@inproceedings{18891,
abstract = {Deep neural networks (DNNs) exhibit a surprising structure in their final layer
known as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon
called deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.
In contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two
layers or two classes, DNC stops being optimal for the deep unconstrained features
model (DUFM) – the standard theoretical framework for the analysis of collapse.
The main culprit is a low-rank bias of multi-layer regularization schemes: this bias
leads to optimal solutions of even lower rank than the neural collapse. We support
our theoretical findings with experiments on both DUFM and real data, which show
the emergence of the low-rank structure in the solution found by gradient descent.},
author = {Súkeník, Peter and Lampert, Christoph and Mondelli, Marco},
booktitle = {38th Annual Conference on Neural Information Processing Systems},
location = {Vancouver, Canada},
publisher = {Neural Information Processing Systems Foundation},
title = {{Neural collapse versus low-rank bias: Is deep neural collapse really optimal?}},
volume = {37},
year = {2024},
}
@misc{18895,
abstract = {ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file).},
author = {Cadei, Riccardo and Locatello, Francesco and Cremer, Sylvia M and Lindorfer, Lukas and Schmid, Cordelia},
publisher = {Institute of Science and Technology Austria},
title = {{ISTAnt}},
doi = {10.6084/M9.FIGSHARE.26484934.V2},
year = {2024},
}
@inproceedings{18897,
abstract = {Score-based generative models (SGMs) are powerful tools to sample from complex data distributions. Their underlying idea is to (i) run a forward process for time T1 by adding noise to the data, (ii) estimate its score function, and (iii) use such estimate to run a reverse process. As the reverse process is initialized with the stationary distribution of the forward one, the existing analysis paradigm requires T1→∞. This is however problematic: from a theoretical viewpoint, for a given precision of the score approximation, the convergence guarantee fails as T1 diverges; from a practical viewpoint, a large T1 increases computational costs and leads to error propagation. This paper addresses the issue by considering a version of the popular predictor-corrector scheme: after running the forward process, we first estimate the final distribution via an inexact Langevin dynamics and then revert the process. Our key technical contribution is to provide convergence guarantees which require to run the forward process only for a fixed finite time T1. Our bounds exhibit a mild logarithmic dependence on the input dimension and the subgaussian norm of the target distribution, have minimal assumptions on the data, and require only to control the L2 loss on the score approximation, which is the quantity minimized in practice.},
author = {Pedrotti, Francesco and Maas, Jan and Mondelli, Marco},
booktitle = {Transactions on Machine Learning Research},
issn = {2835-8856},
title = {{Improved convergence of score-based diffusion models via prediction-correction}},
year = {2024},
}
@book{18899,
abstract = {The flourishing theory of classical optimal transport concerns mass transportation at minimal cost. This book introduces the reader to optimal transport on quantum structures, i.e., optimal transportation between quantum states and related non-commutative concepts of mass transportation. It contains lecture notes on
classical optimal transport and Wasserstein gradient flows
dynamics and quantum optimal transport
quantum couplings and many-body problems
quantum channels and qubits
These notes are based on lectures given by the authors at the "Optimal Transport on Quantum Structures" School held at the Erdös Center in Budapest in the fall of 2022. The lecture notes are complemented by two survey chapters presenting the state of the art in different research areas of non-commutative optimal transport.},
editor = {Maas, Jan and Rademacher, Simone Anna Elvira and Titkos, Tamás and Virosztek, Daniel},
isbn = {9783031504655},
issn = {2947-9460},
publisher = {Springer Nature},
title = {{Optimal Transport on Quantum Structures}},
doi = {10.1007/978-3-031-50466-2},
volume = {29},
year = {2024},
}
@article{18900,
abstract = {We prove that certain closable derivations on the GNS Hilbert space associated with a non-tracial weight on a von Neumann algebra give rise to GNS-symmetric semigroups of contractive completely positive maps on the von Neumann algebra.},
author = {Wirth, Melchior},
issn = {1687-0247},
journal = {International Mathematics Research Notices},
number = {14},
pages = {10597--10614},
publisher = {Oxford University Press},
title = {{Modular completely Dirichlet forms as squares of derivations}},
doi = {10.1093/imrn/rnae092},
volume = {2024},
year = {2024},
}
@article{18902,
author = {Zagorski, Marcin and Brandenberg, Nathalie and Lutolf, Matthias and Tkačik, Gašper and Bollenbach, Mark Tobias and Briscoe, James and Kicheva, Anna},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Assessing the precision of morphogen gradients in neural tube development}},
doi = {10.1038/s41467-024-45148-8},
volume = {15},
year = {2024},
}
@inproceedings{18906,
abstract = {Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective.
Our extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time.},
author = {Hanauer, Kathrin and Henzinger, Monika H and Münk, Robin and Räcke, Harald and Vötsch, Maximilian},
booktitle = {Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining},
isbn = {9798400704901},
location = {Barcelona, Spain},
pages = {1016--1027},
publisher = {ACM},
title = {{Expander hierarchies for normalized cuts on graphs}},
doi = {10.1145/3637528.3671978},
year = {2024},
}
@article{18908,
abstract = {Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.},
author = {Le Moan, Alan and Stankowski, Sean and Rafajlović, Marina and Ortega-Martinez, Olga and Faria, Rui and Butlin, Roger K and Johannesson, Kerstin},
issn = {2056-3744},
journal = {Evolution Letters},
number = {4},
pages = {575--586},
publisher = {Oxford University Press},
title = {{Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes}},
doi = {10.1093/evlett/qrae014},
volume = {8},
year = {2024},
}
@article{18910,
abstract = {Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.},
author = {Schanda, Paul and Haran, Gilad},
issn = {1936-1238},
journal = {Annual Review of Biophysics},
pages = {247--273},
publisher = {Annual Reviews},
title = {{NMR and single-molecule FRET insights into fast protein motions and their relation to function}},
doi = {10.1146/annurev-biophys-070323-022428},
volume = {53},
year = {2024},
}
@inproceedings{18912,
abstract = {This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.},
author = {Tojo, Kenji and Shamir, Ariel and Bickel, Bernd and Umetani, Nobuyuki},
booktitle = {SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers},
isbn = {9798400705250},
location = {Denver, CO, United States},
publisher = {ACM},
title = {{Fabricable 3D wire art}},
doi = {10.1145/3641519.3657453},
year = {2024},
}
@inproceedings{18913,
abstract = {With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.
By implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols.},
author = {Giuliari, Giacomo and Sonnino, Alberto and Frei, Marc and Streun, Fabio and Kokoris Kogias, Eleftherios and Perrig, Adrian},
booktitle = {Proceedings of the 19th ACM Asia Conference on Computer and Communications Security},
isbn = {9798400704826},
location = {Singapore, Singapore},
pages = {1345--1360},
publisher = {ACM},
title = {{An empirical study of consensus protocols’ DoS resilience}},
doi = {10.1145/3634737.3656997},
year = {2024},
}
@article{18919,
abstract = {The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling.},
author = {Baykusheva, Denitsa Rangelova},
issn = {1745-2481},
journal = {Nature Physics},
number = {5},
pages = {684--685},
publisher = {Springer Nature},
title = {{Through the slopes of a light-induced phase transition}},
doi = {10.1038/s41567-024-02401-7},
volume = {20},
year = {2024},
}
@inproceedings{18922,
abstract = {Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them.},
author = {Georgiadis, Loukas and Italiano, Giuseppe F. and Kosinas, Evangelos},
booktitle = {65th Annual Symposium on Foundations of Computer Science},
isbn = {9798331516741},
location = {Chicago, IL, United States},
pages = {62--85},
publisher = {IEEE},
title = {{Computing the 3-edge-connected components of directed graphs in linear time}},
doi = {10.1109/focs61266.2024.00015},
year = {2024},
}
@inproceedings{18925,
abstract = {Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature.},
author = {Ceylan, Esra and Chatterjee, Krishnendu and Schmid, Stefan and Svoboda, Jakub},
booktitle = {NOMS 2024-2024 IEEE Network Operations and Management Symposium},
isbn = {9798350327946},
issn = {2374-9709},
location = {Seoul, Republic of Korea},
publisher = {IEEE},
title = {{Congestion-free rerouting of network flows: Hardness and an FPT algorithm}},
doi = {10.1109/noms59830.2024.10575579},
year = {2024},
}
@article{18926,
abstract = {We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. },
author = {Hensel, Sebastian and Laux, Tim},
issn = {0022-2518},
journal = {Indiana University Mathematics Journal},
number = {1},
pages = {111--148},
publisher = {Indiana University Mathematics Journal},
title = {{BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness}},
doi = {10.1512/iumj.2024.73.9701},
volume = {73},
year = {2024},
}
@inproceedings{18928,
abstract = {Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.
We investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.
Further, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.
We note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds.},
author = {Henzinger, Monika H and Saha, Barna and Seybold, Martin P. and Ye, Christopher},
booktitle = {15th Innovations in Theoretical Computer Science Conference},
isbn = {9783959773096},
issn = {1868-8969},
location = {Berkeley, CA, United States},
pages = {62:1--62:25},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On the complexity of algorithms with predictions for dynamic graph problems}},
doi = {10.4230/LIPIcs.ITCS.2024.62},
volume = {287},
year = {2024},
}
@article{18934,
abstract = {The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .},
author = {Sárkány, Zsuzsa and Figueiredo, Francisco and Macedo-Ribeiro, Sandra and Martins, Pedro M.},
issn = {1939-4586},
journal = {Molecular Biology of the Cell},
number = {3},
publisher = {American Society for Cell Biology},
title = {{NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation}},
doi = {10.1091/mbc.e23-07-0289},
volume = {35},
year = {2024},
}
@article{18937,
abstract = {A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions.},
author = {Ray, Sujata Kumari and Pati, Anupama and Sahoo, Payala and Sahoo, A.K. and Singh, Saurabh and Takeuchi, Tsunehiro and Dash, S.},
issn = {0921-4526},
journal = {Physica B: Condensed Matter},
publisher = {Elsevier},
title = {{Tunable magnetoelectronic properties in Bi3+ substituted YCrO3}},
doi = {10.1016/j.physb.2024.416018},
volume = {685},
year = {2024},
}
@article{18938,
abstract = {The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.},
author = {Springstein, Benjamin L and Paulo, Joao A. and Park, Hankum and Henry, Kemardo and Fleming, Eleanor and Feder, Zoë and Harper, J. Wade and Hochschild, Ann},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {6},
publisher = {National Academy of Sciences},
title = {{Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics}},
doi = {10.1073/pnas.2317453121},
volume = {121},
year = {2024},
}
@article{18940,
abstract = {BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.},
author = {Knabl, Paul and Schauer, Alexandra and Pomreinke, Autumn P and Zimmermann, Bob and Rogers, Katherine W and Čapek, Daniel and Müller, Patrick and Genikhovich, Grigory},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator}},
doi = {10.7554/elife.80803},
volume = {13},
year = {2024},
}