@misc{9868,
  abstract     = {The raw data file containing the experimental decisions of all our study subjects.},
  author       = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred},
  publisher    = {Public Library of Science},
  title        = {{Experimental data}},
  doi          = {10.1371/journal.pone.0163867.s009},
  year         = {2016},
}

@misc{9869,
  abstract     = {A lower bound on the error of a positional estimator with limited positional information is derived.},
  author       = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper},
  publisher    = {Public Library of Science},
  title        = {{Error bound on an estimator of position}},
  doi          = {10.1371/journal.pone.0163628.s001},
  year         = {2016},
}

@article{987,
  abstract     = {In contrast to bulk FeSe, which exhibits nematic order and low temperature superconductivity, highly doped FeSe reverses the situation, having high temperature superconductivity appearing alongside a suppression of nematic order. To investigate this phenomenon, we study a minimal electronic model of FeSe, with interactions that enhance nematic fluctuations. This model is sign problem free, and is simulated using determinant quantum Monte Carlo (DQMC). We developed a DQMC algorithm with parallel tempering, which proves to be an efficient source of global updates and allows us to access the region of strong interactions. Over a wide range of intermediate couplings, we observe superconductivity with an extended s-wave order parameter, along with enhanced, but short-ranged, q=(0,0) ferro-orbital (nematic) order. These results are consistent with approximate weak-coupling treatments that predict that nematic fluctuations lead to superconducting pairing. Surprisingly, in the parameter range under study, we do not observe nematic long-range order. Instead, at stronger coupling an unusual insulating phase with q=(π,π) antiferro-orbital order appears, which is missed by weak-coupling approximations.},
  author       = {Dumitrescu, Philipp and Serbyn, Maksym and Scalettar, Richard and Vishwanath, Ashvin},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {15},
  publisher    = {American Physical Society},
  title        = {{Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study}},
  doi          = {10.1103/PhysRevB.94.155127},
  volume       = {94},
  year         = {2016},
}

@misc{9870,
  abstract     = {The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.},
  author       = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper},
  publisher    = {Public Library of Science},
  title        = {{Computation of positional information in an Ising model}},
  doi          = {10.1371/journal.pone.0163628.s002},
  year         = {2016},
}

@misc{9871,
  abstract     = {The positional information in a discrete morphogen field with Gaussian noise is computed.},
  author       = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper},
  publisher    = {Public Library of Science},
  title        = {{Computation of positional information in a discrete morphogen field}},
  doi          = {10.1371/journal.pone.0163628.s003},
  year         = {2016},
}

@misc{9873,
  author       = {Boehm, Alex and Arnoldini, Markus and Bergmiller, Tobias and Röösli, Thomas and Bigosch, Colette and Ackermann, Martin},
  publisher    = {Public Library of Science},
  title        = {{Quantification of the growth rate reduction as a consequence of age-specific mortality}},
  doi          = {10.1371/journal.pgen.1005974.s015},
  year         = {2016},
}

@article{22051,
  abstract     = {We construct solutions with prescribed scattering state to the cubic-quintic NLS (mathematical formular)in three spatial dimensions in the class of solutions with (mathematical formular). This models disturbances in an infinite expanse of (quantum) fluid in its quiescent state— the limiting modulus c corresponds to a local minimum in the energy density.
Our arguments build on work of Gustafson, Nakanishi, and Tsai on the (defocusing) Gross–Pitaevskii equation. The presence of an energy-critical nonlinearity and changes in the geometry of the energy
functional add several new complexities. One new ingredient in our argument is a demonstration that
solutions of such (perturbed) energy-critical equations exhibit continuous dependence on the initial data
with respect to the weak topology on H1/x.},
  author       = {Killip, Rowan and Murphy, Jason and Visan, Monica},
  issn         = {1948-206X},
  journal      = {Analysis & PDE},
  keywords     = {final-state problem, wave operators, cubic-quintic NLS, nonvanishing boundary conditions},
  number       = {7},
  pages        = {1523--1574},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{The final-state problem for the cubic-quintic NLS with nonvanishing boundary conditions}},
  doi          = {10.2140/apde.2016.9.1523},
  volume       = {9},
  year         = {2016},
}

@article{22052,
  abstract     = {We consider the focusing cubic nonlinear Schrödinger equation (NLS) in the exterior Ω of a smooth, compact, strictly convex obstacle in three dimensions. We prove that the threshold for global existence and scattering is the same as for the problem posed on Euclidean space. Specifically, we prove that if E(u0)M(u0)<E(Q)M(Q) and ||u0||2||u0||2<\|\nabla Q||2||Q||2, the corresponding solution to the initial value problem with Dirichlet boundary conditions exists globally and scatters to linear evolutions asymptotically in the future and in the past. Here, Q(x) denotes the ground state for the focusing cubic NLS in ℝ3. },
  author       = {Killip, Rowan and Visan, Monica and Zhang, Xiaoyi},
  issn         = {1687-1197},
  journal      = {Applied Mathematics Research eXpress},
  number       = {1},
  pages        = {146--180},
  publisher    = {Oxford University Press},
  title        = {{The focusing cubic NLS on exterior domains in three dimensions}},
  doi          = {10.1093/amrx/abv012},
  volume       = {2016},
  year         = {2016},
}

@article{22073,
  abstract     = {We prove scale-invariant Strichartz inequalities for the Schrödinger equation on rectangular tori (rational or irrational) in all dimensions. We use these estimates to give a simpler treatment of local well-posedness of the energy-critical nonlinear Schrödinger equation in dimensions three and four.},
  author       = {Killip, Rowan and Visan, Monica},
  issn         = {1945-001X},
  journal      = {Mathematical Research Letters},
  number       = {2},
  pages        = {445--472},
  publisher    = {International Press},
  title        = {{Scale-invariant Strichartz estimates on tori and applications}},
  doi          = {10.4310/mrl.2016.v23.n2.a8},
  volume       = {23},
  year         = {2016},
}

@article{1100,
  abstract     = {During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.},
  author       = {Sako, Keisuke and Pradhan, Saurabh and Barone, Vanessa and Inglés Prieto, Álvaro and Mueller, Patrick and Ruprecht, Verena and Capek, Daniel and Galande, Sanjeev and Janovjak, Harald L and Heisenberg, Carl-Philipp J},
  journal      = {Cell Reports},
  number       = {3},
  pages        = {866 -- 877},
  publisher    = {Cell Press},
  title        = {{Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation}},
  doi          = {10.1016/j.celrep.2016.06.036},
  volume       = {16},
  year         = {2016},
}

@article{1321,
  abstract     = {Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.},
  author       = {Leithner, Alexander F and Eichner, Alexander and Müller, Jan and Reversat, Anne and Brown, Markus and Schwarz, Jan and Merrin, Jack and De Gorter, David and Schur, Florian and Bayerl, Jonathan and De Vries, Ingrid and Wieser, Stefan and Hauschild, Robert and Lai, Frank and Moser, Markus and Kerjaschki, Dontscho and Rottner, Klemens and Small, Victor and Stradal, Theresia and Sixt, Michael K},
  journal      = {Nature Cell Biology},
  pages        = {1253 -- 1259},
  publisher    = {Nature Publishing Group},
  title        = {{Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes}},
  doi          = {10.1038/ncb3426},
  volume       = {18},
  year         = {2016},
}

@article{1183,
  abstract     = {Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.},
  author       = {Tarlungeanu, Dora-Clara and Deliu, Elena and Dotter, Christoph and Kara, Majdi and Janiesch, Philipp and Scalise, Mariafrancesca and Galluccio, Michele and Tesulov, Mateja and Morelli, Emanuela and Sönmez, Fatma and Bilgüvar, Kaya and Ohgaki, Ryuichi and Kanai, Yoshikatsu and Johansen, Anide and Esharif, Seham and Ben Omran, Tawfeg and Topcu, Meral and Schlessinger, Avner and Indiveri, Cesare and Duncan, Kent and Caglayan, Ahmet and Günel, Murat and Gleeson, Joseph and Novarino, Gaia},
  journal      = {Cell},
  number       = {6},
  pages        = {1481 -- 1494},
  publisher    = {Cell Press},
  title        = {{Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder}},
  doi          = {10.1016/j.cell.2016.11.013},
  volume       = {167},
  year         = {2016},
}

@inproceedings{1437,
  abstract     = {We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.},
  author       = {Chatterjee, Krishnendu and Goharshady, Amir and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
  location     = {St. Petersburg, FL, USA},
  pages        = {733 -- 747},
  publisher    = {ACM},
  title        = {{Algorithms for algebraic path properties in concurrent systems of constant treewidth components}},
  doi          = {10.1145/2837614.2837624},
  volume       = {20-22},
  year         = {2016},
}

@inproceedings{1386,
  abstract     = {We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.},
  author       = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir},
  location     = {Toronto, Canada},
  pages        = {3 -- 22},
  publisher    = {Springer},
  title        = {{Termination analysis of probabilistic programs through Positivstellensatz's}},
  doi          = {10.1007/978-3-319-41528-4_1},
  volume       = {9779},
  year         = {2016},
}

@article{1106,
  abstract     = {Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.},
  author       = {Isrie, Mala and Breuss, Martin and Tian, Guoling and Hansen, Andi H and Cristofoli, Francesca and Morandell, Jasmin and Kupchinsky, Zachari A and Sifrim, Alejandro and Rodriguez Rodriguez, Celia and Dapena, Elena P and Doonanco, Kurston and Leonard, Norma and Tinsa, Faten and Moortgat, Stéphanie and Ulucan, Hakan and Koparir, Erkan and Karaca, Ender and Katsanis, Nicholas and Marton, Valeria and Vermeesch, Joris R and Davis, Erica E and Cowan, Nicholas J and Keays, David and Van Esch, Hilde},
  journal      = {The American Journal of Human Genetics},
  number       = {6},
  pages        = {790 -- 800},
  publisher    = {Cell Press},
  title        = {{Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type}},
  doi          = {10.1016/j.ajhg.2015.10.014},
  volume       = {97},
  year         = {2015},
}

@article{11073,
  abstract     = {Human cancer cells bear complex chromosome rearrangements that can be potential drivers of cancer development. However, the molecular mechanisms underlying these rearrangements have been unclear. Zhang et al. use a new technique combining live-cell imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent cell cycle.},
  author       = {Hatch, Emily M. and HETZER, Martin W},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {7},
  pages        = {1502--1504},
  publisher    = {Elsevier},
  title        = {{Linking micronuclei to chromosome fragmentation}},
  doi          = {10.1016/j.cell.2015.06.005},
  volume       = {161},
  year         = {2015},
}

@article{11074,
  author       = {Hatch, Emily M. and HETZER, Martin W},
  issn         = {0960-9822},
  journal      = {Current Biology},
  keywords     = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology},
  number       = {10},
  pages        = {PR397--R399},
  publisher    = {Elsevier},
  title        = {{Chromothripsis}},
  doi          = {10.1016/j.cub.2015.02.033},
  volume       = {25},
  year         = {2015},
}

@article{11075,
  abstract     = {Previously, we identified the nucleoporin gp210/Nup210 as a critical regulator of muscle and neuronal differentiation, but how this nucleoporin exerts its function and whether it modulates nuclear pore complex (NPC) activity remain unknown. Here, we show that gp210/Nup210 mediates muscle cell differentiation in vitro via its conserved N-terminal domain that extends into the perinuclear space. Removal of the C-terminal domain, which partially mislocalizes gp210/Nup210 away from NPCs, efficiently rescues the differentiation defect caused by the knockdown of endogenous gp210/Nup210. Unexpectedly, a gp210/Nup210 mutant lacking the NPC-targeting transmembrane and C-terminal domains is sufficient for C2C12 myoblast differentiation. We demonstrate that the endoplasmic reticulum (ER) stress-specific caspase cascade is exacerbated during Nup210 depletion and that blocking ER stress-mediated apoptosis rescues differentiation of Nup210-deficient cells. Our results suggest that the role of gp210/Nup210 in cell differentiation is mediated by its large luminal domain, which can act independently of NPC association and appears to play a pivotal role in the maintenance of nuclear envelope/ER homeostasis.},
  author       = {Gomez-Cavazos, J. Sebastian and HETZER, Martin W},
  issn         = {1540-8140},
  journal      = {Journal of Cell Biology},
  keywords     = {Cell Biology},
  number       = {6},
  pages        = {671--681},
  publisher    = {Rockefeller University Press},
  title        = {{The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis}},
  doi          = {10.1083/jcb.201410047},
  volume       = {208},
  year         = {2015},
}

@article{11076,
  abstract     = {Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.},
  author       = {Ibarra, Arkaitz and HETZER, Martin W},
  issn         = {1549-5477},
  journal      = {Genes & Development},
  keywords     = {Developmental Biology, Genetics},
  number       = {4},
  pages        = {337--349},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Nuclear pore proteins and the control of genome functions}},
  doi          = {10.1101/gad.256495.114},
  volume       = {29},
  year         = {2015},
}

@article{11077,
  abstract     = {Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing.},
  author       = {Jacinto, Filipe V. and Benner, Chris and HETZER, Martin W},
  issn         = {1549-5477},
  journal      = {Genes & Development},
  keywords     = {Developmental Biology, Genetics},
  number       = {12},
  pages        = {1224--1238},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing}},
  doi          = {10.1101/gad.260919.115},
  volume       = {29},
  year         = {2015},
}