Publications

Hsu J*, Nguyen KT*, Bujnowska M, Janes KA, Fallahi-Sichani M. Protocol for iterative indirect immunofluorescence imaging in cultured cells, tissue sections, and metaphase chromosome spreads, STAR Protocols (2024). (PubMed Link) (PDF) [* Equal contributions]

Abecunas C, Kidd AD, Jiang Y, Zong H, Fallahi-Sichani M. Multivariate analysis of metabolic state vulnerabilities across diverse cancer contexts reveals synthetically lethal associations, Cell Reports (2024). (PubMed Link) (PDF)

Abecunas C, Whitehead CE, Ziemke EK, Baumann DG, Frankowski-McGregor CL, Sebolt-Leopold JS, Fallahi-Sichani M. Loss of NF1 in melanoma confers sensitivity to SYK kinase inhibition, Cancer Research (2023). (PubMed Link) (PDF)

Comandante-Lou N*, Baumann DG*, Fallahi-Sichani M. AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells, Cell Reports (2022). (PubMed Link) (PDF) [* Equal contributions]

Khaliq M, Manikkam M, Martinez ED, and Fallahi-Sichani M. Epigenetic modulation reveals differentiation state specificity of oncogene addiction, Nature Communications (2021). (PubMed Link) (PDF)

Shcherbina A, Larouche J, Fraczek P, Yang BA, Brown LA, Markworth JF, Chung CH, Khaliq M, de Silva K, Choi JJ, Fallahi-Sichani M, Chandrasekaran S, Jang YC, Brooks SV, Aguilar CA. Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis, Cell Reports (2020). (PubMed Link) (PDF)

Comandante-Lou N, Khaliq M, Venkat D, Manikkam M and Fallahi-Sichani M. Phenotype-Based Probabilistic Analysis of Heterogeneous Responses to Cancer Drugs and Their Combination Efficacy, PLoS Computational Biology (2020). (PubMed Link) (PDF)

Khaliq M and Fallahi-Sichani M. Epigenetic Mechanisms of Escape from BRAF Oncogene Dependency, Cancers (2019). (PubMed Link) (PDF)

Comandante-Lou N and Fallahi-Sichani M. Models of Cancer Drug Discovery and Response to Therapy, In Wolkenhauer O (Ed.), Systems Medicine: Integrative, Qualitative and Computational Approaches, vol. 3, pp. 269-276. Oxford: Elsevier (2021). (Link)

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma’ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-level cataloging of human cells response to perturbations, Cell Systems (2018). (PubMed Link) (PDF)

Fallahi-Sichani M#, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK#. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly-dividing de-differentiated state, Molecular Systems Biology (2017). (PubMed Link) (PDF) 
(#Co-corresponding authors)

Lin JR, Fallahi-Sichani M, Chen JY, Sorger PK. Cyclic immunofluorescence (CycIF), a highly multiplexed method for single-cell imaging, Current Protocols in Chemical Biology (2016). (PubMed Link) (PDF)

Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon C, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq, Science (2016). (PubMed Link) (PDF)

Moerke N, Fallahi-Sichani M. Reverse phase protein arrays for compound profiling, Current Protocols in Chemical Biology (2016). (PubMed Link) (PDF)

Lin JR, Fallahi-Sichani M, Sorger PK. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method, Nature Communications (2015). (PubMed Link) (PDF)

Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK. Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis, Molecular Systems Biology (2015). (PubMed Link) (PDF)

Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK. Metrics other than potency reveal systematic variation in responses to cancer drugs, Nature Chemical Biology (2013). (PubMed Link) (PDF)

Kirschner DE, Hunt CA, Marino S, Fallahi-Sichani M, Linderman JJ. Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models, WIREs Systems Biology and Medicine (2014). (PubMed Link) (PDF)

Fallahi-Sichani M, Marino S, Flynn JL, Linderman JJ, Kirschner DE. A systems biology approach for understanding granuloma formation and function in tuberculosis, In McFadden J, Beste D, Kierzek A (Ed.), Systems biology of tuberculosis. Springer (2013). (Publisher Link) (PDF)

Fallahi-Sichani M, Kirschner DE, Linderman JJ. NF-kappaB signaling dynamics play a key role in infection control in tuberculosis, Frontiers in Physiology 3:170 (2012). (PubMed Link) (PDF)

Fallahi-Sichani M, Flynn JL, Linderman JJ, Kirschner DE. Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability, Journal of Immunology (2012). (PubMed Link) (PDF)

Marino S, Fallahi-Sichani M, Linderman JJ, Kirschner DE. Mathematical models of anti-TNF therapies and their correlation with tuberculosis, In Pathak Y, Benita S (Ed.), Antibody-mediated drug delivery systems: Concepts, Technology and Applications. John Wiley and Sons (2012). (Publisher Link) (PDF)

Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ. Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation, Journal of Immunology (2011). (PubMed Link) (PDF)

Fallahi-Sichani M, Schaller MA, Kirschner DE, Kunkel SL, Linderman JJ. Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma, PLoS Computational Biology (2010). (PubMed Link) (PDF)

Fallahi-Sichani M, Linderman JJ, Lipid raft-mediated regulation of G-protein coupled receptor signaling by ligands which influence receptor dimerization: A computational study, PLoS ONE (2009). (PubMed Link) (PDF)

Fallahi-Sichani M, Soleimani M, Najafi SMA, Kiani J, Arefian E, Atashi A, In vitro differentiation of cord blood unrestricted somatic stem cells expressing dopamine-associated genes into neuron-like cells, Cell Biology International (2007). (PubMed Link) (PDF)

Mohammadi Y, Soleimani M, Fallahi-Sichani M, Gazme A, Haddadi-Asl V, Arefian E, Kiani J, Moradi R, Atashi A, Ahmadbeigy N. Nanofibrous poly(ε-caprolactone)/poly(vinyl alcohol)/chitosan hybrid scaffolds for bone tissue engineering using mesenchymal stem cells, International Journal of Artificial Organs (2007). (PubMed Link) (PDF)