<h1 id="division-of-biology-and-biological-engineering"><a
href="./">Division of Biology and Biological Engineering</a></h1>
<h2 id="section">(““)</h2>
<h3 id="monographs-from-caltechauthors">Monographs from <a
href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h3>
<ul>
<li>Edwards, Rhodri T.M.; Antoshechkin, Igor; et al. (2025) <a
href="https://authors.library.caltech.edu/records/43cb9-f9w19">Transcriptome
analysis of the winter tick (Dermacentor albipictus) reveals
sex-specific expression patterns</a>; <a
href="https://doi.org/10.1101/2025.02.17.638687">10.1101/2025.02.17.638687</a></li>
<li>Elder, James R.; Zheng, Jie; et al. (2025) <a
href="https://authors.library.caltech.edu/records/dr3rn-kaj17">An
invariant schema emerges within a neural network during hierarchical
learning of visual boundaries</a>; <a
href="https://doi.org/10.1101/2025.01.30.635821">10.1101/2025.01.30.635821</a></li>
<li>Pimmett, Virginia L; McGehee, James; et al. (2024) <a
href="https://authors.library.caltech.edu/records/bp83m-r0028">Optogenetic
manipulation of nuclear Dorsal reveals temporal requirements and
consequences for transcription</a>; <a
href="https://doi.org/10.1101/2024.11.28.623729">10.1101/2024.11.28.623729</a></li>
<li>Bartol, Thomas M.; Ordyan, Mariam; et al. (2024) <a
href="https://authors.library.caltech.edu/records/6e0sn-ana02">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</a>; <a
href="https://doi.org/10.1101/2024.02.02.578696">10.1101/2024.02.02.578696</a></li>
<li>Chen, Peiwei; Pan, Katherine C.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/83m3n-asa28">Escalation
of genome defense capacity enables control of an expanding meiotic
driver</a>; PMCID PMC11195268; <a
href="https://doi.org/10.1101/2024.06.12.598716">10.1101/2024.06.12.598716</a></li>
<li>Chen, Alex B.; Duque, Marc; et al. (2024) <a
href="https://authors.library.caltech.edu/records/k7qr3-2qd45">Norepinephrine
changes behavioral state via astroglial purinergic signaling</a>; PMCID
PMC11142163; <a
href="https://doi.org/10.1101/2024.05.23.595576">10.1101/2024.05.23.595576</a></li>
<li>Rosenthal, Isabelle A.; Bashford, Luke; et al. (2024) <a
href="https://authors.library.caltech.edu/records/yhqsb-0ra69">Visual
context affects the perceived timing of tactile sensations elicited
through intra-cortical microstimulation</a>; PMCID PMC11118490; <a
href="https://doi.org/10.1101/2024.05.13.593529">10.1101/2024.05.13.593529</a></li>
<li>Desingu Rajan, Ayyappa Raja; Huang, Yuanyun; et al. (2024) <a
href="https://authors.library.caltech.edu/records/tkv9m-0sm23">Generation
of a zebrafish neurofibromatosis model via inducible knockout of
nf2</a>; <a
href="https://doi.org/10.1101/2024.04.23.590787">10.1101/2024.04.23.590787</a></li>
<li>Gornet, James A. and Thomson, Matt (2024) <a
href="https://authors.library.caltech.edu/records/e288m-hdm97">Automated
construction of cognitive maps with predictive coding</a>; bioRxiv;
2023.09.18.558369; <a
href="https://doi.org/10.1101/2023.09.18.558369">10.1101/2023.09.18.558369</a></li>
<li>Prywes, Noam; Philips, Naiya R.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/yx22a-92478">A map of
the rubisco biochemical landscape</a>; PMCID PMC11030240; <a
href="https://doi.org/10.1101/2023.09.27.559826">10.1101/2023.09.27.559826</a></li>
<li>Rich, Joseph M.; Moses, Lambda; et al. (2024) <a
href="https://authors.library.caltech.edu/records/gzsw0-46t72">The
impact of package selection and versioning on single-cell RNA-seq
analysis</a>; PMCID PMC11014608; <a
href="https://doi.org/10.1101/2024.04.04.588111">10.1101/2024.04.04.588111</a></li>
<li>Booeshaghi, A. Sina; Galvez-Merchán, Ángel; et al. (2024) <a
href="https://authors.library.caltech.edu/records/e3z09-4wt43">Algorithms
for a Commons Cell Atlas</a>; <a
href="https://doi.org/10.1101/2024.03.23.586413">10.1101/2024.03.23.586413</a></li>
<li>Flynn, Michael James; Mayfield, Acacia M.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/8b5yj-sjn05">Synthetic
dosage-compensating miRNA circuits allow precision gene therapy for Rett
syndrome</a>; bioRxiv; 2024.03.13.584179; PMCID PMC10980028; <a
href="https://doi.org/10.1101/2024.03.13.584179">10.1101/2024.03.13.584179</a></li>
<li>Du, Rongrong; Flynn, Michael J.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/9dhkn-8g759">miRNA
circuit modules for precise, tunable control of gene expression</a>;
bioRxiv; 2024.03.12.583048; PMCID PMC10979901; <a
href="https://doi.org/10.1101/2024.03.12.583048">10.1101/2024.03.12.583048</a></li>
<li>Kubinski, Hannah C.; Despres, Hannah W.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/krzfp-ykm81">Variant
mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered
genomic encapsidation</a>; bioRxiv; 53; PMCID PMC10979914; <a
href="https://doi.org/10.1101/2024.03.08.584120">10.1101/2024.03.08.584120</a></li>
<li>Israel, Uriah; Marks, Markus; et al. (2024) <a
href="https://authors.library.caltech.edu/records/47sqx-33w78">A
Foundation Model for Cell Segmentation</a>; bioRvix; 2023.11.17.567630;
PMCID PMC10690226; <a
href="https://doi.org/10.1101/2023.11.17.567630">10.1101/2023.11.17.567630</a></li>
<li>Wang, Eric; Cohen, Alexander A.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/t9kx7-ggz82">Designed
mosaic nanoparticles enhance cross-reactive immune responses in
mice</a>; PMCID PMC10925254; <a
href="https://doi.org/10.1101/2024.02.28.582544">10.1101/2024.02.28.582544</a></li>
<li>Cohen, Alexander A.; Keeffe, Jennifer R.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/kenyk-gey96">Mosaic
sarbecovirus vaccination elicits cross-reactive responses in
pre-immunized animals</a>; PMCID PMC10871317; <a
href="https://doi.org/10.1101/2024.02.08.576722">10.1101/2024.02.08.576722</a></li>
<li>Flamholz, Avi I.; Goyal, Akshit; et al. (2024) <a
href="https://authors.library.caltech.edu/records/p94bf-gjw45">The
proteome is a terminal electron acceptor</a>; PMCID PMC10862836; <a
href="https://doi.org/10.1101/2024.01.31.578293">10.1101/2024.01.31.578293</a></li>
<li>Huang, Yu Xi; Mahler, Simon; et al. (2024) <a
href="https://authors.library.caltech.edu/records/x8245-s2790">A compact
and cost-effective laser-powered speckle visibility spectroscopy (SVS)
device for measuring cerebral blood flow</a>; PMCID PMC10862935; <a
href="https://doi.org/10.48550/arxiv.2401.16592">10.48550/arxiv.2401.16592</a></li>
<li>Subramanian, Arjuna M. and Thomson, Matt (2023) <a
href="https://authors.library.caltech.edu/records/sv6fh-01002">Unexplored
regions of the protein sequence-structure map revealed at scale by a
library of foldtuned language models</a>; PMCID PMC10769378; <a
href="https://doi.org/10.1101/2023.12.22.573145">10.1101/2023.12.22.573145</a></li>
<li>Polonsky, Michal; Gerhardt, Louisa M. S.; et al. (2023) <a
href="https://authors.library.caltech.edu/records/hx122-ds441">Spatial
transcriptomics defines injury-specific microenvironments in the adult
mouse kidney and novel cellular interactions in regeneration and
disease</a>; bioRxiv; <a
href="https://doi.org/10.1101/2023.11.22.568217">10.1101/2023.11.22.568217</a></li>
<li>Martinez, Zachary A; Murray, Richard M.; et al. (2023) <a
href="https://authors.library.caltech.edu/records/0p6md-nzv84">TRILL:
Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable
Protein Analysis and Engineering</a>; bioRxiv; 2023.10.24.563881; PMCID
PMC10659302; <a
href="https://doi.org/10.1101/2023.10.24.563881">10.1101/2023.10.24.563881</a></li>
<li>Zhang, Shu; Xie, Na; et al. (2023) <a
href="https://authors.library.caltech.edu/records/gyrwr-hfe79">The
Interferon-inducible NAMPT acts as a protein phosphoribosylase to
restrict viral infection</a>; PMCID PMC10614811; <a
href="https://doi.org/10.1101/2023.10.12.562112">10.1101/2023.10.12.562112</a></li>
<li>Wang, Renée Z.; Lonergan, Zachery R.; et al. (2023) <a
href="https://authors.library.caltech.edu/records/gb86g-qpm69">Widespread
detoxifying NO reductases impart a distinct isotopic fingerprint on N₂O
under anoxia</a>; PMCID PMC10592819; <a
href="https://doi.org/10.1101/2023.10.13.562248">10.1101/2023.10.13.562248</a></li>
<li>Bugacov, Helena; Der, Balint; et al. (2023) <a
href="https://authors.library.caltech.edu/records/9js3y-bp315">Canonical
Wnt transcriptional complexes are essential for induction of
nephrogenesis but not maintenance or proliferation of nephron
progenitors</a>; <a
href="https://doi.org/10.1101/2023.08.20.554044">10.1101/2023.08.20.554044</a></li>
<li>Srivastava, Vasudha; Hu, Jennifer L.; et al. (2023) <a
href="https://authors.library.caltech.edu/records/7wsj9-9v221">Configurational
entropy is an intrinsic driver of tissue structural heterogeneity</a>;
PMCID PMC10327153; <a
href="https://doi.org/10.1101/2023.07.01.546933">10.1101/2023.07.01.546933</a></li>
<li>Weatherbee, Bailey A. T.; Gantner, Carlos W.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230629-647980000.1">Transgene
directed induction of a stem cell-derived human embryo model</a>; <a
href="https://doi.org/10.1101/2023.06.15.545082">10.1101/2023.06.15.545082</a></li>
<li>Tran, Martin; Askary, Amjad; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230725-706037000.28">Lineage
motifs: developmental modules for control of cell type proportions</a>;
PMCID PMC10274800; <a
href="https://doi.org/10.1101/2023.06.06.543925">10.1101/2023.06.06.543925</a></li>
<li>Wolin, Erica; Guo, Jimmy K.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230725-706033000.26">SPIDR:
a highly multiplexed method for mapping RNA-protein interactions
uncovers a potential mechanism for selective translational suppression
upon cellular stress</a>; PMCID PMC10274648; <a
href="https://doi.org/10.1101/2023.06.05.543769">10.1101/2023.06.05.543769</a></li>
<li>Huang, Biao; Zeng, Zipeng; et al. (2023) <a
href="https://authors.library.caltech.edu/records/y7n22-pzy74">Modeling
kidney development, disease, and plasticity with clonal expandable
nephron progenitor cells and nephron organoids</a>; <a
href="https://doi.org/10.1101/2023.05.25.542343">10.1101/2023.05.25.542343</a></li>
<li>Gorin, Gennady; Vastola, John J.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257070000.17">Studying
stochastic systems biology of the cell with single-cell genomics
data</a>; PMCID PMC10245677; <a
href="https://doi.org/10.1101/2023.05.17.541250">10.1101/2023.05.17.541250</a></li>
<li>Xiong, Lingyun; Liu, Jing; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257103000.21">Direct
androgen receptor regulation of sexually dimorphic gene expression in
the mammalian kidney</a>; PMCID PMC10187285; <a
href="https://doi.org/10.1101/2023.05.06.539585">10.1101/2023.05.06.539585</a></li>
<li>Prakash, Sharan J.; Van Auken, Kimberly M.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257134000.27">Semantic
Representation of Neural Circuit Knowledge in Caenorhabditis
elegans</a>; PMCID PMC10168330; <a
href="https://doi.org/10.1101/2023.04.28.538760">10.1101/2023.04.28.538760</a></li>
<li>Jiang, Jialong; Chen, Sisi; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257115000.23">D-SPIN
constructs gene regulatory network models from multiplexed scRNA-seq
data revealing organizing principles of cellular perturbation
response</a>; PMCID PMC10153191; <a
href="https://doi.org/10.1101/2023.04.19.537364">10.1101/2023.04.19.537364</a></li>
<li>Mao, Runze; Wackelin, Daniel J.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257200000.36">Enantio-
and Diastereoenriched Enzymatic Synthesis of 1,2,3-Polysubstituted
Cyclopropanes from (Z/E)-Trisubstituted Enol Acetates</a>; PMCID
PMC10120758; <a
href="https://doi.org/10.21203/rs.3.rs-2802333/v1">10.21203/rs.3.rs-2802333/v1</a></li>
<li>Hahn, Joshua; Monavarfeshani, Aboozar; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257286000.41">Evolution
of neuronal cell classes and types in the vertebrate retina</a>; PMCID
PMC10104162; <a
href="https://doi.org/10.1101/2023.04.07.536039">10.1101/2023.04.07.536039</a></li>
<li>Hitz, Benjamin C.; Lee, Jin-Wook; et al. (2023) <a
href="https://authors.library.caltech.edu/records/nep4b-6xt08">The
ENCODE Uniform Analysis Pipelines</a>; <a
href="https://doi.org/10.1101/2023.04.04.535623">10.1101/2023.04.04.535623</a></li>
<li>Kapasiawala, Manisha and Murray, Richard M. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230327-442725000.2">Probing
metabolism in an E. coli-based cell-free system reveals a trade-off
between transcription and translation</a>; <a
href="https://doi.org/10.1101/2023.03.22.533877">10.1101/2023.03.22.533877</a></li>
<li>Sullivan, Delaney K. and Pachter, Lior (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230327-441955000.1">Flexible
parsing and preprocessing of technical sequences with splitcode</a>;
PMCID PMC10055216; <a
href="https://doi.org/10.1101/2023.03.20.533521">10.1101/2023.03.20.533521</a></li>
<li>Dutka, Przemysław; Liu, Yuxi; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230324-517798000.1">Structure
and Function of the Dot/Icm T4SS</a>; <a
href="https://doi.org/10.1101/2023.03.22.533729">10.1101/2023.03.22.533729</a></li>
<li>Booeshaghi, A. Sina; Chen, Xi; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230322-101294000.2">A
machine-readable specification for genomics assays</a>; <a
href="https://doi.org/10.1101/2023.03.17.533215">10.1101/2023.03.17.533215</a></li>
<li>Bernardi, Yanel E.; Sanchez-Vasquez, Estefania; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-181901000.3">Extracellular
vesicle-localized miR-203 mediates neural crest-placode communication
required for trigeminal ganglia formation</a>; <a
href="https://doi.org/10.1101/2023.03.14.532527">10.1101/2023.03.14.532527</a></li>
<li>Stevens, Taylor Anthony; Pinton Tomaleri, Giovani; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-181961000.8">A
nanobody-based strategy for rapid and scalable purification of native
human protein complexes</a>; <a
href="https://doi.org/10.1101/2023.03.09.531980">10.1101/2023.03.09.531980</a></li>
<li>Ji, Jenny; Winnett, Alexander Viloria; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230323-420614000.1">Index
Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More
Transmission to Household Contacts Than Cases Identified by Other Test
Types</a>; <a
href="https://doi.org/10.1101/2023.03.09.23286855">10.1101/2023.03.09.23286855</a></li>
<li>Hills, Rory A.; Tan, Tiong Kit; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182086000.11">Multiviral
Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive
Vaccinology</a>; PMCID PMC9980174; <a
href="https://doi.org/10.1101/2023.02.24.529520">10.1101/2023.02.24.529520</a></li>
<li>Afik, Eldad; Liu, Toni J. B.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182110000.13">Dynamical
states of self-organized waves in a giant single-celled organism feeding
on light</a>; <a
href="https://doi.org/10.1101/2023.02.22.529174">10.1101/2023.02.22.529174</a></li>
<li>Yang, Jie-Yoon; O’Connell, Thomas F.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182203000.19">Restructuring
of olfactory representations in the fly brain around odor relationships
in natural sources</a>; <a
href="https://doi.org/10.1101/2023.02.15.528627">10.1101/2023.02.15.528627</a></li>
<li>Tan, Chieh-Hsiang; Cheng, Kai-Wen; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182235000.22">LINKIN-associated
proteins necessary for tissue integrity during collective cell
migration</a>; <a
href="https://doi.org/10.1101/2023.02.08.527750">10.1101/2023.02.08.527750</a></li>
<li>Santos, Inês B.; Wainman, Alan; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182273000.24">Mob4
is essential for spermatogenesis in Drosophila melanogaster</a>; <a
href="https://doi.org/10.1101/2023.02.05.527206">10.1101/2023.02.05.527206</a></li>
<li>Trautmann, Eric M.; Hesse, Janis K.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182335000.26">Large-scale
brain-wide neural recording in nonhuman primates</a>; <a
href="https://doi.org/10.1101/2023.02.01.526664">10.1101/2023.02.01.526664</a></li>
<li>Wang, Grace Z.; Warren, Elizabeth A.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182348000.27">Staphylococcal
secreted cytotoxins are competition sensing signals for Pseudomonas
aeruginosa</a>; <a
href="https://doi.org/10.1101/2023.01.29.526047">10.1101/2023.01.29.526047</a></li>
<li>Dam, Kim-Marie A.; Fan, Chengcheng; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182374000.28">Structural
characterization of HIV-1 Env heterotrimers bound to one or two CD4
receptors reveals intermediate Env conformations</a>; <a
href="https://doi.org/10.1101/2023.01.27.525985">10.1101/2023.01.27.525985</a></li>
<li>Akella, Prithvi; Ahmadi, Mohamadreza; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-204032253">Barrier-Based
Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid
Specifications</a></li>
<li>Guna, Alina; Page, Katharine R.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182439000.33">A
dual sgRNA library design to probe genetic modifiers using genome-wide
CRISPRi screens</a>; PMCID PMC9882262; <a
href="https://doi.org/10.1101/2023.01.22.525086">10.1101/2023.01.22.525086</a></li>
<li>Gorin, Gennady and Pachter, Lior (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182495000.36">The
telegraph process is not a subordinator</a>; <a
href="https://doi.org/10.1101/2023.01.17.524309">10.1101/2023.01.17.524309</a></li>
<li>Haloi, Nandan; Huang, Shan; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182493000.35">Interactive
computational and experimental approaches improve the sensitivity of
periplasmic binding protein-based nicotine biosensors for measurements
in biofluids</a>; <a
href="https://doi.org/10.1101/2023.01.16.524298">10.1101/2023.01.16.524298</a></li>
<li>Fry, Michelle Y.; Navarro, Paula P.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182139000.16">In
situ architecture of Opa1-dependent mitochondrial cristae
remodeling</a>; <a
href="https://doi.org/10.1101/2023.01.16.524176">10.1101/2023.01.16.524176</a></li>
<li>Kahan, Anat; Coughlin, Gerard M.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182503000.37">Dysregulated
mammalian estrus cycle rescued by timed activation of VIP neurons in the
circadian pacemaker and late afternoon light exposure</a>; <a
href="https://doi.org/10.1101/2023.01.14.524075">10.1101/2023.01.14.524075</a></li>
<li>Ding, Xiaozhe; Chen, Xinhong; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182523000.38">Fast,
accurate ranking of engineered proteins by receptor binding propensity
using structural modeling</a>; <a
href="https://doi.org/10.1101/2023.01.11.523680">10.1101/2023.01.11.523680</a></li>
<li>De Jonghe, Joachim; Kaminski, Tomasz S.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182577000.43">spinDrop:
a droplet microfluidic platform to maximise single-cell sequencing
information content</a>; <a
href="https://doi.org/10.1101/2023.01.12.523500">10.1101/2023.01.12.523500</a></li>
<li>Shay, Timothy F.; Sullivan, Erin E.; et al. (2023) <a
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