Extbase Variable Dump
array(14 items) uid => 912 (integer) title => '3D Genome Reconstruction from Partially Phased Hi-C Data' (56 chars) abstract => 'The 3-dimensional (3D) structure of the genome is of significant importance
for many cellular processes. In this paper, we study the problem of reconstr
ucting the 3D structure of chromosomes from Hi-C data of diploid organisms,
which poses additional challenges compared to the better-studied haploid set
ting. With the help of techniques from algebraic geometry, we prove that a s
mall amount of phased data is sufficient to ensure finite identifiability, b
oth for noiseless and noisy data. In the light of these results, we propose
a new 3D reconstruction method based on semidefinite programming, paired wit
h numerical algebraic geometry and local optimization. The performance of th
is method is tested on several simulated datasets under different noise leve
ls and with different amounts of phased data. We also apply it to a real dat
aset from mouse X chromosomes, and we are then able to recover previously kn
own structural features.' (936 chars) authors => array(5 items) 0 => array(3 items) last_name => 'Cifuentes' (9 chars) first_name => 'Diego' (5 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Jan' (3 chars) first_name => 'Draisma' (7 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Henriksson' (10 chars) first_name => 'Oskar' (5 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Korchmaros' (10 chars) first_name => 'Annachiara' (10 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Kubjas' (6 chars) first_name => 'Kaie' (4 chars) sorting => 5 (integer) type => '0' (1 chars) keywords => '3D genome organization, Diploid organisms, Hi-C, Applied algebraic geometry,
Numerical algebraic geometry, Mathematics Subject Classification, 92E10, 92
-08, 13P25, 14P05, 65H14, 90C90' (183 chars) year => 2024 (integer) affiliation => 0 (integer) link_paper => '' (0 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => '' (0 chars) doi => '' (0 chars) preprint => '-1' (2 chars)
3D Genome Reconstruction from Partially Phased Hi-C Data
2024: Diego Cifuentes; Draisma Jan; Oskar Henriksson; Annachiara Korchmaros; Kaie KubjasThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruction method based on semidefinite programming, paired with numerical algebraic geometry and local optimization. The performance of this method is tested on several simulated datasets under different noise levels and with different amounts of phased data. We also apply it to a real dataset from mouse X chromosomes, and we are then able to recover previously known structural features.
Keywords: 3D genome organization, Diploid organisms, Hi-C, Applied algebraic geometry, Numerical algebraic geometry, Mathematics Subject Classification, 92E10, 92-08, 13P25, 14P05, 65H14, 90C90Extbase Variable Dump
array(14 items) uid => 1 (integer) title => 'Annotation-Free Identification of Potential Synteny Anchors' (60 chars) abstract => '' (0 chars) authors => array(3 items) 0 => array(3 items) last_name => 'Käther' (7 chars) first_name => 'Karl' (4 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Lemke' (5 chars) first_name => 'Steffen' (7 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 3 (integer) type => '0' (1 chars) keywords => '' (0 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://link.springer.com/content/pdf/10.1007/978-3-031-34953-9_17' (66 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Bioinformatics and Biomedical Engineering; Lecture Notes in Computer Science' (76 chars) doi => '10.1007/978-3-031-34953-9_17' (28 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 13 (integer) title => 'Best Match Graphs With Binary Trees' (35 chars) abstract => '' (0 chars) authors => array(4 items) 0 => array(3 items) last_name => 'Schaller' (8 chars) first_name => 'David' (5 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Geiß' (5 chars) first_name => 'Manüla' (7 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Hellmuth' (8 chars) first_name => 'Marc' (4 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 4 (integer) type => '0' (1 chars) keywords => 'Applied Mathematics, Genetics, Biotechnology' (44 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'http://xplorestaging.ieee.org/ielx7/8857/10144451/09684987.pdf?arnumber=9684
987' (79 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'IEEE/ACM Transactions on Computational Biology and Bioinformatics' (65 chars) doi => '10.1109/tcbb.2022.3143870' (25 chars) preprint => '-1' (2 chars)
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array(14 items) uid => 2 (integer) title => 'Comparison of Atom Maps' (23 chars) abstract => 'The computation of reliable, chemically correct atom maps from educt/product
pairs has turned out to be a difficult problem in cheminformatics because t
he chemically correct solution is not necessarily an optimal solution for co
mbinatorial formulations such as maximum common subgraph problems. As a cons
equence, competing models have been devised and compared in extensive benchm
arking studies. Due to isomorphisms among products and educts it is not imme
diately obvious, however, when two atom maps for a given educt/product pairs
are the same. We formalize here the equivalence of atom maps and show that
equivalence of atom maps is in turn equivalent to the isomorphism of labeled
auxiliary graphs. In particular, we demonstrate that Fujita's Imaginary Tra
nsition State can be used for this purpose. Numerical experiments show that
practical feasibility. Generalizations to the equivalence of subgraph matche
s, double pushout graph transformation rules, and mechanisms of multi-step r
eactions are discussed briefly.' (1019 chars) authors => array(4 items) 0 => array(3 items) last_name => 'Gonzalez Laffitte' (17 chars) first_name => 'Marcos E.' (9 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Beier' (5 chars) first_name => 'Nora' (4 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Domschke' (8 chars) first_name => 'Nico' (4 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 4 (integer) type => '0' (1 chars) keywords => 'Applied Mathematics, Computational Theory and Mathematics, Computer Science
Applications, General Chemistry' (107 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://match.pmf.kg.ac.rs/issues/m90n1/m90n1_75-102.html' (57 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Match Communications in Mathematical and in Computer Chemistry' (62 chars) doi => '10.46793/match.90-1.075g' (24 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 893 (integer) title => 'Defining the landscape of circular RNAs in neuroblastoma unveils a global su
ppressive function of MYCN' (102 chars) abstract => 'Circular RNAs (circRNAs) are a regulatory RNA class. While cancer-driving fu
nctions have been identified for single circRNAs, how they modulate gene exp
ression in cancer is not well understood. We investigate circRNA expression
in the pediatric malignancy, neuroblastoma, through deep whole-transcriptome
sequencing in 104 primary neuroblastomas covering all risk groups. We demon
strate that MYCN amplification, which defines a subset of high-risk cases,
causes globally suppressed circRNA biogenesis directly dependent on the DHX9
RNA helicase. We detect similar mechanisms in shaping circRNA expression in
the pediatric cancer medulloblastoma implying a general MYCN effect. Compar
isons to other cancers identify 25 circRNAs that are specifically upregulate
d in neuroblastoma, including circARID1A. Transcribed from the ARID1A tumor
suppressor gene, circARID1A promotes cell growth and survival, mediated by
direct interaction with the KHSRP RNA-binding protein. Our study highlights
the importance of MYCN regulating circRNAs in cancer and identifies molecula
r mechanisms, which explain their contribution to neuroblastoma pathogenesis
.' (1141 chars) authors => array(30 items) 0 => array(3 items) last_name => 'Fuchs' (5 chars) first_name => 'Steffen' (7 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Danßmann' (9 chars) first_name => 'Clara' (5 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Klironomos' (10 chars) first_name => 'Filippos' (8 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Winkler' (7 chars) first_name => 'Annika' (6 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Fallmann' (8 chars) first_name => 'Jörg' (5 chars) sorting => 5 (integer) 5 => array(3 items) last_name => 'Krützfeldt' (11 chars) first_name => 'Louisa Marie' (12 chars) sorting => 6 (integer) 6 => array(3 items) last_name => 'Szymansky' (9 chars) first_name => 'Annabell' (8 chars) sorting => 7 (integer) 7 => array(3 items) last_name => 'Naderi' (6 chars) first_name => 'Julian' (6 chars) sorting => 8 (integer) 8 => array(3 items) last_name => 'Bernhart' (8 chars) first_name => 'Stephan H. F.' (14 chars) sorting => 9 (integer) 9 => array(3 items) last_name => 'Grunewald' (9 chars) first_name => 'Laura' (5 chars) sorting => 10 (integer) 10 => array(3 items) last_name => 'Helmsaür' (9 chars) first_name => 'Konstantin' (10 chars) sorting => 11 (integer) 11 => array(3 items) last_name => 'Rodrigüz Fos' (13 chars) first_name => 'Elias' (5 chars) sorting => 12 (integer) 12 => array(3 items) last_name => 'Kirchner' (8 chars) first_name => 'Marieluise' (10 chars) sorting => 13 (integer) 13 => array(3 items) last_name => 'Mertins' (7 chars) first_name => 'Philipp' (7 chars) sorting => 14 (integer) 14 => array(3 items) last_name => 'Astrahantseff' (13 chars) first_name => 'Kathy' (5 chars) sorting => 15 (integer) 15 => array(3 items) last_name => 'Sünkel' (7 chars) first_name => 'Christin' (8 chars) sorting => 16 (integer) 16 => array(3 items) last_name => 'Todling' (7 chars) first_name => 'Jorn' (4 chars) sorting => 17 (integer) 17 => array(3 items) last_name => 'Meggetto' (8 chars) first_name => 'Fabienne' (8 chars) sorting => 18 (integer) 18 => array(3 items) last_name => 'Remke' (5 chars) first_name => 'Marc' (4 chars) sorting => 19 (integer) 19 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 20 (integer) 20 => array(3 items) last_name => 'Hundsdorfer' (11 chars) first_name => 'Patrick' (7 chars) sorting => 21 (integer) 21 => array(3 items) last_name => 'Deubzer' (7 chars) first_name => 'Hedwig E.' (9 chars) sorting => 22 (integer) 22 => array(3 items) last_name => 'Künkele' (8 chars) first_name => 'Annette' (7 chars) sorting => 23 (integer) 23 => array(3 items) last_name => 'Lang' (4 chars) first_name => 'Peter' (5 chars) sorting => 24 (integer) 24 => array(3 items) last_name => 'Fuchs' (5 chars) first_name => 'Jörg' (5 chars) sorting => 25 (integer) 25 => array(3 items) last_name => 'Henssen' (7 chars) first_name => 'Anton G.' (8 chars) sorting => 26 (integer) 26 => array(3 items) last_name => 'Eggert' (6 chars) first_name => 'Angelika' (8 chars) sorting => 27 (integer) 27 => array(3 items) last_name => 'Rajewsky' (8 chars) first_name => 'Nikolaus' (8 chars) sorting => 28 (integer) 28 => array(3 items) last_name => 'Hertwig' (7 chars) first_name => 'Falk' (4 chars) sorting => 29 (integer) 29 => array(3 items) last_name => 'Schulte' (7 chars) first_name => 'Johannes H.' (11 chars) sorting => 30 (integer) type => '0' (1 chars) keywords => 'General Physics and Astronomy, General Biochemistry, Genetics and Molecular
Biology, General Chemistry, Multidisciplinary' (121 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://www.nature.com/articles/s41467-023-38747-4.pdf' (54 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Nature Communications' (21 chars) doi => '10.1038/s41467-023-38747-4' (26 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 4 (integer) title => 'Led-Seq: ligation-enhanced double-end sequence-based structure analysis of
RNA' (79 chars) abstract => 'Structural analysis of RNA is an important and versatile tool to investigate
the function of this type of molecules in the cell as well as in vitro. Sev
eral robust and reliable procedures are available, relying on chemical modif
ication inducing RT stops or nucleotide misincorporations during reverse tra
nscription. Others are based on cleavage reactions and RT stop signals. Howe
ver, these methods address only one side of the RT stop or misincorporation
position. Here, we describe Led-Seq, a new approach based on lead-induced cl
eavage of unpaired RNA positions, where both resulting cleavage products are
A ligases. In a deep sequencing analysis, the cleavage sites are identified
as ligation positions, avoiding possible false positive signals based on pre
mature RT stops. With a benchmark set of transcripts in Escherichia coli, we
show that Led-Seq is an improved and reliable approach based on metal ion-i
nduced phosphodiester hydrolysis to investigate RNA structures in vivo.' (1135 chars) authors => array(7 items) 0 => array(3 items) last_name => 'Kolberg' (7 chars) first_name => 'Tim' (3 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Von Lohneysen' (13 chars) first_name => 'Sarah' (5 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Ozerova' (7 chars) first_name => 'Iuliia' (6 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Wellner' (7 chars) first_name => 'Karolin' (7 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Hartmann' (8 chars) first_name => 'Roland K.' (9 chars) sorting => 5 (integer) 5 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 6 (integer) 6 => array(3 items) last_name => 'Mörl' (5 chars) first_name => 'Mario' (5 chars) sorting => 7 (integer) type => '0' (1 chars) keywords => 'Genetics' (8 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://academic.oup.com/nar/article-pdf/51/11/e63/50669469/gkad312.pdf' (71 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Nucleic Acids Research' (22 chars) doi => '10.1093/nar/gkad312' (19 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 3 (integer) title => 'Local RNA Folding Revisisted' (28 chars) abstract => '' (0 chars) authors => array(7 items) 0 => array(3 items) last_name => 'Waldl' (5 chars) first_name => 'Maria' (5 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Spicher' (7 chars) first_name => 'Thomas' (6 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Lorenz' (6 chars) first_name => 'Ronny' (5 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Beckmann' (8 chars) first_name => 'Irene K.' (8 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Hofacker' (8 chars) first_name => 'Ivo L.' (6 chars) sorting => 5 (integer) 5 => array(3 items) last_name => 'Von Lohneysen' (13 chars) first_name => 'Sarah' (5 chars) sorting => 6 (integer) 6 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 7 (integer) type => '0' (1 chars) keywords => 'Computer Science Applications, Molecular Biology, Biochemistry' (62 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://www.worldscientific.com/doi/pdf/10.1142/S0219720023500166' (65 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Journal of Bioinformatics and Computational Biology' (51 chars) doi => '10.1142/s0219720023500166' (25 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 5 (integer) title => 'Planar median graphs and cubesquare-graphs' (42 chars) abstract => '' (0 chars) authors => array(4 items) 0 => array(3 items) last_name => 'Seemann' (7 chars) first_name => 'Carsten R.' (10 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Moulton' (7 chars) first_name => 'Vincent' (7 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Hellmuth' (8 chars) first_name => 'Marc' (4 chars) sorting => 4 (integer) type => '0' (1 chars) keywords => 'Applied Mathematics, Discrete Mathematics and Combinatorics' (59 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://api.elsevier.com/content/article/PII:S0166218X23000203?httpAccept=te
xt/xml' (82 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Discrete Applied Mathematics' (28 chars) doi => '10.1016/j.dam.2023.01.022' (25 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 6 (integer) title => 'Quasi-best match graphs' (23 chars) abstract => '' (0 chars) authors => array(4 items) 0 => array(3 items) last_name => 'Korchmaros' (10 chars) first_name => 'Annachiara' (10 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Schaller' (8 chars) first_name => 'David' (5 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Hellmuth' (8 chars) first_name => 'Marc' (4 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 4 (integer) type => '0' (1 chars) keywords => 'Applied Mathematics, Discrete Mathematics and Combinatorics' (59 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://api.elsevier.com/content/article/PII:S0166218X23000173?httpAccept=te
xt/xml' (82 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => 'Discrete Applied Mathematics' (28 chars) doi => '10.1016/j.dam.2023.01.015' (25 chars) preprint => '-1' (2 chars)
Extbase Variable Dump
array(14 items) uid => 725 (integer) title => 'Relative Timing Information and Orthology inEvolutionary Scenarios' (66 chars) abstract => 'Background: Evolutionary scenarios describing the evolution of a family of g
enes within a collection of species comprise the mapping of the vertices of
a gene tree T to vertices and edges of a species tree S. The relative timing
of the last common ancestors of two extant genes (leaves of T) and the last
common ancestors of the two species (leaves of S) in which they reside is i
ndicative of horizontal gene transfers (HGT) and ancient duplications. Ortho
logous gene pairs, on the other hand, require that their last common ancesto
rs coincides with a corresponding speciation event. The relative timing info
rmation of gene and species divergences is captured by three colored graphs
that have the extant genes as vertices and the species in which the genes ar
e found as vertex colors: the equal-divergence-time (EDT) graph, the later-d
ivergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which
together form an edge partition of the complete graph. Results: Here we giv
e a complete characterization in terms of informative and forbidden triples
that can be read off the three graphs and provide a polynomial time algorith
m for constructing an evolutionary scenario that explains the graphs, provid
ed such a scenario exists. While both LDT and PDT graphs are cographs, this
is not true for the EDT graph in general. We show that every EDT graph is pe
rfect. While the information about LDT and PDT graphs is necessary to recogn
ize EDT graphs in polynomial-time for general scenarios, this extra informat
ion can be dropped in the HGT-free case. However, recognition of EDT graphs
without knowledge of putative LDT and PDT graphs is NP-complete for general
scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We
finally connect the EDT graph to the alternative definitions of orthology th
at have been proposed for scenarios with horizontal gene transfer. With one
exception, the corresponding graphs are shown to be colored cographs.' (1969 chars) authors => array(6 items) 0 => array(3 items) last_name => 'Schaller' (8 chars) first_name => 'David' (5 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Hartmann' (8 chars) first_name => 'Tom' (3 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Lafond' (6 chars) first_name => 'Manül' (6 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Wieseke' (7 chars) first_name => 'Nicolas' (7 chars) sorting => 5 (integer) 5 => array(3 items) last_name => 'Hellmuth' (8 chars) first_name => 'Marc' (4 chars) sorting => 6 (integer) type => '0' (1 chars) keywords => '' (0 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://www.researchsquare.com/article/rs-2678762/v1' (52 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => '' (0 chars) doi => '10.21203/rs.3.rs-2678762/v1' (27 chars) preprint => '-1' (2 chars)