<h1 id="division-of-biology-and-biological-engineering"><a
href="./">Division of Biology and Biological Engineering</a></h1>
<h2 id="section">(““)</h2>
<p><a href="https://www.bbe.caltech.edu/"
class="uri">https://www.bbe.caltech.edu/</a></p>
<h3 id="combined-from-caltechauthors">combined from <a
href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h3>
<ul>
<li>Askary, Amjad; Chen, Wei; et al. (2025) <a
href="https://authors.library.caltech.edu/records/ptmsd-9g284">The lives
of cells, recorded</a>; Nature Reviews Genetics; Vol. 26; 203–222; <a
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<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>Swartwood, Brea (2025) <a
href="https://authors.library.caltech.edu/records/xh66z-82844">Stability
analysis of traveling wave fronts in a model for tumor growth</a>;
Nonlinear Analysis: Real World Applications; Vol. 81; 104176; <a
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<li>Urzúa Lehuedé, Tomás; Berdion Gabarain, Victoria; et al. (2025) <a
href="https://authors.library.caltech.edu/records/1y466-f1f68">Two
antagonistic gene regulatory networks drive Arabidopsis root hair growth
at low temperature linked to a low‐nutrient environment</a>; New
Phytologist; <a
href="https://doi.org/10.1111/nph.20406">10.1111/nph.20406</a></li>
<li>Yang, Xi; Yan, An; et al. (2025) <a
href="https://authors.library.caltech.edu/records/4q5w6-zbx77">Single
cell derived multicellular meristem: insights into male-to-hermaphrodite
conversion and de novo meristem formation in ceratopteris</a>;
Development; <a
href="https://doi.org/10.1242/dev.204411">10.1242/dev.204411</a></li>
<li>Lin, Chujun; Keles, Umit; et al. (2025) <a
href="https://authors.library.caltech.edu/records/68gh4-h7n95">How trait
impressions of faces shape subsequent mental state inferences</a>;
Nature Human Behaviour; Vol. 9; 208–226; <a
href="https://doi.org/10.1038/s41562-024-02059-4">10.1038/s41562-024-02059-4</a></li>
<li>Morais, Livia H.; de Castro Fonseca, Matheus; et al. (2025) <a
href="https://authors.library.caltech.edu/records/b8ggc-xy695">The gut
microbiome in animal models of Parkinson’s disease</a>; ISBN
9780443135507; Integrative Omics in Parkinson’s Disease; Academic Press:
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<li>Merk, Liana N.; Shur, Andrey S.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/4kyba-3mm91">Diagnostic
and Therapeutic Microbial Circuit with Application to Intestinal
Inflammation</a>; ACS Synthetic Biology; Vol. 13; No. 12; 3885–3896; <a
href="https://doi.org/10.1021/acssynbio.3c00668">10.1021/acssynbio.3c00668</a></li>
<li>Sánchez-Guardado, Luis; Razavi, Peyman Callejas; et al. (2024) <a
href="https://authors.library.caltech.edu/records/e2mgn-vgp08">Projection
neurons are necessary for the maintenance of the mouse olfactory
circuit</a>; eLife; Vol. 13; <a
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<li>Sakai, Alexandra; Singh, Gagandeep; et al. (2024) <a
href="https://authors.library.caltech.edu/records/hy9vj-3dr12">Inhibition
of SARS-CoV-2 growth in the lungs of mice by a peptide-conjugated
morpholino oligomer targeting viral RNA</a>; Moleclar Therapy - Nucleic
Acids; Vol. 35; No. 4; 102331; <a
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<li>Cao, Runnan; Dubois, Julien; et al. (2024) <a
href="https://authors.library.caltech.edu/records/v4b3d-hj608">Domain-specific
representation of social inference by neurons in the human amygdala and
hippocampus</a>; Science Advances; Vol. 10; No. 49; <a
href="https://doi.org/10.1126/sciadv.ado6166">10.1126/sciadv.ado6166</a></li>
<li>Haghi, Benyamin; Aflalo, Tyson; et al. (2024) <a
href="https://authors.library.caltech.edu/records/emwed-ap219">Enhanced
control of a brain–computer interface by tetraplegic participants via
neural-network-mediated feature extraction</a>; Nature Biomedical
Engineering; <a
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<li>DeLaitsch, Andrew T.; Keeffe, Jennifer R.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/d2dj5-06650">Neutralizing
antibodies elicited in macaques recognize V3 residues on altered
conformations of HIV-1 Env trimer</a>; npj Vaccines; Vol. 9; No. 1; 240;
<a
href="https://doi.org/10.1038/s41541-024-01038-0">10.1038/s41541-024-01038-0</a></li>
<li>Jing, Zeyu and Meister, Markus (2024) <a
href="https://authors.library.caltech.edu/records/dtcph-c8p37">A Fast
Algorithm for All-Pairs-Shortest-Paths Suitable for Neural Networks</a>;
Neural Computation; Vol. 36; No. 12; 2710-2733; <a
href="https://doi.org/10.1162/neco_a_01716">10.1162/neco_a_01716</a></li>
<li>Squyres, Georgia R and Newman, Dianne (2024) <a
href="https://authors.library.caltech.edu/records/9try3-cyw51">Biofilms
as more than the sum of their parts: lessons from developmental
biology</a>; Current Opinion in Microbiology; Vol. 82; 102537; <a
href="https://doi.org/10.1016/j.mib.2024.102537">10.1016/j.mib.2024.102537</a></li>
<li>Felce, Catherine; Gorin, Gennady; et al. (2024) <a
href="https://authors.library.caltech.edu/records/fsw5x-9ty83">Biophysical
model for joint analysis of chromatin and RNA sequencing data</a>;
Physical Review E; Vol. 110; No. 6; 064405; <a
href="https://doi.org/10.1103/physreve.110.064405">10.1103/physreve.110.064405</a></li>
<li>Castillo-Ramírez, Luis A.; Herget, Ulrich; et al. (2024) <a
href="https://authors.library.caltech.edu/records/v5p73-51823">Early-life
challenge enhances cortisol regulation in zebrafish larvae</a>; Biology
Open; Vol. 13; No. 12; <a
href="https://doi.org/10.1242/bio.061684">10.1242/bio.061684</a></li>
<li>Nayak, Rohit; Duan, Mengtong; et al. (2024) <a
href="https://authors.library.caltech.edu/records/6fx9y-j4k93">Harmonic
imaging for nonlinear detection of acoustic biomolecules</a>; APL
Bioengineering; Vol. 8; No. 4; 046110; <a
href="https://doi.org/10.1063/5.0214306">10.1063/5.0214306</a></li>
<li>Srivastava, Aruesha; Nair, Aryana; et al. (2024) <a
href="https://authors.library.caltech.edu/records/vr30s-p7m50">Structures
of Trichomonas vaginalis macrophage migratory inhibitory factor</a>;
Acta Crystallographica. Section F; Vol. 80; No. 12; 341-347; <a
href="https://doi.org/10.1107/s2053230x24011105">10.1107/s2053230x24011105</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>Watanabe, Kiichi; Chiu, Hui; et al. (2024) <a
href="https://authors.library.caltech.edu/records/q0dwg-m3483">Whole-brain
in situ mapping of neuronal activation in Drosophila during social
behaviors and optogenetic stimulation</a>; eLife; Vol. 12; <a
href="https://doi.org/10.7554/elife.92380">10.7554/elife.92380</a></li>
<li>Ciemniecki, John A.; Ho, Chia-Lun; et al. (2024) <a
href="https://authors.library.caltech.edu/records/f791y-k9a09">Mechanistic
study of a low-power bacterial maintenance state using high-throughput
electrochemistry</a>; Cell; Vol. 187; No. 24; 6882-6895.e8; <a
href="https://doi.org/10.1016/j.cell.2024.09.042">10.1016/j.cell.2024.09.042</a></li>
<li>Wang, Tongtong; Teng, Bochuan; et al. (2024) <a
href="https://authors.library.caltech.edu/records/mzwp5-r8p90">Organ-specific
sympathetic innervation defines visceral functions</a>; Nature; <a
href="https://doi.org/10.1038/s41586-024-08269-0">10.1038/s41586-024-08269-0</a></li>
<li>Jaeger, Eliza C.B.; Vijatovic, David; et al. (2024) <a
href="https://authors.library.caltech.edu/records/ycgaf-qrk68">Adeno-associated
viral tools to trace neural development and connectivity across
amphibians</a>; Developmental Cell; <a
href="https://doi.org/10.1016/j.devcel.2024.10.025">10.1016/j.devcel.2024.10.025</a></li>
<li>Perez, Andrew A.; Goronzy, Isabel N.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/nskhx-1k517">ChIP-DIP
maps binding of hundreds of proteins to DNA simultaneously and
identifies diverse gene regulatory elements</a>; Nature Genetics; Vol.
56; 2827–2841; <a
href="https://doi.org/10.1038/s41588-024-02000-5">10.1038/s41588-024-02000-5</a></li>
<li>Feng, Shu; Xie, Na; et al. (2024) <a
href="https://authors.library.caltech.edu/records/br891-6cj18">Cryptic
phosphoribosylase activity of NAMPT restricts the virion incorporation
of viral proteins</a>; Nature Metabolism; Vol. 6; 2300–2318; <a
href="https://doi.org/10.1038/s42255-024-01162-0">10.1038/s42255-024-01162-0</a></li>
<li>Kirby, Emily; Bernier, Alexander; et al. (2024) <a
href="https://authors.library.caltech.edu/records/76n5r-79b06">Data
sharing ethics toolkit: The Human Cell Atlas</a>; Nature Communications;
Vol. 15; No. 1; 9901; <a
href="https://doi.org/10.1038/s41467-024-54300-3">10.1038/s41467-024-54300-3</a></li>
<li>Kapasiawala, Manisha and Murray, Richard M. (2024) <a
href="https://authors.library.caltech.edu/records/nwqa7-8hz87">Metabolic
Perturbations to an Escherichia coli-based Cell-Free System Reveal a
Trade-off between Transcription and Translation</a>; ACS Synthetic
Biology; Vol. 13; No. 12; 3976–3990; <a
href="https://doi.org/10.1021/acssynbio.4c00361">10.1021/acssynbio.4c00361</a></li>
<li>Amit, Ido; Ardlie, Kristin; et al. (2024) <a
href="https://authors.library.caltech.edu/records/m3h3f-bx245">The
commitment of the human cell atlas to humanity</a>; Nature
Communications; Vol. 15; No. 1; 10019; <a
href="https://doi.org/10.1038/s41467-024-54306-x">10.1038/s41467-024-54306-x</a></li>
<li>Santorelli, Marco; Bhamidipati, Pranav S.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/qkjf6-g0038">Control
of spatio-temporal patterning via cell growth in a multicellular
synthetic gene circuit</a>; Nature Communications; Vol. 15; 9867; <a
href="https://doi.org/10.1038/s41467-024-53078-8">10.1038/s41467-024-53078-8</a></li>
<li>Ladinsky, Mark S.; Zhu, Li; et al. (2024) <a
href="https://authors.library.caltech.edu/records/7xpn1-ydf37">Electron
tomography visualization of HIV-1 virions trapped by fusion inhibitors
to host cells in infected tissues</a>; Journal of Virology; Vol. 98;
No. 11; e01432-24; PMCID PMC11575291; <a
href="https://doi.org/10.1128/jvi.01432-24">10.1128/jvi.01432-24</a></li>
<li>Zhao, Bingqian; He, Xiaolong; et al. (2024) <a
href="https://authors.library.caltech.edu/records/htqch-sg711">Multi-touch
microcapsules/silicone-polyacrylate hybrid hydrogels with precise
self-healing ability and their self-powered sensing applications in
emergency rescue</a>; Chemical Engineering Journal; Vol. 500; 157149; <a
href="https://doi.org/10.1016/j.cej.2024.157149">10.1016/j.cej.2024.157149</a></li>
<li>Horak, Richard D.; Ciemniecki, John A.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/2jjh1-b6827">Bioenergetic
suppression by redox-active metabolites promotes antibiotic tolerance in
Pseudomonas aeruginosa</a>; Proceedings of the National Academy of
Sciences; Vol. 121; No. 46; e2406555121; <a
href="https://doi.org/10.1073/pnas.2406555121">10.1073/pnas.2406555121</a></li>
<li>Tamborini, Alessio and Gharib, Morteza (Mory) (2024) <a
href="https://authors.library.caltech.edu/records/fj56e-wda77">Listening
to heart sounds through the pressure waveform</a>; Scientific Reports;
Vol. 14; No. 1; 26824; <a
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<li>Sun, Jiaqiu Vince; Jing, Zeyu; et al. (2024) <a
href="https://authors.library.caltech.edu/records/13gs9-f1j05">Perceptual
tri-stability, measured and fitted as emergent from a model for bistable
alternations</a>; Hearing Research; Vol. 453; 109123; <a
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<li>Sader, John E.; Gomez, Alfredo; et al. (2024) <a
href="https://authors.library.caltech.edu/records/4zdw5-mp771">Data-driven
fingerprint nanoelectromechanical mass spectrometry</a>; Nature
Communications; Vol. 15; No. 1; 8800; <a
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<li>Hadas, Ron; Rubinstein, Hernan; et al. (2024) <a
href="https://authors.library.caltech.edu/records/wgy1x-2tf47">Temporal
BMP4 effects on mouse embryonic and extraembryonic development</a>;
Nature; Vol. 634; 652–661; <a
href="https://doi.org/10.1038/s41586-024-07937-5">10.1038/s41586-024-07937-5</a></li>
<li>Shin, Boyoung; Chang, Samantha J.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/8g24g-3gt04">Transcriptional
network dynamics in early T cell development</a>; Journal of
Experimental Medicine; Vol. 221; No. 10; e20230893; <a
href="https://doi.org/10.1084/jem.20230893">10.1084/jem.20230893</a></li>
<li>Zhang, Mark G.; Seyedolmohadesin, Maedeh; et al. (2024) <a
href="https://authors.library.caltech.edu/records/s3rqe-9t165">Sensory
integration of food and population density during the diapause exit
decision involves insulin-like signaling in Caenorhabditis elegans</a>;
Proceedings of the National Academy of Sciences; Vol. 121; No. 40;
e2405391121; <a
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<li>Lu, Chenyue; Pankaj, Amaya; et al. (2024) <a
href="https://authors.library.caltech.edu/records/wjyhf-peh09">HCC
spatial transcriptomic profiling reveals significant and potentially
targetable cancer-endothelial interactions</a>; Hepatology
Communications; Vol. 8; No. 10; e0533; <a
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<li>Huang, Buwei; Abedi, Mohamad; et al. (2024) <a
href="https://authors.library.caltech.edu/records/vg97s-rq795">Designed
endocytosis-inducing proteins degrade targets and amplify signals</a>;
Nature; No. 8031; <a
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<li>Varshavsky, Alexander (2024) <a
href="https://authors.library.caltech.edu/records/7sxh5-9ty59">N-degron
pathways</a>; Proceedings of the National Academy of Sciences; Vol. 121;
No. 39; e2408697121; <a
href="https://doi.org/10.1073/pnas.2408697121">10.1073/pnas.2408697121</a></li>
<li>Agrawal, Parul; Knudsen, Maria L.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/zyjk6-2nv88">Short
CDRL1 in intermediate VRC01-like mAbs is not sufficient to overcome key
glycan barriers on HIV-1 Env</a>; Journal of Virology; <a
href="https://doi.org/10.1128/jvi.00744-24">10.1128/jvi.00744-24</a></li>
<li>Polonsky, Michal; Gerhardt, Louisa M. S.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/0j638-jx111">Spatial
transcriptomics defines injury specific microenvironments and cellular
interactions in kidney regeneration and disease</a>; Nature
Communications; Vol. 15; No. 1; 7010; PMCID PMC11377535; <a
href="https://doi.org/10.1038/s41467-024-51186-z">10.1038/s41467-024-51186-z</a></li>
<li>Coppinger, Macey; Liu, Yang; et al. (2024) <a
href="https://authors.library.caltech.edu/records/6mrrp-vss30">Transient
infection of Euprymna scolopes with an engineered D-alanine auxotroph of
Vibrio fischeri</a>; Applied and Environmental Microbiology; e01298-24;
<a
href="https://doi.org/10.1128/aem.01298-24">10.1128/aem.01298-24</a></li>
<li>Flamholz, Avi I.; Goldford, Joshua E.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/2b7eq-e6f31">Annotation-free
prediction of microbial dioxygen utilization</a>; mSystems; e00763-24;
<a
href="https://doi.org/10.1128/msystems.00763-24">10.1128/msystems.00763-24</a></li>
<li>Iton, Zachery W. B.; Irving-Singh, Zion; et al. (2024) <a
href="https://authors.library.caltech.edu/records/sjez0-mxg64">Modular
MPS₃-Based Frameworks for Superionic Conduction of Monovalent and
Multivalent Ions</a>; Journal of the American Chemical Society; Vol.
146; No. 35; 24398–24414; <a
href="https://doi.org/10.1021/jacs.4c06263">10.1021/jacs.4c06263</a></li>
<li>Der, Balint; Bugacov, Helena; et al. (2024) <a
href="https://authors.library.caltech.edu/records/r141a-y3457">Cadherin
Adhesion Complexes Direct Cell Aggregation in the Epithelial Transition
of Wnt-Induced Nephron Progenitor Cells</a>; Development; Vol. 151;
No. 18; dev202303; <a
href="https://doi.org/10.1242/dev.202303">10.1242/dev.202303</a></li>
<li>Bugacov, Helena; Der, Balint; et al. (2024) <a
href="https://authors.library.caltech.edu/records/hm5da-j0y83">Dose-dependent
responses to canonical Wnt transcriptional complexes in the regulation
of mammalian nephron progenitors</a>; Development; Vol. 151; No. 18;
dev202279; <a
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<li>Niu, Xubo; Melendez, Delmy L.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/8wea3-q4s67">A
conserved transcription factor regulatory program promotes tendon
fate</a>; Developmental Cell; Vol. 59; 1-18; <a
href="https://doi.org/10.1016/j.devcel.2024.08.006">10.1016/j.devcel.2024.08.006</a></li>
<li>Zhang, Oumeng; Alcalde, Reinaldo E.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/xb3nm-mp669">Investigating
3D microbial community dynamics of the rhizosphere using quantitative
phase and fluorescence microscopy</a>; Proceedings of the National
Academy of Sciences; Vol. 121; No. 33; e2403122121; <a
href="https://doi.org/10.1073/pnas.2403122121">10.1073/pnas.2403122121</a></li>
<li>Kim, Sunghyun; Koppitch, Kari; et al. (2024) <a
href="https://authors.library.caltech.edu/records/vyc94-44e78">Comparative
single-cell analyses identify shared and divergent features of human and
mouse kidney development</a>; Developmental Cell; <a
href="https://doi.org/10.1016/j.devcel.2024.07.013">10.1016/j.devcel.2024.07.013</a></li>
<li>Dong, Zhenyu; Mahler, Simon; et al. (2024) <a
href="https://authors.library.caltech.edu/records/84yvb-jx277">Non-invasive
laser speckle contrast imaging (LSCI) of extra-embryonic blood vessels
in intact avian eggs at early developmental stages</a>; Biomedical
Optics Express; Vol. 15; No. 8; 4605-4624; <a
href="https://doi.org/10.1364/boe.530366">10.1364/boe.530366</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
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<li>Garibyan, Mher; Hoffman, Tyler; et al. (2024) <a
href="https://authors.library.caltech.edu/records/81t8j-xc538">Engineering
programmable material-to-cell pathways via synthetic notch receptors to
spatially control differentiation in multicellular constructs</a>;
Nature Communications; Vol. 15; 5891; PMCID PMC11246427; <a
href="https://doi.org/10.1038/s41467-024-50126-1">10.1038/s41467-024-50126-1</a></li>
<li>Kitchen, Sheila A.; Naragon, Thomas H.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/8n92k-h7b39">The
genomic and cellular basis of biosynthetic innovation in rove
beetles</a>; Cell; Vol. 187; No. 14; 1-22; <a
href="https://doi.org/10.1016/j.cell.2024.05.012">10.1016/j.cell.2024.05.012</a></li>
<li>Treidel, Lisa A.; Deem, Kevin D.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/0yz0e-t8s96">Insect
Flight: State of the Field and Future Directions</a>; Integrative And
Comparative Biology; icae106; <a
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