Publications
Megason Lab: Jia BZ, Yitong Q, Wong-Campos JD, Megason SG*, Cohen AE*. “A bioelectrical phase transition patterns the first beats of a vertebrate heart.” bioarxiv. Link
Springer Lab: Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. “Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants.” Nat Biomed Eng. Link
Paulsson Lab: Chen H, Xu J, Wang Y, Wang D, Ferrer-Espada R, Wang Y, Zhou J, Pedrazo-Tardajos A, Yang M, Tan JH, Yang X, Zhang L, Sychugov I, Chen S, Bals S, Paulsson J, Yang Z. “Color-Switchable Nanosilicon Fluorescent Probes.” ACS Nano. Link
Lahav Lab: Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G. “Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations”.Mol Syst Biol. Link
Klein Lab: Cambra HM, Tallapragada NP, Mannam P, Breault DT, Klein AM. “Triple-Decker Sandwich Cultures of Intestinal Organoids for Long-Term Live Imaging, Uniform Perturbation, and Statistical Sampling.” Current Protocols. Link
Higgins Lab: Foy BH, Sundt TM, Carlson JCT, Aguirre AD, Higgins JM. “Human acute inflammatory recovery is defined by co-regulatory dynamics of white blood cell and platelet populations.” Nat Commun. Link
2023
Basan Lab: Severin Schink, Constantin Ammar, Yu-Fang Chang, Ralf Zimmer, and Markus Basan. In Press. “Analysis of proteome adaptation reveals a key role 1 of the bacterial envelope in starvation survival.” Molecular systems biology, 18, Pp. e11160. Link
Mitchison & Kirschner Labs: Elizabeth S Van Itallie, Christine M Field, Timothy J Mitchison, Marc W Kirschner. “Dorsal lip maturation and initial archenteron extension depend on Wnt11 family ligands “ Dev Biol, Jan 2023, Pg 67-79. Link
This list is not all encompassing!
Check out each labs’ website for a complete list of their publications
2022
Basan Lab: Jeffrey Abbott, Avik Mukherjee, Wenxuan Wu, Tianyang Ye, Han Sae Jung, Kevin M. Cheung, Rona S. Gertner, Markus Basan, Donhee Ham, and Hongkun Park. 3/10/2022. “Multi-parametric functional imaging of cell cultures and tissues with a CMOS microelectrode array.” Lab on a Chip. Link
Silver Lab: Ng TL, Olson EJ, Yoo TY, Weiss HS, Koide Y, Koch PD, Rollins NJ, Mach P, Meisinger T, Bricken T, Chang TZ, Molloy CW, Zurcher J, Mitchison T, Glass JI, Marks DS, Way JC, Silver PA. “High content screening and computational prediction reveal viral genes that suppress innate immune response.” mSystems. Link
Kirschner Lab: Xili Liu, Seungeun Oh, Marc W. Kirschner. “The uniformity and stability of cellular mass density in mammalian cell culture” Front Cell Dev Biol. Link
Fontana Lab: Andersen JL, Fagerberg R, Flamm C, Fontana W, Kolčák J, Laurent CVFP, Merkle D, Nøjgaard N. “Representing Catalytic Mechanisms with Rule Composition.” J Chem Inf Model. Link
Sorger Lab: Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK. “Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop.” Nat Commun. Link
Gunawardena Lab: U Cetiner, J Gunawardena "Reformulating non-equilibrium steady-states and generalised Hopfield discrimination"
Phys Rev E. Link
2021
Mitchison & Megason Labs: Munjal A, Hanezzo E, Tsai TY, Mitchison TJ, Megason SG. (2021). “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis”, Cell, 184(26):6313-25. Link
Marks Lab: Jonathan Frazer, Pascal Notin, Mafalda Dias, Aidan Gomez, Joseph K Min, Kelly Brock, Yarin Gal, Debora S Marks “Disease variant prediction with deep generative models of evolutionary data” Nature. Link
Oyler-Yaniv Lab: Jennifer Oyler- Yaniv*, Alon Oyler-Yaniv*, Evan Maltz, and Roy Wollman. “TNF controls a speed-accuracy tradeoff in apoptotic decision to restrict viral spread. “ Nat. Comms. Link
Lahav Lab: Tsabar M, Lovitch SB, Jambhekar A, Lahav G. “Connecting Timescales in Biology: Can Early Dynamical Measurements Predict Long-Term Outcomes?” Trends Cancer. Link
DePace Lab: Bowdish D, Desai TA, DePace A, Haswell ES, Baltrus D, García AJ, Deans T, Lage K, Wittkopp P. “Leadership.” Cell Syst. Link
2020
Lahav Lab: Tsabar M, Mock CS, Venkatachalam V, Reyes J, Karhohs KW, Oliver TG, Regev A, Jambhekar A, Lahav G. “A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest.” Cell Rep. Link
Lu Lab: Rui Fang, Jason Hon, Mengying Zhou and Ying Lu* “An empirical energy landscape reveals the mechanism of proteasome in polypeptide translocation.” eLife. Link
Klein Lab: Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, Klein AM, Lowell S, Camargo FD. “Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis.” Nature. Link
DePace Lab: López-Rivera F, Foster Rhoades OK, Vincent BJ, Pym ECG, Bragdon MDJ, Estrada J, DePace AH, Wunderlich Z. “A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences.” G3. Link
Silver Lab & Springer Lab: Qian J, Lu Z, Mancuso CP, Jhuang H, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. “Barcoded Microbial System for High-Resolution Object Provenance.” Science. Link
Basan Lab & Paulsson Lab: Basan M, Honda T, Christodoulou D, Hörl M, Chang YF, Leoncini E, Mukherjee A, Okano H, Taylor BR, Silverman JM, Sanchez C, Williamson JR, Paulsson J, Hwa T, Sauer U. “A universal trade-off between growth and lag in fluctuating environments.” Nature. Link
2019
Kirschner Lab: Peshkin L, Boukhali M, Haas W, Kirschner MW, Yampolsky LY. “Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex.” Proteomics. Link
DePace Lab: Scholes C, Biette KM, Harden TT, DePace AH. “Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo.” Cell Rep. Link
Marks Lab: Thomas A Hopf, Anna G Green, Benjamin Schubert, Sophia Mersmann, Charlotta PI Schärfe, John B Ingraham, Agnes Toth-Petroczy, Kelly Brock, Adam J Riesselman, Perry Palmedo, Chan Kang, Robert Sheridan, Eli J Draizen, Christian Dallago, Chris Sander, Debora S Marks. “The EVcouplings Python framework for coevolutionary sequence analysis” Bioinformatics. Link
Paulsson Lab: Lord ND, Norman TM, Yuan R, Bakshi S, Losick R, Paulsson J. “Stochastic antagonism between two proteins governs a bacterial cell fate switch.” Science. Link
Klein Lab: Wolock SL, Lopez R, Klein AM. “Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data.” Cell Syst. Link
Gunawardena & DePace Labs: Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MD, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH. “Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity.” Elife. Link
Paulsson & Silver Labs: Riglar DT, Richmond DL, Potvin-Trottier L, Verdegaal AA, Naydich AD, Bakshi S, Leoncini E, Lyon LG, Paulsson J, Silver PA. “Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator.” Nat Commun. Link
Fontana Lab: Ross RJH, Strandkvist C, Fontana W. “Random walker's view of networks whose growth it shapes.” Phys Rev E. Link
Mootha Lab: Flicker D, Sancak Y, Mick E, Goldberger O, Mootha VK. “Exploring the In Vivo Role of the Mitochondrial Calcium Uniporter in Brown Fat Bioenergetics.” Cell Rep Link
Mitchison Lab: Gasic I, Boswell SA, Mitchison TJ. “Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues.” PLoS Biol. Link
2018
Klein & Kirschner Labs: Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. “The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.” Science. Link
Mitchison Lab: Jun HJ, Appleman VA, Wu HJ, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A. “A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine.” Nat Commun. Link
DePace Lab: Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH. “Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos.” PLoS Genet. Link
Gunawardena Lab: Wong F, Amir A, Gunawardena J. “Energy-speed-accuracy relation in complex networks for biological discrimination.” Phys Rev E. Link
Marks Lab: Megan Sjodt, Kelly P Brock, Genevieve Dobihal, Patricia DA Rohs, Anna G Green, Thomas A Hopf, Alexander J Meeske, Veerasak Srisuknimit, Daniel Kahne, Suzanne Walker, Debora S Marks, Thomas G Bernhardt, David Z Rudner, Andrew C Kruse. “Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis” Nature. Link
Sorger Lab: Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK. “Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.” Cell Syst. Link
Fontana Lab: Boutillier P, Maasha M, Li X, Medina-Abarca HF, Krivine J, Feret J, Cristescu I, Forbes AG, Fontana W. “The Kappa platform for rule-based modeling.” Bioinformatics. Link