@article{22959,
  abstract     = {With this status report, we aim to provide a timely snapshot of the protein engineering field as a broad and rapidly advancing discipline that integrates computational, molecular biology, structure-guided, evolutionary, and synthetic approaches to create new and improved proteins with tailored structures and useful functions. The report is organized into eight thematic areas spanning core methodologies and major application domains, including enzymes, therapeutics, detection, synthetic biology, and materials. Contributions from experts across these areas highlight both the historical foundations and recent advances in their respective fields, with particular emphasis on the growing influence of machine learning and artificial intelligence-based methods. Emerging from this broad overview is a central message: protein engineering appears to be entering a golden age, defined by a rapidly accelerating pace of progress, even as significant challenges in design, screening, and real-world application remain. Looking ahead, the continued integration of computational and experimental strategies is poised to further accelerate the impact of protein engineering across an expanding range of economically and societally important sectors, from therapeutics and molecular imaging to diagnostics, plastic recycling, and industrial chemistry.},
  author       = {Ai, Hui-wang and Arnold, Frances H and Barrick, Doug and Bayley, Hagan and Brownless, Alfie-Louise R and Campbell, Robert E and Castells-Graells, Roger and Chaiyen, Pimchai and Chica, Roberto A and Chisholm, Lauren O and Christ, Daniel and Chu, Guo-Chao and Chungyoun, Michael and Eijsink, Vincent G H and Elowitz, Michael B and Fansher, Douglas J and Fasan, Rudi and Foley, Gabriel and Frei, Michelle S and Gagsteiger, Andreas and Gao, Ruiyan and Gillam, Elizabeth M J and Gray, Jeffrey J and Guerra, Luis F and Höcker, Birte and Jin, Zhiyang and Kamerlin, Shina Caroline Lynn and Koga, Nobuyasu and Kontermann, Roland E and Kuhlman, Brian and Langlois, Olivia A and Li, Dongyang and Lins, Roberto D and Liu, Chang C and Liu, Lei and López Barreiro, Diego and Lu, Peilong and Mehta, Sohum and Miyazaki, Ikumi and Müller, Manuel M and Muyldermans, Serge and Nemoto, Naoto and Nivala, Jeff and Nuñez, James K and Ornelas, Izaiah J and Pelletier, Joelle N and Plückthun, Andreas and Porth, Owen T and Prakinee, Kridsadakorn and Qing, Yujia and Reisenbauer, Julia and Schmidt, Sandy and Seifert, Oliver and Shapiro, Mikhail G and Sharma, Rachna and Singh, Nilmani and Smith, Benjamin J and Spangler, Jamie B and Tatsumi-Koga, Rie and Terai, Takuya and Terholsen, Henrik and Tolhurst, Mattias and Tripp, Katherine W and Trossmann, Vanessa Tanja and Tucker, Chandra L and Turak, Onur and Van Deventer, James A and Várnai, Anikó and Viana, Isabelle F T and Weeks, Amy M and Wittrup, K Dane and Wong, Kingsley L-J and Xi, Chenggang and Yeates, Todd O and Yeh, Andy Hsien-Wei and Zhang, Jin and Zhang, Tiger S and Zhao, Huimin and Zheng, Fang and Zhu, Jingyi and Zinn, Sacha},
  issn         = {1741-0134},
  journal      = {Protein Engineering, Design and Selection},
  publisher    = {Oxford University Press},
  title        = {{Protein engineering: Status report}},
  doi          = {10.1093/protein/gzag020},
  volume       = {39},
  year         = {2026},
}

@phdthesis{21198,
  abstract     = {In recent years there has been a massive increase in the amount of data generated in a
decentralized manner. Ever more powerful edge devices, such as smartphones, have become
ubiquitous in most societies on earth. Through text typed, photos taken and apps used,
these devices, which we refer to as clients, generate enormous amounts of high quality and
complex data. Moreover, the nature of these devices means the data they generate is often
sensitive and privacy concerns prevent it being gathered and stored in a central location. This
presents a challenge to the modern machine learning paradigm that requires central access
to large amounts of data. Federated learning (FL) has emerged as one of the answers to
this problem. Rather than bringing the data to the model, FL sends the model to the data.
Model training takes place on device, with periodically synchronized updates, allowing data to
remain locally stored. While this approach offers significant privacy advantages it comes with
its own set of unique challenges. These include: data heterogeneity, the notion that different
devices generate data in distinct ways which can negatively impact training dynamics; systems
heterogeneity, meaning that different devices may have differing hardware specifications; high
communication costs, which are induced by the repeated transferring of models over the
network and low device computational power, which limits the use of larger models on device.
In this thesis we present a range of methods for federated learning. We focus primarily on
the challenge of data heterogeneity, though the methods presented are designed to be well
adapted to the other challenges of a federated setting, such as the constraints of limited
compute and communication overhead. We first present a method for explicitly modeling client
data heterogeneity. The approach formulates clients as samples from a certain probability
distribution and infers the parameters of this distribution from the available training clients.
This learned distribution then represents the heterogeneity present among the clients and can
be sampled from in order to create new simulated clients that are similar to the real clients we
have observed so far. Following this we present two methods for directly dealing with data
heterogeneity through personalization. Highly heterogeneous client data distributions can mean
that learning a single global model becomes suboptimal, and some form of personalization of
models to each individual client is required. Our approaches are based around hypernetworks,
which we use to generate personalized model parameters without the need for additional
training or finetuning. In the first approach we focus on generating full parameterizations of
client models using learned embeddings of client data and labels, with a hypernetwork located
on the central server. In the second approach we address the more challenging scenario where
we want to generate a personalized model for a client without any label information. The
hypernetwork is trained to generate a low dimensional representation of a client’s personalized
model parameters, allowing it to be transferred to and run on the client devices. In our final
presented method, we change our focus and rather than aim to directly address the challenge
of data heterogeneity, we instead ensure we are unaffected by it. This is done in the context
of k-means clustering and we present a method for federated clustering with a focus on added
privacy guarantees.},
  author       = {Scott, Jonathan A},
  issn         = {2663-337X},
  pages        = {158},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data heterogeneity and personalization in federated learning}},
  doi          = {10.15479/AT-ISTA-21198},
  year         = {2026},
}

@phdthesis{21854,
  abstract     = {As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.

First, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.

},
  author       = {Iofinova, Eugenia B},
  issn         = {2663-337X},
  pages        = {237},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{On the utility and effects of efficiency in artificial neural networks}},
  doi          = {10.15479/AT-ISTA-21854},
  year         = {2026},
}

@article{22960,
  abstract     = {We construct and characterize a sample of 146 little red dots (LRDs) across 2.0<z<9.3, selecting all sources with v-shaped
ultraviolet (UV)–optical continua from James Webb Space Telescope (JWST) NIRSpec/PRISM spectra and compact morphologies in NIRCam/F444W imaging. We show that LRD continuum spectra are well described by modified blackbodies
across ∼ 0.4 − 1.0 µm, with typical T ∼ 5000 K (λpeak ∼ 0.65 µm) across 2 dex in luminosity, and a tail toward T ∼ 2000 K.
LRDs therefore trace a locus in the Hertzsprung–Russell diagram that is analogous to stars on the Hayashi track, strongly
supporting the picture that LRDs are active galactic nucleus (AGN) embedded in optically thick dense gas envelopes.
Hotter LRDs with λpeak < 0.65 µm typically have strong Balmer breaks, redder UV slopes, and high optical luminosities;
other LRDs show weak or no Balmer breaks, and wide variety in βUV and L5100. Crucially, we demonstrate that the UV–
optical continua are strongly linked to the Hα, Hβ, [O iii], and O i line properties. There is a tight linear relation between
the Hα and optical continuum luminosities, as well as Hα and O i λ8446, indicating that Balmer, O i, and optical emission
must primarily be powered by the same source. The Balmer decrement increases strongly toward higher LHα, L5100, and
Balmer break strength, providing key evidence for luminosity-dependent effects of collisional (de-)excitation and resonant
scattering in the gaseous envelopes. In contrast, we show that [O iii] emission likely originates from star-forming host
galaxies, with strong variation in the AGN-to-host ratio among the LRD population. Our work presents an empirical
description of the nature and structure of LRDs, defining a new benchmark for ongoing LRD model developments.},
  author       = {de Graaff, Anna and Hviding, Raphael E and Naidu, Rohan P and Greene, Jenny E and Miller, Tim B and Leja, Joel and Matthee, Jorryt J and Brammer, Gabriel and Katz, Harley and Bezanson, Rachel and Boogaard, Leindert A and Bose, Sownak and Chisholm, John and Cleri, Nikko J and Dayal, Pratika and Feldmann, Robert and Fudamoto, Yoshinobu and Fujimoto, Seiji and Furtak, Lukas J and Glazebrook, Karl and Gottumukkala, Rashmi and Heintz, Kasper E and Kokorev, Vasily and Labbe, Ivo and Maseda, Michael V and McConachie, Ian and Nanayakkara, Themiya and Nelson, Erica and Nowaczyk, Przemysław and Oesch, Pascal A and Rix, Hans-Walter and Setton, David J and Torralba Torregrosa, Alberto and Walter, Fabian and Wang, Bingjie and Weibel, Andrea and van der Wel, Arjen},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  number       = {3},
  publisher    = {Oxford University Press},
  title        = {{Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy}},
  doi          = {10.1093/mnras/stag1567},
  volume       = {551},
  year         = {2026},
}

@article{21982,
  abstract     = {A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces.},
  author       = {Diaz Melian, Vicente L and Lenton, Isaac C and Binysh, Jack and Souslov, Anton and Waitukaitis, Scott R},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Geometry of the vapor layer under a Leidenfrost hydrogel sphere}},
  doi          = {10.1103/m7gr-2t6j},
  volume       = {113},
  year         = {2026},
}

@phdthesis{23005,
  abstract     = {When a Leidenfrost droplet floats on its own vapor layer, the interplay between vapor pressure, surface tension, and gravity determines its shape, and in the stable regime the underside of the droplet exhibits curvature inversion. Using interferometric imaging, we observe a different behavior for a levitated hydrogel sphere. Curvature inversion appears briefly after deposition, but the continuous vaporization process removes this feature, leading first to an oscillatory regime and eventually to a steady state without curvature inversion. We demonstrate the essential role of vaporization in shaping the hydrogel underbelly, where direct mass loss has a stronger influence than the balance between vapor pressure and elastic forces.},
  author       = {Diaz Melian, Vicente L},
  issn         = {2663-337X},
  pages        = {114},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The morphology underneath a levitated hydrogel sphere}},
  doi          = {10.15479/AT-ISTA-23005},
  year         = {2026},
}

@phdthesis{22981,
  author       = {Gruber, Nathalie},
  issn         = {2663-337X},
  pages        = {102},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Genetic strategies enabling bacterial adaptation to selective pressures}},
  doi          = {10.15479/AT-ISTA-22981},
  year         = {2026},
}

@article{21743,
  abstract     = {We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden–Weinstein structure. Our method integrates the Liouville 1-form of the Marsden–Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures.},
  author       = {Bauer, Martin and Ishida, Sadashige and Michor, Peter W.},
  issn         = {1432-1467},
  journal      = {Journal of Nonlinear Science},
  number       = {2},
  publisher    = {Springer Nature},
  title        = {{Symplectic structures on the space of space curves}},
  doi          = {10.1007/s00332-026-10266-8},
  volume       = {36},
  year         = {2026},
}

@article{14703,
  abstract     = {We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.},
  author       = {Ishida, Sadashige and Lavenant, Hugo},
  issn         = {1615-3383},
  journal      = {Foundations of Computational Mathematics},
  keywords     = {Optimal transport, Hamilton-Jacobi equation, convex optimization},
  pages        = {349--384},
  publisher    = {Springer Nature},
  title        = {{Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation}},
  doi          = {10.1007/s10208-024-09686-3},
  volume       = {26},
  year         = {2026},
}

@article{20657,
  abstract     = {The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². },
  author       = {Edelsbrunner, Herbert and Pach, János},
  issn         = {1432-0444},
  journal      = {Discrete & Computational Geometry},
  pages        = {597--624},
  publisher    = {Springer Nature},
  title        = {{Maximum Betti numbers of Čech complexes}},
  doi          = {10.1007/s00454-025-00796-5},
  volume       = {75},
  year         = {2026},
}

@article{20585,
  abstract     = {Motivated by applications in medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided.},
  author       = {Cultrera di Montesano, Sebastiano and Draganov, Ondrej and Edelsbrunner, Herbert and Saghafian, Morteza},
  issn         = {2639-8001},
  journal      = {Foundations of Data Science},
  keywords     = {Topological data analysis, Delaunay mosaic, alpha complex, chromatic sets, persistent homology, kernel/image/cokernel persistent homology, radius function, discrete Morse theory, exact sequences},
  pages        = {30--62},
  publisher    = {AIMS},
  title        = {{Chromatic alpha complexes}},
  doi          = {10.3934/fods.2025003},
  volume       = {8},
  year         = {2026},
}

@phdthesis{22804,
  abstract     = {Embryo cleavage — a series of rapid, reductive cell divisions — is the first morphogenetic movement following fertilisation. It lays the foundation for subsequent developmental events, including gastrulation, germ layer specification, organogenesis, and the establishment of the overall body plan. Two major modes of cleavage exist in the animal kingdom: holoblastic (complete) and meroblastic (incomplete) cleavage. Because holoblastic cleavage resembles canonical cytokinesis, its biochemical and mechanical basis has been extensively studied — an annular contractile ring forms at the equator and constricts in a purse-string-like manner, leading to the complete separation of two daughter cells. In contrast, although meroblastic cleavage occurs widely across the animal kingdom (e.g. in fish, reptiles, birds, and cephalopod molluscs), its mechanical basis remains largely unclear. During meroblastic cleavage, the cytokinetic furrow forms only at one pole and does not traverse the entire embryo, raising the question of how cytokinesis proceeds in the absence of a closed contractile ring. Moreover, the resulting daughter cells are not fully separated from the underlying yolk compartment, and how these blastomeres are subsequently cellularised remains unknown. This thesis takes the zebrafish as a model organism to address both questions. The first part characterises the biochemical and mechanical mechanisms underlying non-canonical meroblastic cleavage, revealing a two-phase process in which actomyosin cable contraction and cadherin-mediated membrane adhesion act sequentially to drive furrow ingression and invagination. The second part sheds light on the spatiotemporal dynamics by which individual blastomeres become cellularised, and uncovers a previously unrecognised contribution of central blastomeres to the yolk syncytial layer.},
  author       = {Tong, Xin},
  isbn         = {978-3-99078-080-0},
  issn         = {2663-337X},
  keywords     = {meroblastic cleavage, cytokinesis, active gel theory, embryogenesis, zebrafish, adhesion},
  pages        = {121},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Towards a deeper understanding of meroblastic cleavage}},
  doi          = {10.15479/AT-ISTA-22804},
  year         = {2026},
}

@misc{22777,
  author       = {Tong, Xin},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Towards a deeper understanding of meroblastic cleavage - supplementary movies}},
  doi          = {10.15479/AT-ISTA-22777},
  year         = {2026},
}

@article{22964,
  abstract     = {We investigate whether the nonaccreting phases found in thin, locally isothermal circumbinary disks survive when the disk thermodynamics are evolved self-consistently. We present grid-based hydrodynamics simulations of circumbinary accretion with an energy equation that includes viscous and hydrodynamic heating coupled to radiative blackbody cooling in the high-Mach number regime. We find that, although gas accumulates and heats at the far edge of the circumbinary cavity, the regions that launch accretion streams remain comparatively cold, leading to potentially long-lived suppression of the binary accretion rate as the large-scale feeding rate is reduced towards the Eddington limit. This runaway nonaccretion problem, however, is weakened relative to locally isothermal solutions. Despite their low accretion rates, binaries interacting with disks in a nonaccreting phase can remain sufficiently luminous and variable at optical and near-infrared frequencies to be detectable in upcoming wide-field surveys such as LSST and the Roman Space Telescope. Because of the effective truncation of the surrounding disk, though, such systems are comparatively faint in high energy, photoionizing emission, and may therefore appear as intrinsically X-ray–weak active galactic nuclei with weak or absent emission line features. We additionally suggest an update to grid-based sink prescriptions for approximating mass loss across an unresolved horizon when including an energy conservation equation.},
  author       = {Tiede, Christopher and O'Neill, David W and D’Orazio, Daniel J.},
  issn         = {1538-4357},
  journal      = {The Astrophysical Journal},
  number       = {1},
  publisher    = {IOP Publishing},
  title        = {{Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks}},
  doi          = {10.3847/1538-4357/ae914e},
  volume       = {1008},
  year         = {2026},
}

@article{22965,
  abstract     = {Manganese-based aqueous zinc-ion batteries (AZIBs) have emerged as promising candidates for large-scale energy storage owing to their low cost, intrinsic safety, and the abundance of constituent elements. However, their practical deployment is still restricted by severe capacity fading caused by Jahn–Teller-induced structural instability and sluggish Zn2+ transport in the cathode. Although surface coating, heteroatom doping, and structural regulation have been widely explored to improve Mn-based cathodes, these approaches may suffer from increased interfacial resistance, compositional complexity, or limited control over the intrinsic electronic structure. In this context, oxygen-vacancy engineering offers a more direct route to modulate local coordination environments and accelerate Zn2+/H+ storage kinetics. Herein, lattice-level defect engineering of a dense Mn2O3 host is achieved through a metal–organic framework-derived synthesis followed by mild secondary annealing. The introduced oxygen vacancies regulate the local electronic structure and coordination environment, thereby facilitating Zn2+ diffusion, accelerating charge-transfer kinetics, and improving electrochemical reversibility. Combined experimental and theoretical investigations further show that oxygen-vacancy engineering enhances electronic conductivity, reduces the Zn2+ migration barrier, and enables a reversible dual-ion storage mechanism involving both H+ and Zn2+. Benefiting from these effects, the Zn‖Vo-Mn2O3 battery delivers a high specific capacity of 359 mAh g−1 at 0.3 A g−1, maintains 210 mAh g−1 at 6 A g−1, and retains 74.3% of its capacity after 10 000 cycles at 12 A g−1 after only 150 s of initial preconditioning. This work highlights oxygen-vacancy engineering as an effective route to enhancing the kinetic and structural stability of Mn-based cathodes for advanced AZIBs.},
  author       = {Yu, Ao and Chang, Xingqi and Lu, Xuan and He, Ren and Yang, Linlin and Chai, Jiali and Bi, Xiaoyu and Chacón-Borrero, Jesús and Mejia-Centeno, Karol V. and Llorca, Jordi and Villalobos-Portillo, Eduardo and Liu, Qirong and Shang, Jian and Cabot, Andreu},
  issn         = {2050-7496},
  journal      = {Journal of Materials Chemistry A},
  publisher    = {Royal Society of Chemistry},
  title        = {{Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries}},
  doi          = {10.1039/d6ta05844b},
  year         = {2026},
}

@article{22967,
  abstract     = {Alkali salts are widely used in solution processing, yet the corresponding cations are often assumed to remain in the liquid phase. Here, we show that alkali ions introduced during the solution synthesis of SnSe are retained through particle isolation and continue to influence the material during subsequent thermal processing, where they shape the evolution of the final polycrystalline material. Different SnSe powders were prepared using Li+, Na+, and K+ precursors, as well as tetramethylammonium (TMA+) precursors as a nonalkali reference for comparison, and all samples were consolidated under identical conditions. Although all three alkali ions were found in the matrix, at grain boundaries, and in segregated nanoscale regions, they partitioned differently and resulted in distinct grain sizes, defect distributions, and therefore transport properties. Li induced the strongest grain size heterogeneity and the lowest energy barriers, Na the best overall balance between carrier concentration and mobility, and K the broadest alkali-rich grain boundary regions along with the strongest interfacial penalty to charge carrier transport. These results show that residual alkali ions are not just remnants of solution synthesis but active determinants of microstructure and thermoelectric performance in SnSe.},
  author       = {Fiedler, Christine and Horta, Sharona and Navita, Navita and Maji, Krishnendu and Kleinhanns, Tobias and Llorca, Jordi and Wang, Qi and Ramon, Maria Garcia and Das, Sambit and Gavini, Vikram and Liu, Yu and Ibáñez, Maria},
  issn         = {1520-5002},
  journal      = {Chemistry of Materials},
  number       = {18},
  pages        = {9323–9332},
  publisher    = {American Chemical Society},
  title        = {{Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe}},
  doi          = {10.1021/acs.chemmater.6c01284},
  volume       = {38},
  year         = {2026},
}

@article{22972,
  abstract     = {Genomic measurements of DNA methylation, gene expression or protein levels are becoming more prevalent and are increasingly used to study health outcomes. However, most proposed association testing methods consider only marginal effects of each feature on a single outcome variable and are not set up to handle highly correlated, continuous data. Here, we introduce MAJA, a method to learn shared and outcome-specific effects for multiple traits in multi-omics data. MAJA determines the unique contribution of individual loci, genes, or molecular pathways to variation in one or more traits, conditional on all other measured “omics” data genome-wide. Simulations show MAJA accurately finds shared and distinct associations between omics-data and multiple traits and estimates omics-specific (co)variances, allowing for sparsity and correlations within the data. Applying MAJA to 12 outcome traits in Generation Scotland methylation data (n = 18 264), we find novel shared epigenetic probes among cholesterol metabolism, osteoarthritis, blood pressure and asthma. In contrast to marginal testing, we find only 10 CpG probes with significant effects above the genome-wide background. This highlights the need for joint association testing in highly correlated methylation data from whole blood and for studies of increased sample size in order to refine epigenomic associations in observational data.},
  author       = {Krätschmer, Ilse and Smith, Hannah M and McCartney, Daniel L and Bernabeu, Elena and Mahmoudi, Mahdi and Campbell, Archie and Corley, Janie and Harris, Sarah E and Cox, Simon R and Marioni, Riccardo E and Robinson, Matthew Richard},
  issn         = {2635-0041},
  journal      = {Bioinformatics Advances},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes}},
  doi          = {10.1093/bioadv/vbag231},
  volume       = {6},
  year         = {2026},
}

@article{22963,
  abstract     = {Although studies of tumor invasion have mainly emphasized the evolution of genetic and epigenetic heterogeneity, cellular behaviors also depend on the physical microenvironment. Yet, the tumor microenvironment is both complex and continuously remodeled, making it hard to rigorously test its causal influence on tumor dissemination. Here, we adopted a reductionist approach to studying tumor cell invasion in microengineered environments of tunable patterned geometries. We find that not only the presence of obstacles but more unexpectedly their spatial disorder causes a drastic shift from a collective to a single-cell mode of invasion—comparable in strength to loss of cell-cell adhesion. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell dissemination results both from local geometrical constraints and a global integration of spatial disorder over time. We identify generic universality classes of invasion dynamics dependent on environmental geometry, enabling us to identify quantitative physical principles for tumor dissemination.},
  author       = {Dunajova, Zuzana and Tasciyan, Saren and Majek, Juraj and Merrin, Jack and Jenkins, Robert P. and Sahai, Erik and Sixt, Michael K and Hannezo, Edouard B},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {37},
  publisher    = {AAAS},
  title        = {{Substrate heterogeneity promotes cancer cell dissemination through interface roughening}},
  doi          = {10.1126/sciadv.aed0587},
  volume       = {12},
  year         = {2026},
}

@article{22976,
  abstract     = {<jats:p>The influence of chiral molecular potentials on phase-coherent transport in superconducting Josephson junctions is investigated. Within a Bogoliubov–de Gennes tight-binding framework, a superconducting-normal-superconducting (SNS) junction functionalized by adsorbed chiral molecules is modeled, where electrostatic gradients generated by the molecules induce spin-orbit coupling in the normal region. The equilibrium charge current-phase relation is found to remain largely insensitive to molecular chirality in symmetric, zero-field configurations. In contrast, the spin-polarized equilibrium current exhibits a pronounced chirality-dependent response, with opposite enantiomers producing distinct and anisotropic spin-polarized Josephson currents. The resulting handedness contrast can be enhanced through control parameters such as molecular orientation and the strength of the induced spin-orbit coupling. The temperature dependence of these currents further shows that the chirality-dependent signatures persist across a range of temperatures well below the superconducting critical temperature. These results identify Josephson interferometry as a phase-sensitive setting for probing chirality-dependent spin structure and highlight spin-polarized superconducting transport as a controlled route toward integrating chiral molecular functionality into superconducting spintronic devices.</jats:p>},
  author       = {Kuliashov, Oleg and Cappellaro, Alberto and Millo, Oded and Paltiel, Yossi and Lemeshko, Mikhail and Al Hyder, Ragheed},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {15},
  publisher    = {American Physical Society},
  title        = {{Supercurrents in Josephson junctions with chiral molecular potentials}},
  doi          = {10.1103/s1jn-fq4d},
  volume       = {114},
  year         = {2026},
}

@article{22975,
  abstract     = {Conjugated molecules with diradical character have emerged as promising building blocks for high-conductance single-molecule electronics because of their behavior as 1D topological insulators. However, the impact of antiaromaticity on these radical-based edge states has not been explored. Here, we introduce thiophene-based molecular wires that exhibit intrinsic diradical character in their ground state under ambient conditions and systematically investigate how their conductance responds to changes in aromaticity upon the oxidation of fluorene-based flanking moieties. Using scanning tunneling microscopy-based break junction (STM-BJ) techniques, we show that the conductance increases with molecular length in the neutral state, supporting one-dimensional topological behavior. We further examine the effect of oxidation on conductance through three complementary methods, revealing substantial conductance enhancements that we attribute to an increase in the antiaromatic character of the wires. Together, these findings establish a rational design strategy for highly conducting, electrochemically switchable molecular junctions, with implications for single-molecule electronics.},
  author       = {Lee, Woojung and Shi, Wanzhuo and Kwon, Junho and Low, Jonathan and Wei, Sujun and Yin, Xiaodong and Campos, Luis M. and Venkataraman, Latha},
  issn         = {1520-5126},
  journal      = {Journal of the AmericanChemical Society},
  number       = {37},
  pages        = {40536–40542},
  publisher    = {American Chemical Society},
  title        = {{Redox-driven antiaromaticity enables multistate conductancein 1D topological insulators}},
  doi          = {10.1021/jacs.6c15721},
  volume       = {148},
  year         = {2026},
}