@article{802,
  abstract     = {Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.},
  author       = {Engel, Jakob and Schmalhorst, Philipp S and Kruger, Anke and Muller, Christina and Buettner, Falk and Routier, Françoise},
  journal      = {Glycobiology},
  number       = {12},
  pages        = {1423 -- 1430},
  publisher    = {Oxford University Press},
  title        = {{Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis}},
  doi          = {10.1093/glycob/cwv059},
  volume       = {25},
  year         = {2015},
}

@article{814,
  abstract     = {Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.},
  author       = {Florian Schur and Hagen, Wim J and Rumlová, Michaela and Ruml, Tomáš and Müller B and Kraüsslich, Hans Georg and Briggs, John A},
  journal      = {Nature},
  number       = {7535},
  pages        = {505 -- 508},
  publisher    = {Nature Publishing Group},
  title        = {{Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution}},
  doi          = {10.1038/nature13838},
  volume       = {517},
  year         = {2015},
}

@article{815,
  abstract     = {The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.
},
  author       = {Schur, Florian and Dick, Robert and Hagen, Wim and Vogt, Volker and Briggs, John},
  journal      = {Journal of Virology},
  number       = {20},
  pages        = {10294 -- 10302},
  publisher    = {ASM},
  title        = {{The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly}},
  doi          = {10.1128/JVI.01502-15},
  volume       = {89},
  year         = {2015},
}

@unpublished{8183,
  abstract     = {We study conditions under which a finite simplicial complex $K$ can be mapped to $\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\to \mathbb R^d$ such that the images of any $r$
pairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of
the $(d+1)(r-1)$-simplex in $\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\geq 3r$) based on a series of papers by M. \"Ozaydin, M. Gromov, P. Blagojevi\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\to \mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\to \mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \sqcup S^3\sqcup S^3\to \mathbb R^5$ up to ornament
concordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.},
  author       = {Avvakumov, Sergey and Mabillard, Isaac and Skopenkov, A. and Wagner, Uli},
  booktitle    = {arXiv},
  title        = {{Eliminating higher-multiplicity intersections, III. Codimension 2}},
  year         = {2015},
}

@inproceedings{1481,
  abstract     = {Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. },
  author       = {Ahmed, Umair and Chatterjee, Krishnendu and Gulwani, Sumit},
  booktitle    = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence},
  location     = {Austin, TX, USA},
  pages        = {745 -- 752},
  publisher    = {AAAI Press},
  title        = {{Automatic generation of alternative starting positions for simple traditional board games}},
  volume       = {2},
  year         = {2015},
}

@inproceedings{1483,
  abstract     = {Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes.},
  author       = {Reininghaus, Jan and Huber, Stefan and Bauer, Ulrich and Kwitt, Roland},
  location     = {Boston, MA, USA},
  pages        = {4741 -- 4748},
  publisher    = {IEEE},
  title        = {{A stable multi-scale kernel for topological machine learning}},
  doi          = {10.1109/CVPR.2015.7299106},
  year         = {2015},
}

@inproceedings{1495,
  abstract     = {Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. },
  author       = {Edelsbrunner, Herbert and Iglesias Ham, Mabel and Kurlin, Vitaliy},
  booktitle    = {Proceedings of the 27th Canadian Conference on Computational Geometry},
  location     = {Ontario, Canada},
  pages        = {128--135},
  publisher    = {Queen's University},
  title        = {{Relaxed disk packing}},
  volume       = {2015-August},
  year         = {2015},
}

@article{1497,
  abstract     = {Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.},
  author       = {Andergassen, Daniel and Dotter, Christoph and Kulinski, Tomasz and Guenzl, Philipp and Bammer, Philipp and Barlow, Denise and Pauler, Florian and Hudson, Quanah},
  journal      = {Nucleic Acids Research},
  number       = {21},
  publisher    = {Oxford University Press},
  title        = {{Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data}},
  doi          = {10.1093/nar/gkv727},
  volume       = {43},
  year         = {2015},
}

@inproceedings{1498,
  abstract     = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.},
  author       = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien},
  isbn         = {978-3-939897-80-4 },
  location     = {Asilomar, CA, United States},
  pages        = {90 -- 102},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{The need for language support for fault-tolerant distributed systems}},
  doi          = {10.4230/LIPIcs.SNAPL.2015.90},
  volume       = {32},
  year         = {2015},
}

@inproceedings{1499,
  abstract     = {We consider weighted automata with both positive and negative integer weights on edges and
study the problem of synchronization using adaptive strategies that may only observe whether
the current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.},
  author       = {Kretinsky, Jan and Larsen, Kim and Laursen, Simon and Srba, Jiří},
  location     = {Madrid, Spain},
  pages        = {142 -- 154},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Polynomial time decidability of weighted synchronization under partial observability}},
  doi          = {10.4230/LIPIcs.CONCUR.2015.142},
  volume       = {42},
  year         = {2015},
}

@misc{1500,
  abstract     = {In this poster, we present methods for randomly generating hybrid automata with affine differential equations, invariants, guards, and assignments. Selecting an arbitrary affine function from the set of all affine functions results in a low likelihood of generating hybrid automata with diverse and interesting behaviors, as there are an uncountable number of elements in the set of all affine functions. Instead, we partition the set of all affine functions into potentially interesting classes and randomly select elements from these classes. For example, we partition the set of all affine differential equations by using restrictions on eigenvalues such as those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior (guards, assignments, and invariants) to allow either time-dependent or state-dependent switching, and in particular provide the ability to generate subclasses of piecewise-affine hybrid automata. Our preliminary experimental results with a prototype tool called HyRG (Hybrid Random Generator) illustrate the feasibility of this generation method to automatically create standard hybrid automaton examples like the bouncing ball and thermostat.},
  author       = {Nguyen, Luan V and Christian Schilling and Sergiy Bogomolov and Johnson, Taylor T},
  booktitle    = {HSCC: Hybrid Systems - Computation and Control},
  pages        = {289 -- 290},
  publisher    = {Springer},
  title        = {{Poster: HyRG: A random generation tool for affine hybrid automata}},
  doi          = {10.1145/2728606.2728650},
  year         = {2015},
}

@article{1501,
  abstract     = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Daca, Przemyslaw},
  journal      = {Formal Methods in System Design},
  number       = {2},
  pages        = {230 -- 264},
  publisher    = {Springer},
  title        = {{CEGAR for compositional analysis of qualitative properties in Markov decision processes}},
  doi          = {10.1007/s10703-015-0235-2},
  volume       = {47},
  year         = {2015},
}

@inproceedings{1502,
  abstract     = {We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.},
  author       = {Beneš, Nikola and Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Nickovic, Dejan},
  isbn         = {978-1-4503-3471-6},
  location     = {Montreal, QC, Canada},
  pages        = {101 -- 110},
  publisher    = {ACM},
  title        = {{Complete composition operators for IOCO-testing theory}},
  doi          = {10.1145/2737166.2737175},
  year         = {2015},
}

@article{1503,
  abstract     = {A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles.},
  author       = {Sadel, Christian},
  journal      = {Ergodic Theory and Dynamical Systems},
  number       = {5},
  pages        = {1582 -- 1591},
  publisher    = {Cambridge University Press},
  title        = {{A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles}},
  doi          = {10.1017/etds.2013.103},
  volume       = {35},
  year         = {2015},
}

@article{1504,
  abstract     = {Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones.},
  author       = {Bao, Zhigang and Lin, Liang and Pan, Guangming and Zhou, Wang},
  journal      = {Annals of Statistics},
  number       = {6},
  pages        = {2588 -- 2623},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Spectral statistics of large dimensional spearman s rank correlation matrix and its application}},
  doi          = {10.1214/15-AOS1353},
  volume       = {43},
  year         = {2015},
}

@article{1505,
  abstract     = {This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.},
  author       = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
  journal      = {Annals of Statistics},
  number       = {1},
  pages        = {382 -- 421},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Universality for the largest eigenvalue of sample covariance matrices with general population}},
  doi          = {10.1214/14-AOS1281},
  volume       = {43},
  year         = {2015},
}

@article{1506,
  abstract     = {Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).},
  author       = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
  journal      = {Bernoulli},
  number       = {3},
  pages        = {1600 -- 1628},
  publisher    = {Bernoulli Society for Mathematical Statistics and Probability},
  title        = {{The logarithmic law of random determinant}},
  doi          = {10.3150/14-BEJ615},
  volume       = {21},
  year         = {2015},
}

@article{1508,
  abstract     = {We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential.},
  author       = {Erdös, László and Yau, Horng},
  journal      = {Journal of the European Mathematical Society},
  number       = {8},
  pages        = {1927 -- 2036},
  publisher    = {European Mathematical Society},
  title        = {{Gap universality of generalized Wigner and β ensembles}},
  doi          = {10.4171/JEMS/548},
  volume       = {17},
  year         = {2015},
}

@article{1509,
  abstract     = {The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.},
  author       = {Michalko, Jaroslav and Dravecka, Marta and Bollenbach, Tobias and Friml, Jirí},
  journal      = {F1000 Research },
  publisher    = {F1000 Research},
  title        = {{Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene}},
  doi          = {10.12688/f1000research.7143.1},
  volume       = {4},
  year         = {2015},
}

@inproceedings{1510,
  abstract     = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. },
  author       = {Franek, Peter and Krcál, Marek},
  location     = {Eindhoven, Netherlands},
  pages        = {842 -- 856},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{On computability and triviality of well groups}},
  doi          = {10.4230/LIPIcs.SOCG.2015.842},
  volume       = {34},
  year         = {2015},
}