiation. Research Square. May 19 2022; DOI: 10.21203/rs.3.rs-1632074/v1

142. LaCroix R, Lin B, Kang TY, Levchenko A. Complex effects of kinase localization revealed by compartment-specific regulation of protein kinase A activity. Elife. Feburary 24 2022; 11: 3e66869; DOI: 10.7554/eLife.66869

141. Scanlon VM, Kochugaeva M, Lawton BM, Xavier-Ferrucio J, Kang E, Eskow NM, Lu Y, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel SM, Reed F, Pena-Carmona G, Ubbelohde A, Lee JP, Boobalan S, Oppong Y, Anderson R, Maynard C, Sahirul K, Lajeune C, Ivathraya V, Addy T, Sanchez P, Holbrook C, Ho ATV, Blau HM, Levchenko A, Krause DS. Single-cell tracking by time lapse imaging confirms thrombopoietin promotes megakaryocytic-erythroid progenitor self renewal, but does not instruct lineage commitment. Blood. November 15 2021; 138(S1): 3270-3270; DOI: 10.1182/blood-2021-154360

140. Wagner GP, Kshitiz, Dighe A, Levchenko A. The coevolution of placentation and cancer. Annual Review of Animal Biosciences. November 15 2021; 10: 1; DOI: 10.1146/annurev-animal-020420-031544

139. Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cazares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Reports. July 20 2021; 36(3): 109416; DOI: 10.1016/j.celrep.2021.109416

138. Mukherjee R, Vanaja K, Boyer JA, Gadal S, Solomon H, Chandarlapaty S, Levchenko A, Rosen N. Regulation of PTEN translation by PI3K signaling maintains pathway homeostasis. Molecular Cell. February 18 2021; 81(4): 708-723.e5; DOI: 10.1016/j.molcel.2021.01.033

137. Vanaja K, Mukherjee R, Rosen N, Levchenko A. A computational model for the PI3K/Akt/mTOR pathway predicts PTEN as a negative feedback loop. Cancer Res. August 15 2020 (80) (16 Supplement) 5506; DOI: 10.1158/1538-7445.AM2020-5506

136. Ozen M, Lipniacki T, Levchenko A, Esmamian ES, Abdi A. Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods. Integrative Biology. May 2020; 12(5):122–138. doi:10.1093/intbio/zyaa009

135. Keyes J, Ganesan A, Molinar-Inglis O, Hamidzadeh A, Ling M, Trejo J, Levchenko A, Zhang J. Signaling Diversity Enabled by Rap1 and cAMP/PKA-Regulated Plasma Membrane ERK with Distinct Temporal Dynamics. The FASEB Journal. 2020; 34(S1):1-1. doi:10.1096/fasebj.2020.34.s1.00680

134. Kshitiz, Afzal J, Maziarz JD, Hamidzadeh A, Liang C, Erkenbrack EM, Kim HN, Haeger JD, Pfarrer C, Hoang T, Ott T, Spencer T, Pavličev M, Antczak DF, Levchenko A, Wagner GP. Evolution of placental invasion and cancer metastasis are causally linked. Nat Ecol Evol. 2019 Dec;3(12):1743-1753. doi: 10.1038/s41559-019-1046-4. Epub 2019 Nov 25. Erratum in: Nat Ecol Evol. 2020 Jan 16;:.

133. Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. Sci Adv. 2019 Dec 4;5(12):eaaw3851. doi: 10.1126/sciadv.aaw3851. eCollection 2019 Dec.

132. Kang TY, Bocci F, Jolly MK, Levine H, Onuchic JN, Levchenko A. Pericytes enable effective angiogenesis in the presence of proinflammatory signals. Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23551-23561. doi: 10.1073/pnas.1913373116. Epub 2019 Nov 4.

131. Suhail Y, Cain MP, Vanaja K, Kurywchak PA, Levchenko A, Kalluri R, Kshitiz. Systems Biology of Cancer Metastasis. Cell Syst. 2019 Aug 28;9(2):109-127. doi: 10.1016/j.cels.2019.07.003. Review.

130. Park J, Kim DH, Shah SR, Kim HN, Kshitiz, Kim P, Quiñones-Hinojosa A, Levchenko A. Switch-like enhancement of epithelial-mesenchymal transition by YAP through feedback regulation of WT1 and Rho-family GTPases. Nat Commun. 2019 Jun 26;10(1):2797. doi: 10.1038/s41467-019-10729-5.

129. Kshitiz, Ellison DD, Suhail Y, Afzal J, Woo L, Kilic O, Spees J, Levchenko A. Dynamic secretome of bone marrow-derived stromal cells reveals a cardioprotective biochemical cocktail. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14374-14383. doi: 10.1073/pnas.1902598116. Epub 2019 Jun 25.

128. Kang TY, Ellison D, Lee SH, Ewald AJ, Levchenko A. 3D Analysis of Multi-cellular Responses to Chemoattractant Gradients. J Vis Exp. 2019 May 24;(147). doi: 10.3791/59226.

127. Kilic O, Yoon A, Shah SR, Yong HM, Ruiz-Valls A, Chang H, Panettieri RA Jr, Liggett SB, Quiñones-Hinojosa A, An SS, Levchenko A. A microphysiological model of the bronchial airways reveals the interplay of mechanical and biochemical signals in bronchospasm. Nat Biomed Eng. 2019 Jul;3(7):532-544. doi: 10.1038/s41551-019-0366-7. Epub 2019 Mar 11.

126. Chu EK, Kilic O, Cho H, Groisman A, Levchenko A. Self-induced mechanical stress can trigger biofilm formation in uropathogenic Escherichia coli. Nat Commun. 2018 Oct 5;9(1):4087. doi: 10.1038/s41467-018-06552-z.

125. Vanaja KG, Timp W, Feinberg AP, Levchenko A. A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network. Mol Cell. 2018 Oct 4;72(1):60-70.e3. doi: 10.1016/j.molcel.2018.08.025. Epub 2018 Sep 20.

124. Kim DH, Ewald AJ, Park J, Kshitiz, Kwak M, Gray RS, Su CY, Seo J, An SS, Levchenko A. Biomechanical interplay between anisotropic re-organization of cells and the surrounding matrix underlies transition to invasive cancer spread. Sci Rep. 2018 Sep 21;8(1):14210. doi: 10.1038/s41598-018-32010-3.

123. Smirnova L, Kleinstreuer N, Corvi R, Levchenko A, Fitzpatrick SC, Hartung T. 3S - Systematic, systemic, and systems biology and toxicology. ALTEX. 2018;35(2):139-162. doi: 10.14573/altex.1804051.

122. Park J, Kim DH, Levchenko A. Topotaxis: A New Mechanism of Directed Cell Migration in Topographic ECM Gradients. Biophys J. 2018 Mar 27;114(6):1257-1263. doi: 10.1016/j.bpj.2017.11.3813. Review.

121. Shah SR, David JM, Tippens ND, Mohyeldin A, Martinez-Gutierrez JC, Ganaha S, Schiapparelli P, Hamilton DH, Palena C, Levchenko A, Quiñones-Hinojosa A. Brachyury-YAP Regulatory Axis Drives Stemness and Growth in Cancer. Cell Rep. 2017 Oct 10;21(2):495-507. doi: 10.1016/j.celrep.2017.09.057

120. Park J, Holmes WR, Lee SH, Kim HN, Kim DH, Kwak MK, Wang CJ, Edelstein-Keshet L, Levchenko A. Mechanochemical feedback underlies coexistence of qualitatively distinct cell polarity patterns within diverse cell populations. Proc Natl Acad Sci U S A.  2017 Jul 11;114(28):E5750-E5759. doi: 10.1073/pnas.1700054114

119. Nishimura S, Mishra-Gorur K, Park J, Surovtseva YV, Sebti SM, Levchenko A, Louvi A, Gunel M. Combined HMG-COA reductase and prenylation inhibition in treatment of CCM. Proc Natl Acad Sci U S A . 2017 May 12. pii: 201702942. doi: 10.1073/pnas.1702942114.

118. Holmes WR, Park J, Levchenko A, Edelstein-Keshet L. A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns. PLoS Comput Biol. 2017 May 4;13(5):e1005524.

117. Habibi I, Cheong R, Lipniacki T, Levchenko A, Emamian ES, Abdi A.. Computation and measurement of cell decision making errors using single cell data. PLoS Comput Biol. 2017 Apr 5;13(4):e1005436. doi: 10.1371/journal.pcbi.1005436.

116. Kilic O, Pamies D, Lavell E, Schiapparelli P, Feng Y, Hartung T, Bal-Price A, Hogberg HT, Quinones-Hinojosa A, Guerrero-Cazares H, Levchenko A. Brain-on-a-chip model enables analysis of human neuronal differentiation and chemotaxis. Lab Chip. 2016 Oct 18;16(21):4152-4162.

115. Conlon P, Gelin-Licht R, Ganesan A, Zhang J, Levchenko A. Single-cell dynamics and variability of MAPK activity in a yeast differentiation pathway. Proc Natl Acad Sci U S A. (2016) Sep 20. pii: 201610081

114. Foxman EF, Storer JA, Vanaja K, Levchenko A, Iwasaki A. Two interferon-independent double-stranded RNA-induced host defense strategies suppress the common cold virus at warm temperature. Proc Natl Acad Sci U S A. (2016) Jul 11. pii: 201601942.

113. Smith CL, Kilic O, Schiapparelli P, Guerrero-Cazares H, Kim DH, Sedora-Roman NI, Gupta S, O’Donnell T, Chaichana KL, Rodriguez FJ, Abbadi S, Park J, Quiñones-Hinojosa A, Levchenko A. Migration Phenotype of Brain-Cancer Cells Predicts Patient Outcomes. Cell Rep. (2016) Jun 9. pii: S2211-1247(16)30625-8

112. Smith T, Fancher S, Levchenko A, Nemenman I, Mugler A. Role of spatial averaging in multicellular gradient sensing. Phys Biol. (2016) May 20;13(3):035004.

111. Park J, Kim DH, Kim HN, Wang CJ, Kwak MK, Hur E, Suh KY, An SS, Levchenko A. Directed migration of cancer cells guided by the graded texture of the underlying matrix. Nat Ma​ter (2016) Mar 14

110. Noren DP, Chou WH, Lee SH, Qutub AA, Warmflash A, Wagner DS, Popel AS, Levchenko A. Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses. Sci Signal (2016) Feb 23;9(416):ra20

109. Molitoris JM, Paliwal S, Sekar RB, Blake R, Park J, Trayanova NA, Tung L, Levchenko A. Precisely parameterized experimental and computational models of tissue organization. Integr Biol (Camb) (2016) Feb;8(2):230-42.

108.  Ellison D, Mugler A, Brennan MD, Lee SH, Huebner RJ, Shamir ER, Woo LA, Kim J, Amar P, Nemenman I, Ewald AJ, Levchenko A.Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. Proc Natl Acad Sci U S A (2016) Feb 9;113(6):E679-88. 

107. Mugler A, Levchenko A, Nemenman. Limits to the precision of gradient sensing with spatial communication and temporal integration. Proc Natl Acad Sci U S A (2016) Feb 9;113(6):E689-95. 

106. Yaniv Y, Ganesan A, Yang D, Ziman BD, Lyashkov AE, Levchenko A, Zhang J, Lakatta EG. Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells: Kinetics of PKA activation in heart pacemaker cells. J Mol Cell Cardiol  (2015) Sep;86:168-78

105. Lin B, Levchenko A. Spatial manipulation with microfluidics. Front Bioeng Biotechnol. (2015) Apr 8;3:39.

104. Lin B, Yin T, Wu YI, Inoue T, Levchenko A. Interplay between chemotaxis and contact inhibition of locomotion determines exploratory cell migration. Nat Commun. (2015) Apr 8;6:6619.

103. Kshitiz, Afzal J, Suhail Y, Ahn EH, Goyal R, Hubbi ME, Hussaini Q, Ellison DD, Goyal J, Nacev B, Kim DH, Lee JH, Frankel S, Gray K, Bankoti R, Chien AJ, Levchenko A. Control of the interface between heterotypic cell populations reveals the mechanism of intercellular transfer of signaling proteins. Integr Biol (Camb). (2015) Mar;7(3):364-72.

102. Smith CL, Chaichana KL, Lee YM, Lin B, Stanko KM, O’Donnell T, Gupta S, Shah SR, Wang J, Wijesekera O, Delannoy M, Levchenko A, Quiñones-Hinojosa A. Pre-exposure of human adipose mesenchymal stem cells to soluble factors enhances their homing to brain cancer. Stem Cells Transl Med. (2015) Mar;4(3):239-51.

101. Rhee A, Cheong R, Levchenko A. Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters. Proc Natl Acad Sci U S A. (2014) Dec 2;111(48):17330-5.

100. Zhu M, Feng Y, Dangelmajer S, Guerrero-Cázares H, Chaichana KL, Smith CL, Levchenko A, Lei T, Quiñones-Hinojosa A. Human cerebrospinal fluid regulates proliferation and migration of stem cells through insulin-like growth factor-1. Stem Cells Dev. (2015) Jan 15;24(2):160-71.

99. Luo W, Lin B, Wang Y, Zhong J, O’Meally R, Cole RN, Pandey A, Levchenko A, Semenza GL. PHD3-mediated prolyl hydroxylation of nonmuscle actin impairs polymerization and cell motility. Mol Biol Cell. (2014) Sep 15;25(18):2788-96.

98. Abbadi S, Rodarte JJ, Abutaleb A, Lavell E, Smith CL, Ruff W, Schiller J, Olivi A, Levchenko A, Guerrero-Cazares H, Quinones-Hinojosa A. Glucose-6-phosphatase is a key metabolic regulator of glioblastoma invasion. Mol Cancer Res. (2014) Nov;12(11):1547-59.

97. Levchenko A, Nemenman I. Cellular noise and information transmission. Curr Opin Biotechnol. (2014) Aug;28:156-64.

96. Li Q, Wijesekera O, Salas SJ, Wang JY, Zhu M, Aprhys C, Chaichana KL, Chesler DA, Zhang H, Smith CL, Guerrero-Cazares H, Levchenko A, Quinones-Hinojosa A. Mesenchymal stem cells from human fat engineered to secrete BMP4 are nononcogenic, suppress brain cancer, and prolong survival. Clin Cancer Res. (2014) May 1;20(9):2375-87.

95. Kshitiz, Afzal J, Kim DH, Levchenko A. Concise review: Mechanotransduction via p190RhoGAP regulates a switch between cardiomyogenic and endothelial lineages in adult cardiac progenitors. Stem Cells. (2014) Aug;32(8):1999-2007.

94. Ahn EH, Kim Y, Kshitiz, An SS, Afzal J, Lee S, Kwak M, Suh KY, Kim DH, Levchenko A. Spatial control of adult stem cell fate using nanotopographic cues. Biomaterials. (2014) Mar;35(8):2401-10.

93. Chang H, Levchenko A. Adaptive molecular networks controlling chemotactic migration: dynamic inputs and selection of the network architecture. Philos Trans R Soc Lond B Biol Sci. (2013) Sep 23;368(1629):20130117.

92. Howard JD, Moriarty WF, Park J, Riedy K, Panova IP, Chung CH, Suh KY, Levchenko A, Alani RM. Notch signaling mediates melanoma-endothelial cell communication and melanoma cell migration. Pigment Cell Melanoma Res. (2013) Sep;26(5):697-707.

91. Kundu A, Micholt L, Friedrich S, Rand DR, Bartic C, Braeken D, Levchenko A. Superimposed topographic and chemical cues synergistically guide neurite outgrowth. Lab Chip. (2013) Aug 7;13(15):3070-81.

90. Lin YC, Niewiadomski P, Lin B, Nakamura H, Phua SC, Jiao J, Levchenko A, Inoue T, Rohatgi R, Inoue T. Chemically inducible diffusion trap at cilia reveals molecular sieve-like barrier. Nat Chem Biol. (2013) Jul;9(7):437-43.

89. Hubbi ME, Hu H, Kshitiz, Ahmed I, Levchenko A, Semenza GL. Chaperone-mediated autophagy targets hypoxia-inducible factor-1α (HIF-1α) for lysosomal degradation. J Biol Chem. (2013) Apr 12;288(15):10703-14.

88. Suhail Y, Kshitiz, Lee J, Walker M, Kim DH, Brennan MD, Bader JS, Levchenko A. Modeling intercellular transfer of biomolecules through tunneling nanotubes. Bull Math Biol. (2013) Aug;75(8):1400-16.

87. Hubbi ME, Kshitiz, Gilkes DM, Rey S, Wong CC, Luo W, Kim DH, Dang CV, Levchenko A, Semenza GL. A nontranscriptional role for HIF-1α as a direct inhibitor of DNA replication. Sci Signal. (2013) Feb 12;6(262):ra10.

86. Chaturvedi P, Gilkes DM, Wong CC; Kshitiz, Luo W, Zhang H, Wei H, Takano N, Schito L, Levchenko A, Semenza GL. Hypoxia-inducible factor-dependent breast cancer-mesenchymal stem cell bidirectional signaling promotes metastasis. J Clin Invest. (2013) Jan;123(1):189-205

85. Lin B, Holmes WR, Wang CJ, Ueno T, Harwell A, Edelstein-Keshet L, Inoue T, Levchenko A. Synthetic spatially graded Rac activation drives cell polarization and movement. Proc Natl Acad Sci U S A. (2012) Dec 26;109(52):E3668-77.

84. Brennan MD, Cheong R, Levchenko A. Systems biology. How information theory handles cell signaling and uncertainty. Science. (2012) Oct 19;338(6105):334-5.

83. Kshitiz, Park J, Kim P, Helen W, Engler AJ, Levchenko A, Kim DH. Control of stem cell fate and function by engineering physical microenvironments. Integr Biol (Camb). (2012) Sep;4(9):1008-18. Review.

82. Gorelik M, Orukari I, Wang J, Galpoththawela S, Kim H, Levy M, Gilad AA, Bar-Shir A, Kerr DA, Levchenko A, Bulte JW, Walczak P. Use of MR cell tracking to evaluate targeting of glial precursor cells to inflammatory tissue by exploiting the very late antigen-4 docking receptor. Radiology. (2012) Oct;265(1):175-85.

81. Kim DH, Kshitiz, Smith RR, Kim P, Ahn EH, Kim HN, Marbán E, Suh KY, Levchenko A. Nanopatterned cardiac cell patches promote stem cell niche formation and myocardial regeneration. Integr Biol (Camb). (2012) Sep;4(9):1019-33.

80. Rhee A, Cheong R, Levchenko A. The application of information theory to biochemical signaling systems. Phys Biol. (2012) Aug;9(4):045011

79. Gelin-Licht R, Paliwal S, Conlon P, Levchenko A, Gerst JE. Scp160-dependent mRNA trafficking mediates pheromone gradient sensing and chemotropism in yeast. Cell Reports 1(5):483-94 (2012)

78. Holmes WR, Lin B, Levchenko A, Edelstein-Keshet L. Modelling cell polarization driven by synthetic spatially graded Rac activation. Plos computational Biology ;8(6):e1002366 (2012)

77. Kshitiz, Hubbi ME, Ahn EH, Downey J, Afzal J, Kim DH, Rey S, Chang C, Kundu A, Semenza GL, Abraham RM, Levchenko A. Matrix rigidity controls endothelial differentiation and morphogenesis of cardiac precursors. Science Signaling 5(227):ra41 (2012)

76. Lin B, Levchenko A. Microfluidic technologies for studying synthetic circuits. Curr Opin Chem Biol(2012)

75. Garzon-Muvdi T, Schiapparelli P, ap Rhys C, Guerrero-Cazares H, Smith C, Kim DH, Kone L, Farber H, Lee DY, An SS, Levchenko A, Quiñones-Hinojosa A. Regulation of brain tumor dispersal by NKCC1 through a novel role in focal adhesion regulation. Plos Biology 10(5):e1001320 (2012)

74. Kim DH, Provenzano PP, Smith CL, Levchenko A. Matrix nanotopography as a regulator of cell function. Journal of Cell Biology 197(3):351-60 (2012)

73. Ganesan A, Levchenko A. Principles of model building: an experimentation-aided approach to development of models for signaling networks. Methods Cell Biol 110:1-17 (2012)

72. Bankoti R, Gupta K, Levchenko A, Stäger S. Marginal zone B cells regulate antigen-specific T cell responses during infection. Journal of Immunology 188(8):3961-71 (2012)

71. Wang CJ, Bergmann A, Lin B, Kim K, Levchenko A. Diverse sensitivity thresholds in dynamic signaling responses by social amoebae. Science Signaling 5(213):ra17 (2012)

70. Cromer Berman SM, Kshitiz, Wang CJ, Orukari I, Levchenko A, Bulte JW, Walczak P. Cell motility of neural stem cells is reduced after SPIO-labeling, which is mitigated after exocytosis. Magn Reson Med 29(8):399-408 (2012)

69. Vanaja KG, Feinberg AP, Levchenko A. Stem cell differentiation as a renewal-reward process: predictions and validation in the colonic crypt. Adv Exp Med Biol 736:199-209 (2012)

68. Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. Information transduction capacity of noisy biochemical signaling networks. Science 334(6054):354-8 (2011)

67. Park J, Kim HN, Kim DH, Levchenko A, Suh KY. Quantitative analysis of the combined effect of substrate rigidity and topographic guidance on cell morphology. IEEE Trans Nanobioscience 11(1):28-36 (2011)

66. Kshitiz, Kim DH, Beebe DJ, Levchenko A. Micro- and nanoengineering for stem cell biology: the promise with a caution. Trends in Biotechnology 29(8):399-408 (2011)

65. Hur EM, Yang IH, Kim DH, Byun J, Saijilafu, Xu WL, Nicovich PR, Cheong R, Levchenko A, Thakor N, Zhou FQ. Engineering neuronal growth cones to promote axon regeneration over inhibitory molecules. Proceedings of the National Academy of Science USA 108(12):5057-62 (2011)

64. Stine MJ, Wang CJ, Moriarty WF, Ryu B, Cheong R, Westra WH, Levchenko A, Alani RM. Integration of genotypic and phenotypic screening reveals molecular mediators of melanoma-stromal interaction. Cancer Research 71(7):2433-44 (2011)

63. Compani B, Su T, Chang I, Cheng J, Shah KH, Whisenant T, Dou Y, Bergmann A, Cheong R, Wold B, Bardwell L, Levchenko A, Baldi P, Mjolsness E. A scalable and integrative system for pathway bioinformatics and systems biology. Adv Exp Med Biol 680:523-34 (2010)

62. Cheong R, Paliwal S, Levchenko A. Models at the single cell level. Wiley Interdiscip Rev Syst Biol Med 2(1):34-48 (2010)

61. Cheong, R. and Levchenko, A. Oscillatory signaling processes: the how, the why and the where. Current Opinion in Genetics and Development 20(6):665-9 (2010)

60. Yin, Z., Tao, S.-C., Cheong, R., Zhu, H. and Levchenko, A. An integrated micro-electro-fluidic and protein arraying system for parallel analysis of cell responses to controlled microenvironments. Integrative Biology 2(9): 416 - 423 (2010)

59. Ni, Q.*, Ganesan, A.*, Aye-Han, N.N.*, Gao, X., Levchenko, A., and Zhang, J. Signaling diversity of PKA achieved via a Ca2+-cAMP-PKA oscillatory circuit. Nature Chemical Biology 7(1):34-40 (2010)

58. You, M.-H., Kwak, M. K., Kim, D.H., Kim, K., Levchenko, A., Kim, D.-Y. and Suh, K.Y., Synergistically enhanced osteogenic differentiation of human mesenchymal stem cells by culture on nanostructured surfaces with induction media. Biomacromolecules 11: 1856–1862 (2010)

57. Gupta, K., Kim, D.H., Ellison, D., Smith, C., Kundu, A., Tuan, J., Suh, K.Y. and Levchenko, A. Lab-on-a-chip devices as an emerging platform for stem cell biology. Lab on a Chip 10(16): 2019-2031(2010)

56. Park. J., Kim, D.H., Kim,G., Kim, Y., Choi, E. and Levchenko, A. Simple haptotactic gradient generation within a triangular microfluidic channel. Lab on a Chip 10(16): 2130-2138 (2010)

55. Cheong, R., Paliwal, S. and Levchenko, A. High-content screening in microfluidic devices. Expert Opinion on Drug Discovery 5(8): 715–72 (2010)

54. Melke, P., Sahlin, P., Levchenko, A. and Jönsson, H. A cell-based model for quorum sensing in heterogeneous bacterial colonies. PLoS Computational Biology 6(6): e1000819 (2010)

53. Fan., D., Yin, Z., Cheong, R., Zhu, F.Q., Cammarata, R.C., Chien, C.L. and Levchenko, A. Subcellular-resolution delivery of a cytokine through precisely manipulated nanowires. Nature Nanotechnology 5(7):545-51 (2010)

52. Kim, D.H., Lee, H.J., Lee, Y.K., Nam, J.M. and Levchenko, A. Biomimetic nanopatterns as enabling tools for analysis and control of live cells. Advanced Materials (2010)

  • Featured on the cover and highlighted in the News and Views in the journal

51. Fosbrink, M., Aye-Han, N.-N., Cheong, R., Levchenko, A. and Zhang, J. Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor. Proceedings of the National Academy of Science USA 107(12):5459-64 (2010) 

50. Kim, D.H., Lipke, E., Kim, P., Cheong, R., Edmonds, S., Delannoy, M., Suh., K.Y., Tung, L and Levchenko, Nanoscale cues regulate the structure and function of macroscopic cardiac tissue constructs. Proceedings of the National Academy of Science USA 107(2): 565–570 (2010)  

49. Rey, S., Lee, K.-A., Wang, C.J., Gupta, K., Chen, S., McMillan, A., Bhise, N., Levchenko, A. and Semenza, G.L. Synergistic effect of HIF-1alpha gene therapy and HIF-1-activated bone marrow-derived angiogenic cells in a mouse model of limb ischemia. Proceedings of the National Academy of Science USA 106(48): 20399-20404 (2009)  

48. Kim DH, Wong PK, Park J, Levchenko A, Sun Y. Microengineered platforms for cell mechanobiology. Annual Rev. Biomed. Eng. 11:203-33 (2009)  

47. Wang CJ, Levchenko A. Microfluidics technology for systems biology research. Methods Mol. Biol. 500:203-19 (2009)  

46. Cheong R, Wang CJ, Levchenko A. Using a microfluidic device for high-content analysis of cell signaling. Science Signaling 2(75):pl2 (2009)  

45. Ellison D, Munden A, Levchenko A. Computational model and microfluidic platform for the investigation of paracrine and autocrine signaling in mouse embryonic stem cells. Molecular Biosystems 5(9):1004-1012 (2009)   

44. Kim DH, Han K, Gupta K, Kwon KW, Suh KY, Levchenko A. Mechanosensitivity of fibroblast cell shape and movement to anisotropic substratum topography gradients. Biomaterials 30(29):5433-44 (2009)  

43. Kim DH, Seo CH, Han K, Kwon KW, Levchenko A, Suh KY. Guided Cell Migration on Microtextured Substrates with Variable Local Density and Anisotropy. Advanced Functional Materials 19(10):1579-1586 (2009)

42. Polinkovsky M, Gutierrez E, Levchenko A, Groisman A. Fine temporal control of the medium gas content and acidity and on-chip generation of series of oxygen concentrations for cell cultures. Lab on a Chip 9(8):1073-1084 (2009) 

41. Cheong R, Wang CJ, Levchenko A. High content cell screening in a microfluidic device. Mol & Cell Proteomics 8(3):433-442 (2009)

40. Niu XL, Gupta K, Yang JT, Shamblott MJ, Levchenko A. Physical transfer of membrane and cytoplasmic components as a general mechanism of cell-cell communication. Journal of Cell Science 122(5):600-610 (2009)  

39. Timp W, Levchenko A, Feinberg AP. A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction. Cell Cycle 8(3):383-390 (2009)  

38. Yin ZZ, Noren D, Wang CJ, Hang R, Levchenko A. Analysis of pairwise cell interactions using an integrated dielectrophoretic-microfluidic system. Mol Syst Biol. 4:232 (2008)   

37. Williams JW, Cui XH, Levchenko A, Stevens AM. Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops. Mol Syst Biol. 4:234 (2008) 

36. Hilioti Z, Sabbagh W, Paliwal S, Bergmann A, Goncalves MD, Bardwell L, Levchenko A. Oscillatory phosphorylation of yeast Fus3 MAP kinase controls periodic gene expression and morphogenesis. Current Biology 18(21):1700-1706 (2008) 

35. Paliwal S, Wang CJ, Levchenko A. Pulsing cells: how fast is too fast? HFSP Journal 2(5):251-256 (2008)   

34. Cheong R, Hoffmann A, Levchenko A. Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol. 4:192 (2008) 

33. Cheong R, Levchenko A. Wires in the soup: quantitative models of cell signaling. Trends Cell Biol. 18(3):112-8 (2008) 

32. Joanne Wang C, Li X, Lin B, Shim S, Ming GL, Levchenko A. A microfluidics-based turning assay reveals complex growth cone responses to integrated gradients of substrate-bound ECM molecules and diffusible guidance cues. Lab Chip. 8(2):227-37 (2008) 

31. Kaneda A, Wang CJ, Cheong R, Timp W, Onyango P, Wen B, Iacobuzio-Donahue CA, Ohlsson R, Andraos R, Pearson MA, Sharov AA, Longo DL, Ko MS, Levchenko A, Feinberg AP. Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci U S A 104(52):20926-31 (2007) 

30. Cho H, Jönsson H, Campbell K, Melke P, Williams JW, Jedynak B, Stevens AM, Groisman A, Levchenko A. Self-organization in high-density bacterial colonies: efficient crowd control. PLoS Biol.5(11):e302 (2007) 

29. Socolovsky M, Murrell M, Liu Y, Pop R, Porpiglia E, Levchenko A. Negative autoregulation by FAS mediates robust fetal erythropoiesis. PLoS Biol. 5(10):e252 (2007)  

28. O’Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A. A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity. Mol Syst Biol.3:111 (2007) 

27. Paliwal S, Iglesias PA, Campbell K, Hilioti Z, Groisman A, Levchenko A. MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature. 446(7131):46-51 (2007) 

26. Zhang, N.N., Dudgeon, D.D., Paliwal, S., Levchenko, A., Grote, E., Cunningham, K.W. Multiple signaling pathways regulate yeast cell death during the response to mating pheromones. Mol. Biol. Cell. 17(8): 3409-22 (2006) 

25. Cheong, R., Bergmann, A., Werner, S.L., Regal, J., Hoffmann, A. and Levchenko, A. Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. Journal of Biological Chemistry 281(5):2945-50(2006) 

  • Reviewed in: Infectious Intruder ‘Alarm’ Yields Clues to Immune System Behavior JohnsHopkins Gazette 35(24) (2006)

24. Koh, X., Srinivasan, B, Ching, H.S. and Levchenko, A. A 3D Monte Carlo analysis of the role of dyadic space geometry in spark generation. Biophysical Journal 90(6):1999-2014 (2006)

  • The work leading up to the publication has been featured in: Healthy Heartbeat JohnsHopkins Gazette 33(25) (2004)

23. Prill, R., Iglesias, P.A. and Levchenko, A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biology 3(11): e343 (2005) 

  • Selected as ‘Recommended’ by Faculty1000 (‘This enlightening paper offers a first glimpse at fundamental design principles that may underlie the structure of biological networks’)

Reviewed in a PLoS Biology comment: Doyle, J. and Csete, M Motifs, control, and stability. PLoS Biol. 3(11):e392 (2005)

22. Groisman, A., Lobo, C., Cho, H.J., Campbell, J. K., Dufour, Y.S., Stevens, A.M. and Levchenko, A. A microfluidic chemostat for experiments with bacterial and yeast cells. Nature Methods 2(9): 685-689 (2005) 

  • Reviewed in a Nature Methods comment: Balaban, N.Q. Szilard’s dream Nature Methods 2 (9): 648-649 (2005)

21. Levchenko, A. Proteomics takes stem cell analyses to another level. Nature Biotechnology23(7):828-30 (2005)  

  • Invited review, not refereed.

20. Barken, D.*, Wang, C.C.*, Kearns, J., Cheong, R., Hoffmann, A., Levchenko, A. Comment on “Oscillations in NF-kappaB signaling control the dynamics of gene expression”. Science308(5718):52 (2005)   

19. Levchenko*, A., Mehta*, B.M., Niu, X., Kang, G., Villafania, L., Way, D., Sadelain, M. and Larson, S.M. Intercellular transfer of P-glycoprotein mediates acquired multidrug resistance in tumor cells. Proceedings of the NationalAcademy of Science, 102(6):1933-38 (2005) 

  • Reviewed in a comment in Nature Reviews Drug Discovery: Owens, J. Drug resistance - Passing on protection Nature Reviews Drug Discovery 4 (3): 191-191 (2005)
  • Reviewed in Trends in Pharmacological Sciences: Ambudkar SV, Sauna ZE, Gottesman MM, et al. A novel way to spread drug resistance in tumor cells: functional intercellular transfer of P-glycoprotein (ABCB1) Trends in Pharmacological Sciences 26 (8): 385-387 (2005)
  • Reviewed in “Research Sheds Fresh Light on How Cancer Cells Become Resistant to Treatment”, Johns Hopkins Gazette, 34(19) (2005)
  • Reviewed in multiple other media outlets across the globe

18. Jönsson, H. and Levchenko, A. An explicit spatial model of yeast microcolony growth. SIAMMultiscale Modeling and Simulation 3(2): 346-361 (2005)

17. Murrell, M.P., Yarema, K. J. and Levchenko, A. The systems biology of glycosylation. ChemBioChem 5: 1334-1347 (2004)  

  • Cover story

16. Levchenko, A., Bruck, J., Sternberg, P.W. Biphasic response as a criterion for identification of regulatory modules in biological systems. Systems Biology 1(1): 139-148 (2004) (Journal later renamed IEE Proceedings in Systems Biology)

  • Inaugural Issue

15. Paliwal, S.,* Ma, L.,* Krishnan, J., Levchenko, A. and Iglesias, P.A. Responding to directional cues: A tale of two cells. IEEE Control Systems Magazine 24(4): 77-90 (2004)

14. Hilioti, Z., Gallagher, D.A., Low-Nam, S. T., Ramaswamy, P., Gajer, P., Kingsbury, T.J., Birchwood, C.J., Levchenko, A., and Cunningham, K.W. GSK-3 kinases enhance calcineurin signaling by phosphorylation of RCNs. Genes and Development 18: 35-47 (2004)   

13. Levchenko A. Allovalency: a case of molecular entanglement. Current Biology 13(22):R876-8 (2003)  
Invited review, not refereed

12. Levchenko, A. Dynamical and integrative cell signaling: new challenges for the new biology.Biotechnology and Bioengineering 84: 773–782 (2003)  

11. Shapiro, B.E, Levchenko, A., Meyerowitz E., Wold, B.J, and Mjolsness, E.D. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19(5):677-678 (2003)  

10. Hoffmann, A.*, Levchenko, A..*, Scott, M.L. and Baltimore, D. The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science, 298: 1241-1245 (2002) 

  • The Hot Paper according to The Scientist magazine (cited significantly more than its peers in the same or similar journals)
  • Exceptional paper by Faculty of 1000
  • Reviewed in a comment in Science:
    Ting, A.Y. and Endy, D. Signal transduction. Decoding NF-kappaB signaling. Science. 298(5596):1189-90 (2002)
  • Reviewed in “Cellular Pathway Contains a ‘Clock’ That Steers Gene Activity”, Johns HopkinsGazette, 32(12) (2002)
  • Reviewed in multiple printed and online publications across the globe
  • Remains the state of the art computational model used in multiple publications, including 3 recent Science papers.

9. Iglesias P.A., Levchenko, A., Modeling the cell’s guidance system. Science’s STKE (2002) 

8. Levchenko, A., Iglesias, P.A. Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. Biophysical Journal 82: 50-63 (2002)  

7. Levchenko, A. Computational cell biology in the post-genomic era. Molecular Biology Reports28(2):83-9 (2001)   

6. DiResta, G.R., Lee, J., Healey, J.H., Levchenko, A., Larson, S.M., Arbit, E. “Artificial lymphatic system”: a new approach to reduce interstitial hypertension and increase blood flow, pH and pO2 in solid tumors. Ann. Biomed. Eng. 28(5):543-55 (2000)   

5. Levchenko, A., Bruck, J. and Sternberg, P.W. Scaffold proteins can alter multiple parameters of MAP kinase signaling modules. Proceedings of the National Academy of Science. (11):5818-23 (2000)   

4. Levchenko, A., Mehta, B.M., Lee, J., Humm, J.L., Augensen, F., Squire, O., Kothari, P.J., Finn, R.D., Leonard, E.F., Larson, S.M. Using 11C-colchicine for positron emission tomography imaging of multiple drug resistance. J. Nucl. Med. 41(3):493-501 (2000)   

3. Fonti, R., Levchenko, A., Mehta, B.M., Zhang, J.J., Tsuruo, T., Larson, S.M. Measurement of P-glycoprotein expression in human neuroblastoma xenografts using in vitro quantitative autoradiography. Nucl. Med.Biol. 26: 35-41(1999)   

2. Levchenko, A., Mehta, B.M., Spengler, B.A., Narkar, A.A., Fonti, R., Biedler, J.L., Tsuruo, T., Larson, S.M. Measurement of P-glycoprotein expression in multidrug-resistant humanneuroblastoma cell lines using self-competitive binding assay. Anal. Biochem. 236(2):338-343 (1996)  

1. Mehta, B.M., Levchenko, A., Rosa, E., Kim, S.W., Winnick, S., Zhang, J.J., Kalaigian, H., Larson, S.M. Evaluation of carbon-14-colchicine biodistribution with whole-body quantitative autoradiography in colchicine-sensitive and -resistant xenografts. J. Nucl. Med.,37(2):312-314(1996)   

INVITED BOOK CHAPTERS (peer reviewed)

1. Levchenko, A., Bruck, J. and Sternberg, P.W. Combination of the biphasic response regulation and positive feedback as a general regulatory mechanism in homeostasis and signal transduction. In Foundations of Systems Biology, ed. H. Kitano, MIT Press, 2001

2. Shapiro, B.E., Levchenko, A. and Mjolsness, E. Automatic model generation for signal transduction with applications to MAPK pathway. In Foundations of Systems Biology, ed. H. Kitano, MIT Press, 2001.

3. Murrell, M.P., Yarema, K.J., & Levchenko, A., Computational modeling of glycosylation. InHandbook of Carbohydrate Engineering. (K.J. Yarema, ed.) CRC Press (Taylor & Francis Group), Boca Raton, FL, pp 247-288, 2005.

4. Cheong, R. and Levchenko A. Survey of the NFkB Transcription Factor: Function, Structure, Regulation, Pathways, and Applications. In The Encyclopedia of Molecular Cell Biology and Molecular Medicine, ed. R.A. Meyers, Wiley-VCH, pp. 437-472, 2005.