Division of Biology and Biological Engineering (BBE)

Monographs from CaltechAUTHORS

• Edwards, Rhodri T.M.; Antoshechkin, Igor; et al. (2025) Transcriptome analysis of the winter tick (Dermacentor albipictus) reveals sex-specific expression patterns; 10.1101/2025.02.17.638687
• Elder, James R.; Zheng, Jie; et al. (2025) An invariant schema emerges within a neural network during hierarchical learning of visual boundaries; 10.1101/2025.01.30.635821
• Schwarz, Erich M.; Baniya, Anil; et al. (2025) Genomes of the entomopathogenic nematodeSteinernema hermaphroditumand its associated bacteria; 10.1101/2025.01.09.632278
• Raciti, Daniela; Van Auken, Kimberly M.; et al. (2025) Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity; 10.1101/2025.01.06.631539
• Fan, Tzu-Pei; Lee, Jun-Ru; et al. (2024) Deep homology of a brachyury regulatory syntax and origin of the notochord; 10.1101/2024.12.12.628285
• Gill, Shubhroz; Mandigo, Torrey R.; et al. (2024) A conserved role for ALG10/ALG10B and the N-glycosylation pathway in the sleep-epilepsy axis; 10.1101/2024.12.11.24318624
• Pimmett, Virginia L; McGehee, James; et al. (2024) Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription; 10.1101/2024.11.28.623729
• Bartol, Thomas M.; Ordyan, Mariam; et al. (2024) A spatial model of autophosphorylation of Ca²⁺/calmodulin-dependent protein kinase II in a glutamatergic spine reveals dynamics of kinase activation in the first several seconds after a complex synaptic stimulus; 10.1101/2024.02.02.578696
• Chen, Alex B.; Duque, Marc; et al. (2024) Norepinephrine changes behavioral state via astroglial purinergic signaling; PMCID PMC11142163; 10.1101/2024.05.23.595576
• Rosenthal, Isabelle A.; Bashford, Luke; et al. (2024) Visual context affects the perceived timing of tactile sensations elicited through intra-cortical microstimulation; PMCID PMC11118490; 10.1101/2024.05.13.593529
• Desingu Rajan, Ayyappa Raja; Huang, Yuanyun; et al. (2024) Generation of a zebrafish neurofibromatosis model via inducible knockout of nf2; 10.1101/2024.04.23.590787
• Gornet, James A. and Thomson, Matt (2024) Automated construction of cognitive maps with predictive coding; bioRxiv; 2023.09.18.558369; 10.1101/2023.09.18.558369
• Rich, Joseph M.; Moses, Lambda; et al. (2024) The impact of package selection and versioning on single-cell RNA-seq analysis; PMCID PMC11014608; 10.1101/2024.04.04.588111
• Prywes, Noam; Philips, Naiya R.; et al. (2024) A map of the rubisco biochemical landscape; PMCID PMC11030240; 10.1101/2023.09.27.559826
• Booeshaghi, A. Sina; Galvez-Merchán, Ángel; et al. (2024) Algorithms for a Commons Cell Atlas; 10.1101/2024.03.23.586413
• Flynn, Michael James; Mayfield, Acacia M.; et al. (2024) Synthetic dosage-compensating miRNA circuits allow precision gene therapy for Rett syndrome; bioRxiv; 2024.03.13.584179; PMCID PMC10980028; 10.1101/2024.03.13.584179
• Du, Rongrong; Flynn, Michael J.; et al. (2024) miRNA circuit modules for precise, tunable control of gene expression; bioRxiv; 2024.03.12.583048; PMCID PMC10979901; 10.1101/2024.03.12.583048
• Kubinski, Hannah C.; Despres, Hannah W.; et al. (2024) Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation; bioRxiv; 53; PMCID PMC10979914; 10.1101/2024.03.08.584120
• Israel, Uriah; Marks, Markus; et al. (2024) A Foundation Model for Cell Segmentation; bioRvix; 2023.11.17.567630; PMCID PMC10690226; 10.1101/2023.11.17.567630
• Wang, Eric; Cohen, Alexander A.; et al. (2024) Designed mosaic nanoparticles enhance cross-reactive immune responses in mice; PMCID PMC10925254; 10.1101/2024.02.28.582544
• Cohen, Alexander A.; Keeffe, Jennifer R.; et al. (2024) Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals; PMCID PMC10871317; 10.1101/2024.02.08.576722
• Flamholz, Avi I.; Goyal, Akshit; et al. (2024) The proteome is a terminal electron acceptor; PMCID PMC10862836; 10.1101/2024.01.31.578293
• Huang, Yu Xi; Mahler, Simon; et al. (2024) A compact and cost-effective laser-powered speckle visibility spectroscopy (SVS) device for measuring cerebral blood flow; PMCID PMC10862935; 10.48550/arxiv.2401.16592
• Subramanian, Arjuna M. and Thomson, Matt (2023) Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models; PMCID PMC10769378; 10.1101/2023.12.22.573145
• Polonsky, Michal; Gerhardt, Louisa M. S.; et al. (2023) Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease; bioRxiv; 10.1101/2023.11.22.568217
• Martinez, Zachary A; Murray, Richard M.; et al. (2023) TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering; bioRxiv; 2023.10.24.563881; PMCID PMC10659302; 10.1101/2023.10.24.563881
• Zhang, Shu; Xie, Na; et al. (2023) The Interferon-inducible NAMPT acts as a protein phosphoribosylase to restrict viral infection; PMCID PMC10614811; 10.1101/2023.10.12.562112
• Wang, Renée Z.; Lonergan, Zachery R.; et al. (2023) Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N₂O under anoxia; PMCID PMC10592819; 10.1101/2023.10.13.562248
• Bugacov, Helena; Der, Balint; et al. (2023) Canonical Wnt transcriptional complexes are essential for induction of nephrogenesis but not maintenance or proliferation of nephron progenitors; 10.1101/2023.08.20.554044
• Srivastava, Vasudha; Hu, Jennifer L.; et al. (2023) Configurational entropy is an intrinsic driver of tissue structural heterogeneity; PMCID PMC10327153; 10.1101/2023.07.01.546933
• Weatherbee, Bailey A. T.; Gantner, Carlos W.; et al. (2023) Transgene directed induction of a stem cell-derived human embryo model; 10.1101/2023.06.15.545082
• Tran, Martin; Askary, Amjad; et al. (2023) Lineage motifs: developmental modules for control of cell type proportions; PMCID PMC10274800; 10.1101/2023.06.06.543925
• Wolin, Erica; Guo, Jimmy K.; et al. (2023) SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress; PMCID PMC10274648; 10.1101/2023.06.05.543769
• Huang, Biao; Zeng, Zipeng; et al. (2023) Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids; 10.1101/2023.05.25.542343
• Gorin, Gennady; Vastola, John J.; et al. (2023) Studying stochastic systems biology of the cell with single-cell genomics data; PMCID PMC10245677; 10.1101/2023.05.17.541250
• Xiong, Lingyun; Liu, Jing; et al. (2023) Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney; PMCID PMC10187285; 10.1101/2023.05.06.539585
• Prakash, Sharan J.; Van Auken, Kimberly M.; et al. (2023) Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans; PMCID PMC10168330; 10.1101/2023.04.28.538760
• Jiang, Jialong; Chen, Sisi; et al. (2023) D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response; PMCID PMC10153191; 10.1101/2023.04.19.537364
• Mao, Runze; Wackelin, Daniel J.; et al. (2023) Enantio- and Diastereoenriched Enzymatic Synthesis of 1,2,3-Polysubstituted Cyclopropanes from (Z/E)-Trisubstituted Enol Acetates; PMCID PMC10120758; 10.21203/rs.3.rs-2802333/v1
• Hahn, Joshua; Monavarfeshani, Aboozar; et al. (2023) Evolution of neuronal cell classes and types in the vertebrate retina; PMCID PMC10104162; 10.1101/2023.04.07.536039
• Hitz, Benjamin C.; Lee, Jin-Wook; et al. (2023) The ENCODE Uniform Analysis Pipelines; 10.1101/2023.04.04.535623
• Kapasiawala, Manisha and Murray, Richard M. (2023) Probing metabolism in an E. coli-based cell-free system reveals a trade-off between transcription and translation; 10.1101/2023.03.22.533877
• Sullivan, Delaney K. and Pachter, Lior (2023) Flexible parsing and preprocessing of technical sequences with splitcode; PMCID PMC10055216; 10.1101/2023.03.20.533521
• Dutka, Przemysław; Liu, Yuxi; et al. (2023) Structure and Function of the Dot/Icm T4SS; 10.1101/2023.03.22.533729
• Booeshaghi, A. Sina; Chen, Xi; et al. (2023) A machine-readable specification for genomics assays; 10.1101/2023.03.17.533215
• Bernardi, Yanel E.; Sanchez-Vasquez, Estefania; et al. (2023) Extracellular vesicle-localized miR-203 mediates neural crest-placode communication required for trigeminal ganglia formation; 10.1101/2023.03.14.532527
• Stevens, Taylor Anthony; Pinton Tomaleri, Giovani; et al. (2023) A nanobody-based strategy for rapid and scalable purification of native human protein complexes; 10.1101/2023.03.09.531980
• Ji, Jenny; Winnett, Alexander Viloria; et al. (2023) Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types; 10.1101/2023.03.09.23286855
• Hills, Rory A.; Tan, Tiong Kit; et al. (2023) Multiviral Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive Vaccinology; PMCID PMC9980174; 10.1101/2023.02.24.529520
• Afik, Eldad; Liu, Toni J. B.; et al. (2023) Dynamical states of self-organized waves in a giant single-celled organism feeding on light; 10.1101/2023.02.22.529174
• Yang, Jie-Yoon; O’Connell, Thomas F.; et al. (2023) Restructuring of olfactory representations in the fly brain around odor relationships in natural sources; 10.1101/2023.02.15.528627
• Tan, Chieh-Hsiang; Cheng, Kai-Wen; et al. (2023) LINKIN-associated proteins necessary for tissue integrity during collective cell migration; 10.1101/2023.02.08.527750
• Santos, Inês B.; Wainman, Alan; et al. (2023) Mob4 is essential for spermatogenesis in Drosophila melanogaster; 10.1101/2023.02.05.527206
• Trautmann, Eric M.; Hesse, Janis K.; et al. (2023) Large-scale brain-wide neural recording in nonhuman primates; 10.1101/2023.02.01.526664
• Wang, Grace Z.; Warren, Elizabeth A.; et al. (2023) Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa; 10.1101/2023.01.29.526047
• Dam, Kim-Marie A.; Fan, Chengcheng; et al. (2023) Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations; 10.1101/2023.01.27.525985
• Akella, Prithvi; Ahmadi, Mohamadreza; et al. (2023) Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications
• Guna, Alina; Page, Katharine R.; et al. (2023) A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens; PMCID PMC9882262; 10.1101/2023.01.22.525086
• Gorin, Gennady and Pachter, Lior (2023) The telegraph process is not a subordinator; 10.1101/2023.01.17.524309
• Haloi, Nandan; Huang, Shan; et al. (2023) Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids; 10.1101/2023.01.16.524298
• Kahan, Anat; Coughlin, Gerard M.; et al. (2023) Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure; 10.1101/2023.01.14.524075
• Fry, Michelle Y.; Navarro, Paula P.; et al. (2023) In situ architecture of Opa1-dependent mitochondrial cristae remodeling; 10.1101/2023.01.16.524176
• Ding, Xiaozhe; Chen, Xinhong; et al. (2023) Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling; 10.1101/2023.01.11.523680
• De Jonghe, Joachim; Kaminski, Tomasz S.; et al. (2023) spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content; 10.1101/2023.01.12.523500
• Chen, Xinhong; Wolfe, Damien A.; et al. (2023) Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates; 10.1101/2023.01.12.523844
• Carilli, Maria; Gorin, Gennady; et al. (2023) Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data; 10.1101/2023.01.13.523995
• Shay, Timothy F.; Sullivan, Erin E.; et al. (2023) Primate-conserved Carbonic Anhydrase IV and murine-restricted Ly6c1 are new targets for crossing the blood-brain barrier; 10.1101/2023.01.12.523632
• Dylla, Kristina V.; O’Connell, Thomas F.; et al. (2023) Early life experience with natural odors modifies olfactory behavior through an associative process; 10.1101/2023.01.08.523155
• Yamoune, Amel; Zdarska, Marketa; et al. (2023) Cytokinins regulate spatially-specific ethylene production to control root growth in Arabidopsis; 10.1101/2023.01.07.522790
• Bhat, Prashant; Chow, Amy; et al. (2023) 3D genome organization around nuclear speckles drives mRNA splicing efficiency; 10.1101/2023.01.04.522632
• Choe, Mangyu; Einav, Tal; et al. (2022) Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis; 10.1101/2022.12.28.522046
• Hoffmann, Magnus A. G.; Yang, Zhi; et al. (2022) ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses; PMCID PMC9810232; 10.1101/2022.12.26.521940
• Fenelon, Kelli D.; Gao, Fan; et al. (2022) Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos; 10.1101/2022.12.15.519123
• Guan, Charles; Aflalo, Tyson; et al. (2022) Compositional coding of individual finger movements in human posterior parietal cortex and motor cortex enables ten-finger decoding; 10.1101/2022.12.07.22283227
• Palmer, Emily H.; Omoto, Jaison J.; et al. (2022) The role of a population of descending neurons in the optomotor response in flying Drosophila; 10.1101/2022.12.05.519224
• Hjorleifsson, Kristján Eldjárn; Sullivan, Delaney K.; et al. (2022) Accurate quantification of single-nucleus and single-cell RNA-seq transcripts; 10.1101/2022.12.02.518832
• Hjorleifsson, Kristján Eldjárn; Pachter, Lior; et al. (2022) Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes; 10.1101/2022.12.02.518787
• Pleiner, Tino; Hazu, Masami; et al. (2022) A selectivity filter in the EMC limits protein mislocalization to the ER; 10.1101/2022.11.29.518402
• Murali, Ranjani; Yu, Hang; et al. (2022) Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea; 10.1101/2022.11.23.517749
• Spolski, Rosanne; Li, Peng; et al. (2022) Distinct super-enhancer elements differentially control Il2ra gene expression in a cell-type specific fashion; 10.1101/2022.11.18.516445
• Shin, Boyoung; Zhou, Wen; et al. (2022) Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms; 10.1101/2022.11.18.517146
• Findlay, Andrew R.; Paing, May M.; et al. (2022) DNAJB6 Isoform Specific Knockdown: Therapeutic Potential for LGMDD1; 10.1101/2022.11.17.516920
• Marken, John P. and Murray, Richard M. (2022) Addressable and adaptable intercellular communication via DNA messaging; 10.1101/2022.11.17.516988
• Griggs, Whitney S.; Norman, Sumner L.; et al. (2022) Decoding Motor Plans Using a Closed-Loop Ultrasonic Brain-Machine Interface; 10.1101/2022.11.10.515371
• Fornace, Mark E.; Huang, Jining; et al. (2022) NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems; 10.26434/chemrxiv-2022-xv98l
• Wandelt, Sarah K.; Bjånes, David A.; et al. (2022) Online internal speech decoding from single neurons in a human participant; 10.1101/2022.11.02.22281775
• Sockell, Alexandra; Wong, Wing; et al. (2022) A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids; 10.1101/2022.11.01.514733
• Shimojo, Kensuke; Shimojo, Eiko; et al. (2022) Preservation of Conditioned Behavior Based on UV Light Sensitivity in Dissected Tail Halves of Planarians- a Proof by DNN; 10.1101/2022.10.30.514395
• Chen, Peiwei and Aravin, Alexei A. (2022) Genetic control of a sex-specific piRNA program; 10.1101/2022.10.25.513766
• Gorin, Gennady; Yoshida, Shawn; et al. (2022) Transient and delay chemical master equations; 10.1101/2022.10.17.512599
• Danelius, Emma; Porter, Nicholas J.; et al. (2022) MicroED structure of a protoglobin reactive carbene intermediate; 10.1101/2022.10.18.512604
• Badithela, Apurva; Graebener, Josefine B.; et al. (2022) Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows; 10.48550/arXiv.2210.10304
• Badithela, Apurva; Wongpiromsarn, Tichakorn; et al. (2022) Evaluation Metrics for Object Detection for Autonomous Systems; 10.48550/arXiv.2210.10298
• Zhang, Juner; Maggiolo, Ailiena O.; et al. (2022) Chemodivergent C(sp³)–H and C(sp²)–H Cyanomethylation Using Engineered Carbene Transferases; 10.26434/chemrxiv-2022-z6pkw
• Booeshaghi, A. Sina; Min, Kyung Hoi (Joseph); et al. (2022) Quantifying orthogonal barcodes for sequence census assays; 10.1101/2022.10.09.511501
• Pandey, Ayush; Rodriguez, Makena L.; et al. (2022) Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline; 10.1101/2022.10.05.511053
• Santorelli, Marco; Bhamidipati, Pranav S.; et al. (2022) Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit; 10.1101/2022.10.04.510900
• Kreida, Stefan; Narita, Akihiro; et al. (2022) Cryo-EM structure of the Agrobacterium tumefaciens type IV secretion system-associated T-pilus reveals stoichiometric protein-phospholipid assembly; 10.1101/2022.09.25.509369
• Jiménez Otero, Fernanda; Newman, Dianne K.; et al. (2022) Electrochemical disruption of extracellular electron transfer inhibits Pseudomonas aeruginosa cell survival within biofilms and is synergistic with antibiotic treatment; 10.1101/2022.09.15.508205
• Schulte, Samuel J.; Huang, Jining; et al. (2022) HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing; 10.1101/2022.09.18.508442
• Guna, Alina; Stevens, Taylor A.; et al. (2022) MTCH2 is a mitochondrial outer membrane protein insertase; 10.1101/2022.09.15.508165
• Olina, Anna; Agapov, Aleksei; et al. (2022) Bacterial Argonaute proteins aid cell division in the presence of topoisomerase inhibitors in Escherichia coli; 10.1101/2022.09.13.507849
• Athavale, Soumitra V.; Gao, Shilong; et al. (2022) Enzymatic Nitrogen Insertion into Unactivated C–H Bonds; 10.26434/chemrxiv-2022-w8sg3
• Venkei, Zsolt G.; Gainetdinov, Ildar; et al. (2022) Drosophila Males Use 5′-to-3′ Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides; 10.1101/2022.09.12.507655
• Gristick, Harry B.; Hartweger, Harald; et al. (2022) CD4-binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wildtype animals; 10.1101/2022.09.08.507086
• Lisitskaya, Lidiya; Kropocheva, Ekaterina; et al. (2022) Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo; 10.1101/2022.09.09.507302
• Aflalo, Tyson; Chivukula, Srinivas; et al. (2022) Cognition through internal models: Mirror neurons as one manifestation of a broader mechanism; 10.1101/2022.09.06.506071
• Lee, Peter H.; Anaya, Michael; et al. (2022) An extracellular vesicle targeting ligand that binds to Arc proteins and facilitates Arc transport in vivo; 10.1101/2022.09.06.506798
• Boltje, Daan B.; Hoogenboom, Jacob P.; et al. (2022) A cryogenic, coincident fluorescence, electron and ion beam microscope; 10.1101/2022.09.02.506334
• Brugman, Katherine I.; Susoy, Vladislav; et al. (2022) PEZO-1 and TRP-4 mechanosensors are involved in mating behavior in Caenorhabditis elegans; 10.1101/2022.08.31.506045
• Rosenthal, Isabelle A.; Bashford, Luke; et al. (2022) S1 represents multisensory contexts and somatotopic locations within and outside the bounds of the cortical homunculus; 10.1101/2022.08.29.505313
• Braet, Sean M.; Buckley, Theresa S. C.; et al. (2022) Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk and enhanced NTD dynamics; 10.1101/2022.08.26.505369
• Kaplan, Mohammed; Shepherd, Doulin C.; et al. (2022) Structural remodeling of Coxiella burnetii during its biphasic developmental cycle revealed by cryo-electron tomography; 10.1101/2022.08.23.505044
• Granados, Alejandro A.; Kanrar, Nivedita; et al. (2022) Combinatorial expression motifs in signaling pathways; 10.1101/2022.08.21.504714
• Calvó-Tusell, Carla; Liu, Zhen; et al. (2022) Reversing the enantioselectivity of enzymatic carbene N–H insertion through mechanism-guided protein engineering; 10.26434/chemrxiv-2022-f02xh
• Ninova, Maria; Lomenick, Brett; et al. (2022) Pervasive SUMOylation of heterochromatin and piRNA pathway proteins; 10.1101/2022.08.15.504007
• Han, SooJean; Effros, Michelle; et al. (2022) OUTformation: Distributed Data-Gathering with Feedback under Unknown Environment and Communication Delay Constraints; 10.48550/arXiv.2208.06395
• Nichols, Aaron L.; Blumenfeld, Zack; et al. (2022) Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane; 10.1101/2022.08.09.502705
• Flamholz, Avi I.; Saccomano, Samuel; et al. (2022) Optical O₂ sensors also respond to redox active molecules commonly secreted by bacteria; 10.1101/2022.08.08.503264
• Bjånes, David A.; Bashford, Luke; et al. (2022) Multi-channel intra-cortical micro-stimulation yields quick reaction times and evokes natural somatosensations in a human participant; 10.1101/2022.08.08.22278389
• Amadei, Gianluca; Handford, Charlotte E.; et al. (2022) Stem cell-derived mouse embryos develop within an extra-embryonic yolk sac to form anterior brain regions and a beating heart; 10.1101/2022.08.01.502375
• Lau, Kasey Y. C.; Rubinstein, Hernan; et al. (2022) Mouse-embryo model derived exclusively from embryonic stem cells undergo neurulation and heart development; 10.1101/2022.08.01.502371
• Yang, Zhi; Dam, Kim-Marie A.; et al. (2022) Antibody recognition of CD4-induced open HIV-1 Env trimers; 10.1101/2022.07.27.501785
• Miguel, Amanda; Zietek, Matylda; et al. (2022) Modulation of bacterial cell size and growth rate via activation of a cell envelope stress response; 10.1101/2022.07.26.501648
• Truong, Lisa; Chen, Yen-Wei; et al. (2022) Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol; 10.1101/2022.07.21.500524
• Ohdera, Aki H.; Darymple, Justin; et al. (2022) Symbiosis-driven development in an early branching metazoan; 10.1101/2022.07.21.500558
• Boktor, Joseph C.; Sharon, Gil; et al. (2022) Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome; 10.1101/2022.07.20.500694
• Winnett, Alexander Viloria; Akana, Reid; et al. (2022) Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals; 10.1101/2022.07.13.22277513
• Winnett, Alexander Viloria; Akana, Reid; et al. (2022) Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods; 10.1101/2022.07.13.22277113
• Chen, Zibo; Linton, James M.; et al. (2022) A synthetic protein-level neural network in mammalian cells; 10.1101/2022.07.10.499405
• Laso-Pérez, Rafael; Wu, Fabai; et al. (2022) Evolutionary Diversification of Methanotrophic Ca. Methanophagales (ANME-1) and Their Expansive Virome; 10.1101/2022.07.04.498658
• Abdel-Haq, Reem; Schlachetzki, Johannes C. M.; et al. (2022) A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice; 10.1101/2022.06.27.497828
• Salahshoor, Hossein; Yao, Yuxing; et al. (2022) Geometric effects in gas vesicle buckling under ultrasound; 10.1101/2022.06.27.497663
• Fan, Chengcheng; Cohen, Alexander A.; et al. (2022) Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes; 10.1101/2022.06.28.497989
• Hueschen, Christina L.; Dunn, Alexander R.; et al. (2022) Wildebeest Herds on Rolling Hills: Flocking on Arbitrary Curved Surfaces; 10.1101/2022.06.22.497052
• Siepe, Dirk H.; Henneberg, Lukas T.; et al. (2022) Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform; 10.1101/2022.06.22.497261
• Dutka, Przemysław; Metskas, Lauren Ann; et al. (2022) Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET; 10.1101/2022.06.21.496981
• Poceviciute, Roberta; Bogatyrev, Said R.; et al. (2022) Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa; 10.1101/2022.06.17.496478
• Gorin, Gennady; Carilli, Maria; et al. (2022) Spectral neural approximations for models of transcriptional dynamics; 10.1101/2022.06.16.496448
• Gorin, Gennady and Pachter, Lior (2022) Monod: mechanistic analysis of single-cell RNA sequencing count data; 10.1101/2022.06.11.495771
• Hueschen, Christina L.; Segev Zarko, Li-av; et al. (2022) Emergent Actin Flows Explain Diverse Parasite Gliding Modes; 10.1101/2022.06.08.495399
• Hu, Rongfeng K.; Chen, Patrick B.; et al. (2022) Improved Version of ChETA Promotes Aggression in the Medial Amygdala; 10.1101/2022.06.05.493862
• Booeshaghi, A. Sina and Pachter, Lior (2022) Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads; 10.1101/2022.06.04.494845
• Wang, Megan; Sanfiorenzo, Charles; et al. (2022) A universal system for streamlined genome integrations with CRISPR-associated transposases; 10.1101/2022.05.30.494051
• Gálvez-Merchán, Ángel; Min, Kyung Hoi (Joseph); et al. (2022) Metadata retrieval from sequence databases with ffq; 10.1101/2022.05.18.492548
• Luebbert, Laura and Pachter, Lior (2022) Efficient querying of genomic reference databases with gget; 10.1101/2022.05.17.492392
• Tang, Weiyi; Jacobs-Li, Jessica; et al. (2022) Single-cell profiling coupled with lineage analysis reveals distinct sacral neural crest contributions to the developing enteric nervous system; 10.1101/2022.05.09.491197
• Booeshaghi, A. Sina; Hallgrímsdóttir, Ingileif B.; et al. (2022) Depth normalization for single-cell genomics count data; 10.1101/2022.05.06.490859
• Raghavan, Guruprasad and Thomson, Matt (2022) Engineering flexible machine learning systems by traversing functionally invariant paths in weight space; 10.48550/arXiv.2205.00334
• Zhang, Bao; He, Peng; et al. (2022) A human embryonic limb cell atlas resolved in space and time; 10.1101/2022.04.27.489800
• Pool, Allan-Hermann; Poldsam, Helen; et al. (2022) Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data; 10.1101/2022.04.26.489449
• Nair, Aditya; Karigo, Tomomi; et al. (2022) An approximate line attractor in the hypothalamus that encodes an aggressive internal state; 10.1101/2022.04.19.488776
• Esyunina, Daria; Okhtienko, Anastasiia; et al. (2022) Specific targeting of plasmids with Argonaute enables genome editing; 10.1101/2022.04.14.488398
• Pandey, Ayush; Incer, Inigo; et al. (2022) From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology; 10.1101/2022.04.08.487709
• Suresh, Pooja; Galstyan, Vahe; et al. (2022) Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle; 10.1101/2022.04.08.487649
• Li, Ya-tang and Meister, Markus (2022) Functional Cell Types in the Mouse Superior Colliculus; 10.1101/2022.04.01.486789
• Cohen, Alexander A.; van Doremalen, Neeltje; et al. (2022) Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models; PMCID PMC8978945; 10.1101/2022.03.25.485875
• Dam, Kim-Marie A.; Barnes, Christopher O.; et al. (2022) HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design; 10.1101/2022.03.25.485873
• Wang, Sheng; Garcia-Ojalvo, Jordi; et al. (2022) Periodic spatial patterning with a single morphogen; 10.1101/2022.03.21.484932
• Braun, A. L.; Fabian, D. K.; et al. (2022) Virgin Birth: A genetic basis for facultative parthenogenesis; 10.1101/2022.03.13.484157
• Chure, Griffin; Banks, Rachel A.; et al. (2022) Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth; 10.1101/2022.03.04.483053
• Winnett, Alexander Viloria; Porter, Michael K.; et al. (2022) Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking; 10.1101/2022.03.02.22271724
• Lamanna, Francesco; Hervas-Sotomayor, Francisca; et al. (2022) Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas; 10.1101/2022.02.28.482278
• Morton, James T.; Jin, Dong-Min; et al. (2022) Multi-omic analysis along the gut-brain axis points to a functional architecture of autism; 10.1101/2022.02.25.482050
• Whitehead, Samuel C.; Leone, Sofia; et al. (2022) Neuromuscular embodiment of feedback control elements in Drosophila flight; 10.1101/2022.02.22.481344
• Zhao, Wei and Jensen, Grant J. (2022) In situ architecture of human kinetochore-microtubule interface visualized by cryo-electron tomography; 10.1101/2022.02.17.480955
• Gorin, Gennady; Fang, Meichen; et al. (2022) RNA velocity unraveled; 10.1101/2022.02.12.480214
• Luo, Yicheng; He, Peng; et al. (2022) Maternally inherited siRNAs initiate piRNA cluster formation; 10.1101/2022.02.08.479612
• Metskas, Lauren Ann; Ortega, Davi; et al. (2022) Rubisco forms a lattice inside alpha-carboxysomes; 10.1101/2022.01.24.477598
• Daş, Ersin and Murray, Richard M. (2022) Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions; 10.48550/arXiv.2201.05758
• Chuapoco, Miguel R.; Flytzanis, Nicholas C.; et al. (2022) Intravenous gene transfer throughout the brain of infant Old World primates using AAV; 10.1101/2022.01.08.475342
• Henrickson, Amy; Gorbet, Gary E.; et al. (2021) Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions; 10.1101/2021.12.29.474408
• Magkiriadou, S.; Habel, A.; et al. (2021) Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa; 10.1101/2021.12.23.473106
• Inglis, Alison J.; Guna, Alina; et al. (2021) Coupled protein quality control during nonsense mediated mRNA decay; 10.1101/2021.12.22.473893
• Wilbert, Steven A. and Newman, Dianne K. (2021) The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence; 10.1101/2021.12.09.472001
• Gao, Fan and Pachter, Lior (2021) Efficient pre-processing of Single-cell ATAC-seq data; 10.1101/2021.12.08.471788
• Sun, Jennifer J.; Ryou, Serim; et al. (2021) Self-Supervised Keypoint Discovery in Behavioral Videos; 10.48550/arXiv.2112.05121
• Liang, Xuan; Weberling, Antonia; et al. (2021) E-cadherin mediated Apical Membrane Initiation Site localisation; 10.1101/2021.11.30.470571
• Huang, Shan; Wang, Kaihang; et al. (2021) Genome manipulation by guide-directed Argonaute cleavage; 10.1101/2021.11.17.469050
• Reilly, Douglas K.; Schwarz, Erich M.; et al. (2021) Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in C. elegans; 10.1101/2021.10.26.465928
• Banks, Rachel A.; Galstyan, Vahe; et al. (2021) Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies; 10.1101/2021.10.22.465381
• Guan, Charles; Aflalo, Tyson; et al. (2021) Preserved motor representations after paralysis; 10.1101/2021.10.07.463105
• Mondragón-Palomino, Octavio; Poceviciute, Roberta; et al. (2021) 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa; 10.1101/2021.10.07.463215
• Perry, Elena K.; Siozios, Stefanos; et al. (2021) Structure of an ant-myrmecophile-microbe community; 10.1101/2021.10.04.462948
• Clamons, Samuel E. and Murray, Richard M. (2021) How to model DNA replication in stochastic models of synthetic gene circuits (and why); 10.1101/2021.09.26.461880
• Zhang, Tony; Rosenberg, Matthew; et al. (2021) Endotaxis: A Universal Algorithm for Mapping, Goal-Learning, and Navigation; 10.1101/2021.09.24.461751
• Xu, Shuhui; Li, Kai; et al. (2021) Ratiometric RNA labeling allows dynamic multiplexed analysis of gene circuits in single cells; 10.1101/2021.09.23.461487
• Hu, Chelsea Y. and Murray, Richard M. (2021) Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks; 10.1101/2021.09.12.459953
• Ahmadi, Mohamadreza; Rosolia, Ugo; et al. (2021) Risk-Averse Decision Making Under Uncertainty; 10.48550/arXiv.2109.04082
• Gorin, Gennady; Vastola, John J.; et al. (2021) Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments; 10.1101/2021.09.06.459173
• Zhou, Wen; Gao, Fan; et al. (2021) Single-cell perturbation dissects transcription factor control of progression speed and trajectory choice in early T-cell development; 10.1101/2021.09.03.458944
• Kaplan, Mohammed; Oikonomou, Catherine M.; et al. (2021) A novel widespread bacterial structure related to the flagellar type III secretion system; 10.1101/2021.09.03.458937
• Gugel, Zhannetta V.; Maurais, Elizabeth; et al. (2021) Chronic exposure to odors at naturally occurring concentrations triggers limited plasticity in early stages of Drosophila olfactory processing; 10.1101/2021.09.03.458834
• Chari, Tara; Banerjee, Joeyta; et al. (2021) The Specious Art of Single-Cell Genomics; 10.1101/2021.08.25.457696
• Banerjee, Navonil; Shih, Pei-Yin; et al. (2021) Distinct neural circuits establish the same chemosensory behavior in C. elegans; 10.1101/2021.08.17.456617
• Badithela, Apurva and Murray, Richard M. (2021) Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems; 10.48550/arXiv.2108.05911
• Le, Steven Q.; Kan, Shih-hsin; et al. (2021) Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome; 10.1101/2021.08.06.455469
• Speth, Daan R.; Yu, Feiqiao B.; et al. (2021) Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily; 10.1101/2021.08.02.454472
• Gorin, Gennady and Pachter, Lior (2021) Length Biases in Single-Cell RNA Sequencing of pre-mRNA; 10.1101/2021.07.30.454514
• Meister, Markus (2021) Curved Micro-Electrode Arrays; 10.48550/arXiv.2107.13532
• Zhang, Haifeng; Shang, Renjie; et al. (2021) Evolution of a chordate-specific mechanism for myoblast fusion; 10.1101/2021.07.24.453587
• Santorelli, Marco; Bhamidipati, Pranav; et al. (2021) Cell density controls signal propagation waves in a multicellular synthetic gene circuit; 10.48550/arXiv.2107.08116
• Liu, Wenpeng; Polaczek, Piotr; et al. (2021) FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability; 10.1101/2021.07.08.450798
• Luongo, Francisco J.; Liu, Lu; et al. (2021) Mice and primates use distinct strategies for visual segmentation; 10.1101/2021.07.04.451059
• da Veiga Beltrame, Eduardo; Arnaboldi, Valerio; et al. (2021) Single cell tools for WormBase; 10.1101/2021.07.04.451030
• Beery, Sara; Cole, Elijah; et al. (2021) Species Distribution Modeling for Machine Learning Practitioners: A Review; 10.48550/arXiv.2107.10400
• Keleş, Ümit; Kliemann, Dorit; et al. (2021) Atypical gaze patterns in autism are heterogeneous across subjects but reliable within individuals; 10.1101/2021.07.01.450793
• Wang, Zitong Jerry and Thomson, Matt (2021) Signaling receptor localization maximizes cellular information acquisition in spatially-structured, natural environments; 10.48550/arXiv.2107.00806
• Chen, Xiaoqiao; Chen, Sisi; et al. (2021) Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data; 10.1101/2021.06.15.448478
• Andreev, Andrey; Vasnarungruengkul, Pavee; et al. (2021) Open-Source Thermometer, Temperature Controller, and Light Meter for Use in Animal Facilities and During Experiments; 10.1101/2021.05.18.444705
• Brückner, Adrian; Badroos, Jean M.; et al. (2021) Evolutionary assembly of cooperating cell types in an animal chemical defense system; 10.1101/2021.05.13.444042
• McManus, John B.; Bernhards, Casey B.; et al. (2021) A Method for Cost-Effective and Rapid Characterization of Genetic Parts; 10.1101/2021.04.30.440836
• Galton, Riley; Fejes-Tóth, Katalin; et al. (2021) A somatic piRNA pathway regulates epithelial-to-mesenchymal transition of chick neural crest cells; 10.1101/2021.04.30.442165
• Rozowsky, Joel; Drenkow, Jorg; et al. (2021) Multi-tissue integrative analysis of personal epigenomes; 10.1101/2021.04.26.441442
• Takei, Yodai; Zheng, Shiwei; et al. (2021) Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture; 10.1101/2021.04.26.441547
• Kajikawa, Koichiro; Hulse, Brad K.; et al. (2021) Inhibition is the hallmark of CA3 intracellular dynamics around awake ripples; 10.1101/2021.04.20.440699
• Chongtham, Anjalika; Isas, J. Mario; et al. (2021) Sonicated fibrils of huntingtin exon-1 preferentially seed neurons and produce toxic assemblies; 10.1101/2021.04.16.440200
• Yoo, Bryan B.; Griffiths, Jessica A; et al. (2021) Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice; 10.1101/2021.04.12.439539
• Sun, Jennifer J.; Karigo, Tomomi; et al. (2021) The Multi-Agent Behavior Dataset: Mouse Dyadic Social Interactions; 10.48550/arXiv.2104.02710
• Dahlstrom, Kurt M. and Newman, Dianne K. (2021) Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge; 10.1101/2021.03.28.437412
• Graebener, Josefine B.; Phan-Minh, Tung; et al. (2021) Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture; 10.48550/arXiv.2103.12919
• Sierra, Noemie; Olsman, Noah; et al. (2021) A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration; 10.1101/2021.03.22.434850
• She, Liang; Benna, Marcus K.; et al. (2021) The neural code for face memory; 10.1101/2021.03.12.435023
• Muecksch, Frauke; Weisblum, Yiska; et al. (2021) Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies; PMCID PMC7987023; 10.1101/2021.03.07.434227
• Weissbourd, Brandon; Momose, Tsuyoshi; et al. (2021) Functional modules within a distributed neural network control feeding in a model medusa; 10.1101/2021.02.22.432372
• Booeshaghi, A. Sina and Pachter, Lior (2021) Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing; 10.1101/2021.01.25.428188
• Chure, Griffin; Banks, Rachel A.; et al. (2021) The Anthropocene by the Numbers: A Quantitative Snapshot of Humanity’s Influence on the Planet; 10.48550/arXiv.2101.09620
• Gorin, Gennady and Pachter, Lior (2021) Direct simulation of a stochastically driven multi-step birth-death process; 10.1101/2021.01.20.427480
• Qu, Zijie; Jiang, Jialong; et al. (2021) Programming Boundary Deformation Patterns in Active Networks; 10.48550/arXiv.2101.08464
• Thompson, W. H.; Esteban, O.; et al. (2021) Intracranial electrical stimulation alters meso-scale network integration as a function of network topology; 10.1101/2021.01.16.426941
• Keleş, Ümit; Lin, Chujun; et al. (2021) Efficient prediction of trait judgments from faces using deep neural networks; 10.31234/osf.io/t7hw4
• Irizarry, Jihyun; McGehee, James; et al. (2021) High levels of Dorsal transcription factor downregulate, not promote, snail expression by regulating enhancer action; 10.1101/2021.01.11.426256
• Walton, Sophie J.; Clamons, Samuel E.; et al. (2020) Analysis of Circuits for Dosage Control in Microbial Populations; 10.1101/2020.12.18.423556
• Winnett, Alexander; Cooper, Matthew M.; et al. (2020) SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans; PMCID PMC7743094; 10.1101/2020.12.09.20239467
• Zocchi, Dhruv; Ye, Emily S.; et al. (2020) Stimulus-selective lateral signaling between olfactory afferents enables parallel encoding of distinct CO₂ dynamics; 10.1101/2020.12.03.410571
• Cai, Karena X.; Phan-Minh, Tung; et al. (2020) Rules of the Road: Towards Safety and Liveness Guarantees for Autonomous Vehicles; 10.48550/arXiv.2011.14148
• Pandey, Ayush and Murray, Richard M. (2020) A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression; 10.1101/2020.11.25.399287
• Tsypin, Lev M. and Newman, Dianne K. (2020) Bidirectional redox cycling of phenazine-1-carboxylic acid by Citrobacter portucalensis MBL drives increased nitrate reduction; 10.1101/2020.11.23.395335
• Markaki, Yolanda; Chong, Johnny Gan; et al. (2020) Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome; 10.1101/2020.11.22.393546
• Flynn, Michael J.; Snitser, Olga; et al. (2020) A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic; 10.1101/2020.11.19.20234948
• Arango-Gonzalez, Blanca; Sen, Merve; et al. (2020) Inhibition of VCP preserves retinal structure and function in autosomal dominant retinal degeneration; 10.1101/2020.11.17.384669
• Barlow, Ida L.; Mackay, Eirinn; et al. (2020) A genetic screen identifies dreammist as a regulator of sleep; 10.1101/2020.11.18.388736
• Merk, Liana N.; Shur, Andrey S.; et al. (2020) Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions; 10.1101/2020.11.10.377085
• Chen, Yuxiao; Rosolia, Ugo; et al. (2020) Reactive motion planning with probabilistic safety guarantees; 10.48550/arXiv.2011.03590
• Yamamoto, Masahiro and Shimojo, Shinsuke (2020) The Brain Knows enough to take into account Light and Shadow; 10.1101/2020.10.19.344838
• Piacentino, Michael L.; Hutchins, Erica J.; et al. (2020) Temporal changes in plasma membrane lipid content induce endocytosis to regulate developmental epithelial-to-mesenchymal transition; 10.1101/2020.10.18.344523
• Hutchins, Erica J.; Gandhi, Shashank; et al. (2020) RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification; 10.1101/2020.10.14.338715
• Qiao, Mu and Meister, Markus (2020) Factorized linear discriminant analysis and its application in computational biology; 10.48550/arXiv.2010.02171
• Yatsenko, Dimitri; Moreaux, Laurent C.; et al. (2020) Signal separability in integrated neurophotonics; 10.1101/2020.09.27.315556
• Gorin, Gennady and Pachter, Lior (2020) Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production; 10.1101/2020.09.25.312868
• Barnes, Christopher O.; Jette, Claudia A.; et al. (2020) Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies; 10.1101/2020.08.30.273920
• Le, Henry H.; Wrobel, Chester J.; et al. (2020) Modular metabolite assembly in C. elegans lysosome-related organelles; 10.1101/2020.08.22.262956
• Booeshaghi, A. Sina; Tan, Fayth; et al. (2020) Markedly heterogeneous COVID-19 testing plans among US colleges and universities; 10.1101/2020.08.09.20171223
• Hutchins, Erica J.; Piacentino, Michael L.; et al. (2020) P-bodies are sites of rapid RNA decay during the neural crest epithelial-mesenchymal transition; 10.1101/2020.07.31.231860
• Dobreva, Tatyana; Brown, David; et al. (2020) Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood; 10.1101/2020.07.25.210468
• Shehata, Mohammad; Cheng, Miao; et al. (2020) Team flow is a unique brain state associated with enhanced information integration and neural synchrony; 10.1101/2020.06.17.157990
• Flytzanis, Nicholas C.; Goeden, Nick; et al. (2020) Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids; 10.1101/2020.06.16.152975
• McCaffrey, Erin F.; Donato, Michele; et al. (2020) Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood; 10.1101/2020.06.08.140426
• Gao, Xiaojing J.; Chong, Lucy S.; et al. (2020) Engineering multiple levels of specificity in an RNA viral vector
• Cohen, Bruce N.; Nichols, Aaron L.; et al. (2020) Successful Cessation Programs that Reduce Comorbidity May Explain Surprisingly Low Smoking Rates Among Hospitalized COVID-19 Patients; 10.32388/WURFH0
• Gorasia, Dhana G.; Chreifi, Georges; et al. (2020) In situ structure and organisation of the type IX secretion system; 10.1101/2020.05.13.094771
• Jue, Erik and Ismagilov, Rustem F. (2020) Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays; 10.1101/2020.04.28.20077602
• Hesse, Janis K. and Tsao, Doris Y. (2020) Representation of conscious percept without report in the macaque face patch network; 10.1101/2020.04.22.047522
• Jaffari, Matiar; Aflalo, Tyson; et al. (2020) Neural correlates of cognitive motor signals in primary somatosensory cortex; 10.1101/2020.04.20.041269
• Booeshaghi, A. Sina and Pachter, Lior (2020) Decrease in ACE2 mRNA expression in aged mouse lung; 10.1101/2020.04.02.021451
• Liao, Hsin-I; Kashino, Makio; et al. (2020) Transient Pupil Constriction Reflects and Affects Facial Attractiveness; 10.1101/2020.04.02.021436
• Ren, Xinying and Murray, Richard M. (2020) Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations; 10.1101/2020.03.24.006528
• Weaver, Sara J.; Sazinsky, Matthew H.; et al. (2020) CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ; 10.1101/2020.03.03.975896
• Khazaei, Tahmineh; Williams, Rory L.; et al. (2020) Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community; 10.1101/2020.02.28.968941
• Pandey, Ayush and Murray, Richard M. (2020) Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits; 10.1101/2020.02.15.950840
• Marken, John P.; Xiao, Fangzhou; et al. (2020) A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology; 10.1101/2020.02.18.953620
• Borden, Philip M.; Shivange, Amol V.; et al. (2020) A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies; 10.1101/2020.02.07.939504
• Mayalu, Michaëlle N. and Murray, Richard M. (2020) Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli; 10.1101/2020.01.27.921734
• Mohlin, Sofie; Persson, Camilla U.; et al. (2020) Cancer-associated HIF-2α impacts trunk neural crest stemness; 10.1101/2020.01.22.915199
• Bogatyrev, Said R. and Ismagilov, Rustem F. (2020) Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding; 10.1101/2020.01.22.914705
• Chen, Yuxiao; Dathathri, Sumanth; et al. (2020) Counter-example Guided Learning of Bounds on Environment Behavior; 10.48550/arXiv.2001.07233
• Chen, Sisi; Park, Jong H.; et al. (2019) Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations
• Liu, Yang; Perona, Pietro; et al. (2019) PanDA: Panoptic Data Augmentation; 10.48550/arXiv.1911.12317
• Goldberg, Nathaniel; Knight, Anders M.; et al. (2019) Nitrene Transfer Catalyzed by a Non-Heme Iron Enzyme and Enhanced by Non-Native Small-Molecule Cofactors; 10.26434/chemrxiv.10062044.v1
• Singhal, Vipul and Murray, Richard M. (2019) Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability
• Quinn, Robert A.; Thron, Taren; et al. (2019) Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids; 10.1101/654756
• McCardell, Reed D.; Pandey, Ayush; et al. (2019) Control of density and composition in an engineered two-member bacterial community; 10.1101/632174
• Ding, Fangyuan and Elowitz, Michael B. (2018) Quantitative single-cell splicing analysis reveals an ‘economy of scale’ filter for gene expression; 10.1101/457432
• Murrow, Lyndsay M.; Weber, Robert J.; et al. (2018) Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks; 10.1101/430611
• Einav, Tal; Yazdi, Shahrzad; et al. (2018) Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes; 10.1101/406454
• Filippidis, Ioannis and Murray, Richard M. (2017) Hiding variables when decomposing specifications into GR(1) contracts
• Arichega, Nikos; Dathathri, Sumanth; et al. (2017) Fast Automatic Verification of Large-Scale Systems with Lookup Tables
• Dathathri, Sumanth; Livingston, Scott C.; et al. (2016) Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications
• Swaminathan, Anandh; Gomez, Marcella M.; et al. (2016) Stochastic Gene Expression in Single Gene Oscillator Variants
• Hsiao, Victoria; Cheng, Aileen; et al. (2016) Design and application of stationary phase combinatorial promoters
• Sen, Shaunak and Murray, Richard M. (2015) Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty
• Han, Duo; Mo, Yilin; et al. (2015) Synthesis of Distributed Longitudinal Control Protocols for a Platoon of Autonomous Vehicles
• Yeung, Enoch; Kim, Jongmin; et al. (2015) Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks
• Meng, Xianglin; Baetica, Ania A.; et al. (2015) Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively
• Farahani, Samira S.; Raman, Vasumathi; et al. (2015) Robust Model Predictive Control for Signal Temporal Logic Synthesis
• Guo, Shaobin; Hori, Yutaka; et al. (2015) Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo