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The origins of phagocytosis and eukaryogenesis

Natalya Yutin, Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin
2009 Biology Direct  
Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion.
doi:10.1186/1745-6150-4-9 pmid:19245710 pmcid:PMC2651865 fatcat:7xihmqyocffy3mep4b5m55msrq

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin
2008 Biology Direct  
Reviewer's report 2:Dennis Vitkup, Columbia University The paper by Maxim Wolf et al. investigates one of the main puzzles of molecular evolution -the existence of the protein-specific molecular clock.  ...  Y-axis: probability density function.  ... 
doi:10.1186/1745-6150-3-40 pmid:18840284 pmcid:PMC2572155 fatcat:7ylakkr7uzfn3gbneos4creqcm

FRESCo: finding regions of excess synonymous constraint in diverse viruses

Rachel S Sealfon, Michael F Lin, Irwin Jungreis, Maxim Y Wolf, Manolis Kellis, Pardis C Sabeti
2015 Genome Biology  
Below, we highlight a few of the SCEs that also have conserved, stable predicted RNA structures in potato virus Y (PVY), turnip mosaic virus (TuMV), cucumber mosaic virus (CMV), foot-and-mouth disease  ...  elements include splicing sites in bocavirus; known overlapping genes in bluetongue virus, cucumber mosaic virus, hepatitis E virus, infectious bursal disease virus, maize streak virus, potato virus Y,  ... 
doi:10.1186/s13059-015-0603-7 pmid:25853568 pmcid:PMC4376164 fatcat:vw5nznwwivap5fhlttgfxngmpq

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

Lakshminarayan M. Iyer, Vivek Anantharaman, Maxim Y. Wolf, L. Aravind
2008 International Journal of Parasitology  
Comparative genomics of parasitic protists and their free-living relatives are profoundly impacting our understanding of the regulatory systems involved in transcription and chromatin dynamics. While some parts of these systems are highly conserved, other parts are rapidly evolving, thereby providing the molecular basis for the variety in the regulatory adaptations of eukaryotes. The gross number of specific transcription factors and chromatin proteins are positively correlated with proteome
more » ... e in eukaryotes. However, the individual types of specific transcription factors show an enormous variety across different eukaryotic lineages. The dominant families of specific transcription factors even differ between sister lineages, and have been shaped by gene loss and lineage-specific expansions. Recognition of this principle has helped in identifying the hitherto unknown, major specific transcription factors of several parasites, such as apicomplexans, Entamoeba histolytica, Trichomonas vaginalis, Phytophthora and ciliates. Comparative analysis of predicted chromatin proteins from protists allows reconstruction of the early evolutionary history of histone and DNA modification, nucleosome assembly and chromatin-remodeling systems. Many key catalytic, peptide-binding and DNA-binding domains in these systems ultimately had bacterial precursors, but were put together into distinctive regulatory complexes that are unique to the eukaryotes. In the case of histone methylases, histone demethylases and SWI2/SNF2 ATPases, proliferation of paralogous families followed by acquisition of novel domain architectures, seem to have played a major role in producing a diverse set of enzymes that create and respond to an epigenetic code of modified histones. The diversification of histone acetylases and DNA methylases appears to have proceeded via repeated emergence of new versions, most probably via transfers from bacteria to different eukaryotic lineages, again resulting in lineage-specific diversity in epigenetic signals. Even though the key histone modifications are universal to eukaryotes, domain architectures of proteins binding post-translationally modified-histones vary considerably across eukaryotes. This indicates that the histone code might be "interpreted" differently from model organisms in parasitic protists and their relatives. The complexity of domain architectures of chromatin proteins appears to have increased during eukaryotic evolution. Thus, Trichomonas, Giardia, Naegleria and kinetoplastids have relatively simple domain architectures, whereas apicomplexans and oomycetes have more complex architectures. RNA-dependent post-transcriptional silencing systems, which interact with chromatin-level regulatory systems, show considerable variability across parasitic protists, with complete loss in many apicomplexans and partial loss in Trichomonas vaginalis. This evolutionary synthesis offers a robust scaffold for future investigation of transcription and chromatin structure in parasitic protists.
doi:10.1016/j.ijpara.2007.07.018 pmid:17949725 fatcat:ixnwk5ysd5h2hla2fz3hhssxo4

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy [article]

Maria Kousi, Onuralp Soylemez, Aysegul Ozanturk, Sebastian Akle, Irwin Jungreis, Jean Muller, Christopher A Cassa, Harrison Brand, Jill A Rosenfeld, Maxim Y Wolf, Azita Sadeghpour, Kelsey McFadden (+7 others)
2018 bioRxiv   pre-print
The influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remains unclear. We performed a systematic secondary-variant burden analysis of two independent Bardet-Biedl syndrome (BBS) cohorts with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants compared to either
more » ... ion controls or to a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes, a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model paradigm for secondary-variant burden analysis in recessive disorders.
doi:10.1101/362707 fatcat:pl6zxoxi4rexjkdpnyvvk6p5ra

A Statistical Comparative Planetology Approach to Maximize the Scientific Return of Future Exoplanet Characterization Efforts [article]

Jade H. Checlair, Dorian S. Abbot, Robert J. Webber, Y. Katherina Feng, Jacob L. Bean, Edward W. Schwieterman, Christopher C. Stark, Tyler D. Robinson, Eliza Kempton, Olivia D. N. Alcabes, Daniel Apai, Giada Arney, Nicolas Cowan (+27 others)
2019 arXiv   pre-print
This work is of critical importance for maximal exploitation of limited observing time from future exoplanet characterization missions.  ... 
arXiv:1903.05211v1 fatcat:c4vndp3qivh2vfrkf2bjbufiti

GENCODE 2021

Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell (+44 others)
2020 Nucleic Acids Research  
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation
more » ... , bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
doi:10.1093/nar/gkaa1087 pmid:33270111 pmcid:PMC7778937 fatcat:eqyplhdexbdchn53omyqjckpge

Non-monotone Continuous DR-submodular Maximization: Structure and Algorithms

An Bian, Kfir Yehuda Levy, Andreas Krause, Joachim M. Buhmann
2017 Neural Information Processing Systems  
Then we present a non-monotone FRANK-WOLFE variant with 1/e approximation guarantee and sublinear convergence rate.  ...  In this work we study the problem of maximizing non-monotone continuous DRsubmodular functions under general down-closed convex constraints.  ...  1 x NON-CONVEX FRANK-WOLFE(f, P, K 1 , ✏ 1 , x (0) ) ; // x (0) 2 P 2 Q P \ {y 2 R n + | y  ū x}; 3 z NON-CONVEX FRANK-WOLFE(f, Q, K 2 , ✏ 2 , z (0) ) ; // z (0) 2 Q Output: arg max{f (x), f(z)} ; We  ... 
dblp:conf/nips/BianL0B17 fatcat:wcelfk4fbvcrlhdogxvbkwal6q

Online Continuous Submodular Maximization [article]

Lin Chen, Hamed Hassani, Amin Karbasi
2018 arXiv   pre-print
We first propose a variant of the Frank-Wolfe algorithm that has access to the full gradient of the objective functions.  ...  ∇f (x + t(y − x)) − ∇f (x) x − y dt ≤ 1 0 βt x − y 2 dt = β 2 x − y .  ...  The left-hand side of the first inequality is equal to 1 0 ∇f (x + t(y − x)) (x − y)dt − ∇f (x) (x − y) = 1 0 (∇f (x + t(y − x)) − ∇f (x)) (x − y) dt ≤ 1 0 (∇f (x + t(y − x)) − ∇f (x)) (x − y) dt ≤ 1 0  ... 
arXiv:1802.06052v1 fatcat:2szcbuixangxzhzxhm24wfskbq

Modified Numerals as Post-Suppositions [chapter]

Adrian Brasoveanu
2010 Lecture Notes in Computer Science  
Their asserted / at-issue contribution is a maximization operator that introduces the maximal set of entities that satisfies their restrictor and nuclear scope.  ...  [y] = ⇒ x y wolf 1 jasper x y wolf 1 movie 1 x y wolf 1 jasper ⊕ movie 2 x y wolf 2 jasper x y wolf 2 jasper ⊕ agatha x y wolf 2 wolf 3 . . . y=JASPER = ==== ⇒ x y wolf 1 jasper x y wolf 2 jasper . . .  ...  BITE(x,y) ====⇒ x y wolf 1 jasper . . .  ... 
doi:10.1007/978-3-642-14287-1_21 fatcat:37lnynh4rfh2bcwwlb2r4vwka4

Modified Numerals as Post-Suppositions

A. Brasoveanu
2012 Journal of Semantics  
Their asserted / at-issue contribution is a maximization operator that introduces the maximal set of entities that satisfies their restrictor and nuclear scope.  ...  [y] = ⇒ x y wolf 1 jasper x y wolf 1 movie 1 x y wolf 1 jasper ⊕ movie 2 x y wolf 2 jasper x y wolf 2 jasper ⊕ agatha x y wolf 2 wolf 3 . . . y=JASPER = ==== ⇒ x y wolf 1 jasper x y wolf 2 jasper . . .  ...  BITE(x,y) ====⇒ x y wolf 1 jasper . . .  ... 
doi:10.1093/jos/ffs003 fatcat:hlzi5hzmufaqdc3uaqxnhfm6nm

SNEWS 2.0: A Next-Generation SuperNova Early Warning System for Multi-messenger Astronomy

Soud Al Kharusi, Segev Y. BenZvi, Jake Bobowski, Walter Bonivento, Vedran Brdar, Thomas Brunner, Erica Caden, Michael Clark, Alexis Coleiro, Marta Colomer-Molla, José I. Crespo-Anadón, Amanda Depoian (+59 others)
2021 New Journal of Physics  
This document is the product of a workshop in June 2019 towards design of SNEWS 2.0, an upgraded SNEWS with enhanced capabilities exploiting the unique advantages of prompt neutrino detection to maximize  ...  The absolute errors of the reconstructed coordinates x, y, z for a point-like event in the target are virtually the same and depend on the energy as ∼10 cm/ √ E (MeV).  ...  The supernova direction angles, and other parameters, are varied until the total likelihood is maximized.  ... 
doi:10.1088/1367-2630/abde33 fatcat:oayesc6strgirfhfrgyp4dlvwe

Page 915 of Mathematical Reviews Vol. 26, Issue 4 [page]

1963 Mathematical Reviews  
We first find zo and y in G to maximize zo. Then, given y, we solve (*) for x. The first of these steps is, of course, the major one.  ...  The problem considered is the maximization of cT™z+f(y) subject to the constraints Az + F(y) <b, x20 (inadvertently omitted from Equation (1.1)), where z € Ry and y &S, an arbitrary subset of Ry.  ... 

Didstributed source coding authentication of images with affine warping

Yao-Chung Lin, David Varodayan, Bernd Girod
2009 2009 IEEE International Conference on Acoustics, Speech and Signal Processing  
Our approach incorporates an Expectation Maximization algorithm into the Slepian-Wolf decoder.  ...  In both cases, authentication requires a Slepian-Wolf encoded image projection that is supplied to the decoder. We extend our scheme to authenticate images that have undergone affine warping.  ...  It first projects y to Y in the same way as during authentication data generation. A Slepian-Wolf decoder reconstructs Xq from the Slepian-Wolf bitstream S(Xq) using Y as side information.  ... 
doi:10.1109/icassp.2009.4959875 dblp:conf/icassp/LinVG09 fatcat:uzqkcvdedzbqrj5fecmu3ep5km

Continuous DR-submodular Maximization: Structure and Algorithms [article]

An Bian, Kfir Y. Levy, Andreas Krause, Joachim M. Buhmann
2019 arXiv   pre-print
Then we present a non-monotone Frank-Wolfe variant with 1/e approximation guarantee and sublinear convergence rate.  ...  In this work we study the problem of maximizing non-monotone DR-submodular continuous functions under general down-closed convex constraints.  ...  Suppose g is a K α -DR-submodular function, and the K α -DR-submodular maximization problem is max y∈P g(y), where P = {y ∈ R n |h i (y) ≤ b i , ∀i ∈ [m], y Kα 0} is down-closed w.r.t. the conic inequality  ... 
arXiv:1711.02515v4 fatcat:by4uo3vitfdj7kdu5n4v6tcoee
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