---
_id: '9565'
abstract:
- lang: eng
  text: Let D(n,p) be the random directed graph on n vertices where each of the n(n-1)
    possible arcs is present independently with probability p. A celebrated result
    of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton
    cycle, and this is best possible. In this paper, we obtain a strengthening of
    this result, showing that under the same condition, the number of directed Hamilton
    cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version
    of this statement, showing that in the random directed graph process, as soon
    as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n
    directed Hamilton cycles.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Asaf
  full_name: Ferber, Asaf
  last_name: Ferber
- first_name: Matthew Alan
  full_name: Kwan, Matthew Alan
  id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
  last_name: Kwan
  orcid: 0000-0002-4003-7567
- first_name: Benny
  full_name: Sudakov, Benny
  last_name: Sudakov
citation:
  ama: Ferber A, Kwan MA, Sudakov B. Counting Hamilton cycles in sparse random directed
    graphs. <i>Random Structures and Algorithms</i>. 2018;53(4):592-603. doi:<a href="https://doi.org/10.1002/rsa.20815">10.1002/rsa.20815</a>
  apa: Ferber, A., Kwan, M. A., &#38; Sudakov, B. (2018). Counting Hamilton cycles
    in sparse random directed graphs. <i>Random Structures and Algorithms</i>. Wiley.
    <a href="https://doi.org/10.1002/rsa.20815">https://doi.org/10.1002/rsa.20815</a>
  chicago: Ferber, Asaf, Matthew Alan Kwan, and Benny Sudakov. “Counting Hamilton
    Cycles in Sparse Random Directed Graphs.” <i>Random Structures and Algorithms</i>.
    Wiley, 2018. <a href="https://doi.org/10.1002/rsa.20815">https://doi.org/10.1002/rsa.20815</a>.
  ieee: A. Ferber, M. A. Kwan, and B. Sudakov, “Counting Hamilton cycles in sparse
    random directed graphs,” <i>Random Structures and Algorithms</i>, vol. 53, no.
    4. Wiley, pp. 592–603, 2018.
  ista: Ferber A, Kwan MA, Sudakov B. 2018. Counting Hamilton cycles in sparse random
    directed graphs. Random Structures and Algorithms. 53(4), 592–603.
  mla: Ferber, Asaf, et al. “Counting Hamilton Cycles in Sparse Random Directed Graphs.”
    <i>Random Structures and Algorithms</i>, vol. 53, no. 4, Wiley, 2018, pp. 592–603,
    doi:<a href="https://doi.org/10.1002/rsa.20815">10.1002/rsa.20815</a>.
  short: A. Ferber, M.A. Kwan, B. Sudakov, Random Structures and Algorithms 53 (2018)
    592–603.
date_created: 2021-06-18T12:06:28Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-02-23T14:01:03Z
day: '01'
doi: 10.1002/rsa.20815
extern: '1'
external_id:
  arxiv:
  - '1708.07746'
intvolume: '        53'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1708.07746
month: '12'
oa: 1
oa_version: Preprint
page: 592-603
publication: Random Structures and Algorithms
publication_identifier:
  eissn:
  - 1098-2418
  issn:
  - 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting Hamilton cycles in sparse random directed graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 53
year: '2018'
...
---
_id: '9567'
abstract:
- lang: eng
  text: Let P be a graph property which is preserved by removal of edges, and consider
    the random graph process that starts with the empty n-vertex graph and then adds
    edges one-by-one, each chosen uniformly at random subject to the constraint that
    P is not violated. These types of random processes have been the subject of extensive
    research over the last 20 years, having striking applications in extremal combinatorics,
    and leading to the discovery of important probabilistic tools. In this paper we
    consider the k-matching-free process, where P is the property of not containing
    a matching of size k. We are able to analyse the behaviour of this process for
    a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn)
    then this process is likely to terminate in a k-matching-free graph with the maximum
    possible number of edges, as characterised by Erdős and Gallai. We also show that
    these bounds on k are essentially best possible, and we make a first step towards
    understanding the behaviour of the process in the intermediate regime.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
  full_name: Krivelevich, Michael
  last_name: Krivelevich
- first_name: Matthew Alan
  full_name: Kwan, Matthew Alan
  id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
  last_name: Kwan
  orcid: 0000-0002-4003-7567
- first_name: Po‐Shen
  full_name: Loh, Po‐Shen
  last_name: Loh
- first_name: Benny
  full_name: Sudakov, Benny
  last_name: Sudakov
citation:
  ama: Krivelevich M, Kwan MA, Loh P, Sudakov B. The random k‐matching‐free process.
    <i>Random Structures and Algorithms</i>. 2018;53(4):692-716. doi:<a href="https://doi.org/10.1002/rsa.20814">10.1002/rsa.20814</a>
  apa: Krivelevich, M., Kwan, M. A., Loh, P., &#38; Sudakov, B. (2018). The random
    k‐matching‐free process. <i>Random Structures and Algorithms</i>. Wiley. <a href="https://doi.org/10.1002/rsa.20814">https://doi.org/10.1002/rsa.20814</a>
  chicago: Krivelevich, Michael, Matthew Alan Kwan, Po‐Shen Loh, and Benny Sudakov.
    “The Random K‐matching‐free Process.” <i>Random Structures and Algorithms</i>.
    Wiley, 2018. <a href="https://doi.org/10.1002/rsa.20814">https://doi.org/10.1002/rsa.20814</a>.
  ieee: M. Krivelevich, M. A. Kwan, P. Loh, and B. Sudakov, “The random k‐matching‐free
    process,” <i>Random Structures and Algorithms</i>, vol. 53, no. 4. Wiley, pp.
    692–716, 2018.
  ista: Krivelevich M, Kwan MA, Loh P, Sudakov B. 2018. The random k‐matching‐free
    process. Random Structures and Algorithms. 53(4), 692–716.
  mla: Krivelevich, Michael, et al. “The Random K‐matching‐free Process.” <i>Random
    Structures and Algorithms</i>, vol. 53, no. 4, Wiley, 2018, pp. 692–716, doi:<a
    href="https://doi.org/10.1002/rsa.20814">10.1002/rsa.20814</a>.
  short: M. Krivelevich, M.A. Kwan, P. Loh, B. Sudakov, Random Structures and Algorithms
    53 (2018) 692–716.
date_created: 2021-06-18T12:37:40Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-02-23T14:01:07Z
day: '01'
doi: 10.1002/rsa.20814
extern: '1'
external_id:
  arxiv:
  - '1708.01054'
intvolume: '        53'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1708.01054
month: '12'
oa: 1
oa_version: Preprint
page: 692-716
publication: Random Structures and Algorithms
publication_identifier:
  eissn:
  - 1098-2418
  issn:
  - 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The random k‐matching‐free process
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 53
year: '2018'
...
---
_id: '9568'
abstract:
- lang: eng
  text: An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number
    of intercalates in a uniformly random n×n Latin square. We prove that asymptotically
    almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically
    almost surely N≤fn2 for any f→∞). This significantly improves the previous best
    lower and upper bounds. We also give an upper tail bound for the number of intercalates
    in two fixed rows of a random Latin square. In addition, we discuss a problem
    of Linial and Luria on low-discrepancy Latin squares.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
  full_name: Kwan, Matthew Alan
  id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
  last_name: Kwan
  orcid: 0000-0002-4003-7567
- first_name: Benny
  full_name: Sudakov, Benny
  last_name: Sudakov
citation:
  ama: Kwan MA, Sudakov B. Intercalates and discrepancy in random Latin squares. <i>Random
    Structures and Algorithms</i>. 2018;52(2):181-196. doi:<a href="https://doi.org/10.1002/rsa.20742">10.1002/rsa.20742</a>
  apa: Kwan, M. A., &#38; Sudakov, B. (2018). Intercalates and discrepancy in random
    Latin squares. <i>Random Structures and Algorithms</i>. Wiley. <a href="https://doi.org/10.1002/rsa.20742">https://doi.org/10.1002/rsa.20742</a>
  chicago: Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in
    Random Latin Squares.” <i>Random Structures and Algorithms</i>. Wiley, 2018. <a
    href="https://doi.org/10.1002/rsa.20742">https://doi.org/10.1002/rsa.20742</a>.
  ieee: M. A. Kwan and B. Sudakov, “Intercalates and discrepancy in random Latin squares,”
    <i>Random Structures and Algorithms</i>, vol. 52, no. 2. Wiley, pp. 181–196, 2018.
  ista: Kwan MA, Sudakov B. 2018. Intercalates and discrepancy in random Latin squares.
    Random Structures and Algorithms. 52(2), 181–196.
  mla: Kwan, Matthew Alan, and Benny Sudakov. “Intercalates and Discrepancy in Random
    Latin Squares.” <i>Random Structures and Algorithms</i>, vol. 52, no. 2, Wiley,
    2018, pp. 181–96, doi:<a href="https://doi.org/10.1002/rsa.20742">10.1002/rsa.20742</a>.
  short: M.A. Kwan, B. Sudakov, Random Structures and Algorithms 52 (2018) 181–196.
date_created: 2021-06-18T12:47:25Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-02-23T14:01:09Z
day: '01'
doi: 10.1002/rsa.20742
extern: '1'
external_id:
  arxiv:
  - '1607.04981'
intvolume: '        52'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1607.04981
month: '03'
oa: 1
oa_version: Preprint
page: 181-196
publication: Random Structures and Algorithms
publication_identifier:
  eissn:
  - 1098-2418
  issn:
  - 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intercalates and discrepancy in random Latin squares
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 52
year: '2018'
...
---
_id: '9587'
abstract:
- lang: eng
  text: We say a family of sets is intersecting if any two of its sets intersect,
    and we say it is trivially intersecting if there is an element which appears in
    every set of the family. In this paper we study the maximum size of a non-trivially
    intersecting family in a natural “multi-part” setting. Here the ground set is
    divided into parts, and one considers families of sets whose intersection with
    each part is of a prescribed size. Our work is motivated by classical results
    in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and
    by a theorem of Frankl concerning intersecting families in this multi-part setting.
    In the case where the part sizes are sufficiently large we determine the maximum
    size of a non-trivially intersecting multi-part family, disproving a conjecture
    of Alon and Katona.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
  full_name: Kwan, Matthew Alan
  id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
  last_name: Kwan
  orcid: 0000-0002-4003-7567
- first_name: Benny
  full_name: Sudakov, Benny
  last_name: Sudakov
- first_name: Pedro
  full_name: Vieira, Pedro
  last_name: Vieira
citation:
  ama: Kwan MA, Sudakov B, Vieira P. Non-trivially intersecting multi-part families.
    <i>Journal of Combinatorial Theory Series A</i>. 2018;156:44-60. doi:<a href="https://doi.org/10.1016/j.jcta.2017.12.001">10.1016/j.jcta.2017.12.001</a>
  apa: Kwan, M. A., Sudakov, B., &#38; Vieira, P. (2018). Non-trivially intersecting
    multi-part families. <i>Journal of Combinatorial Theory Series A</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.jcta.2017.12.001">https://doi.org/10.1016/j.jcta.2017.12.001</a>
  chicago: Kwan, Matthew Alan, Benny Sudakov, and Pedro Vieira. “Non-Trivially Intersecting
    Multi-Part Families.” <i>Journal of Combinatorial Theory Series A</i>. Elsevier,
    2018. <a href="https://doi.org/10.1016/j.jcta.2017.12.001">https://doi.org/10.1016/j.jcta.2017.12.001</a>.
  ieee: M. A. Kwan, B. Sudakov, and P. Vieira, “Non-trivially intersecting multi-part
    families,” <i>Journal of Combinatorial Theory Series A</i>, vol. 156. Elsevier,
    pp. 44–60, 2018.
  ista: Kwan MA, Sudakov B, Vieira P. 2018. Non-trivially intersecting multi-part
    families. Journal of Combinatorial Theory Series A. 156, 44–60.
  mla: Kwan, Matthew Alan, et al. “Non-Trivially Intersecting Multi-Part Families.”
    <i>Journal of Combinatorial Theory Series A</i>, vol. 156, Elsevier, 2018, pp.
    44–60, doi:<a href="https://doi.org/10.1016/j.jcta.2017.12.001">10.1016/j.jcta.2017.12.001</a>.
  short: M.A. Kwan, B. Sudakov, P. Vieira, Journal of Combinatorial Theory Series
    A 156 (2018) 44–60.
date_created: 2021-06-22T11:42:48Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T14:01:55Z
day: '01'
doi: 10.1016/j.jcta.2017.12.001
extern: '1'
external_id:
  arxiv:
  - '1703.09946'
intvolume: '       156'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1703.09946
month: '05'
oa: 1
oa_version: Preprint
page: 44-60
publication: Journal of Combinatorial Theory Series A
publication_identifier:
  issn:
  - 0097-3165
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-trivially intersecting multi-part families
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 156
year: '2018'
...
---
_id: '9659'
abstract:
- lang: eng
  text: The curvature dependence of interfacial free energy, which is crucial in quantitatively
    predicting nucleation kinetics and the stability of bubbles and droplets, is quantified
    by the Tolman length δ. For solid-liquid interfaces, however, δ has never been
    computed directly due to various theoretical and practical challenges. Here we
    perform a direct evaluation of the Tolman length from atomistic simulations of
    a solid-liquid planar interface in out-of-equilibrium conditions, by first computing
    the surface tension from the amplitude of thermal capillary fluctuations of a
    localized version of the Gibbs dividing surface and by then calculating how much
    the surface energy changes when it is defined relative to the equimolar dividing
    surface. We computed δ for a model potential, and found a good agreement with
    the values indirectly inferred from nucleation simulations. The agreement not
    only validates our approach but also suggests that the nucleation free energy
    of the system can be perfectly described using classical nucleation theory if
    the Tolman length is taken into account.
article_number: '231102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: 'Cheng B, Ceriotti M. Communication: Computing the Tolman length for solid-liquid
    interfaces. <i>The Journal of Chemical Physics</i>. 2018;148(23). doi:<a href="https://doi.org/10.1063/1.5038396">10.1063/1.5038396</a>'
  apa: 'Cheng, B., &#38; Ceriotti, M. (2018). Communication: Computing the Tolman
    length for solid-liquid interfaces. <i>The Journal of Chemical Physics</i>. AIP
    Publishing. <a href="https://doi.org/10.1063/1.5038396">https://doi.org/10.1063/1.5038396</a>'
  chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman
    Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>. AIP
    Publishing, 2018. <a href="https://doi.org/10.1063/1.5038396">https://doi.org/10.1063/1.5038396</a>.'
  ieee: 'B. Cheng and M. Ceriotti, “Communication: Computing the Tolman length for
    solid-liquid interfaces,” <i>The Journal of Chemical Physics</i>, vol. 148, no.
    23. AIP Publishing, 2018.'
  ista: 'Cheng B, Ceriotti M. 2018. Communication: Computing the Tolman length for
    solid-liquid interfaces. The Journal of Chemical Physics. 148(23), 231102.'
  mla: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman
    Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>, vol.
    148, no. 23, 231102, AIP Publishing, 2018, doi:<a href="https://doi.org/10.1063/1.5038396">10.1063/1.5038396</a>.'
  short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018).
date_created: 2021-07-15T07:51:42Z
date_published: 2018-06-21T00:00:00Z
date_updated: 2023-02-23T14:03:57Z
day: '21'
doi: 10.1063/1.5038396
extern: '1'
external_id:
  arxiv:
  - '1803.09140'
  pmid:
  - '29935495'
intvolume: '       148'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1063/1.5038396
month: '06'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
  eissn:
  - 1089-7690
  issn:
  - 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Communication: Computing the Tolman length for solid-liquid interfaces'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 148
year: '2018'
...
---
_id: '9665'
abstract:
- lang: eng
  text: We investigate the thermodynamics and kinetics of a hydrogen interstitial
    in magnetic α-iron, taking account of the quantum fluctuations of the proton as
    well as the anharmonicities of lattice vibrations and hydrogen hopping. We show
    that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly
    from an Arrhenius behavior at and below room temperature. We compare a quantum
    transition state theory to explicit ring polymer molecular dynamics in the calculation
    of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype
    lattice defect. By a sequence of steps in a thought experiment, each involving
    a thermodynamic integration, we are able to separate out the binding free energy
    of a proton to a defect into harmonic and anharmonic, and classical and quantum
    contributions. We find that about 30% of a typical binding free energy of hydrogen
    to a lattice defect in iron is accounted for by finite temperature effects, and
    about half of these arise from quantum proton fluctuations. This has huge implications
    for the comparison between thermal desorption and permeation experiments and standard
    electronic structure theory. The implications are even greater for the interpretation
    of muon spin resonance experiments.
article_number: '225901'
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Anthony T.
  full_name: Paxton, Anthony T.
  last_name: Paxton
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: 'Cheng B, Paxton AT, Ceriotti M. Hydrogen diffusion and trapping in α-iron:
    The role of quantum and anharmonic fluctuations. <i>Physical Review Letters</i>.
    2018;120(22). doi:<a href="https://doi.org/10.1103/physrevlett.120.225901">10.1103/physrevlett.120.225901</a>'
  apa: 'Cheng, B., Paxton, A. T., &#38; Ceriotti, M. (2018). Hydrogen diffusion and
    trapping in α-iron: The role of quantum and anharmonic fluctuations. <i>Physical
    Review Letters</i>. American Physical Society. <a href="https://doi.org/10.1103/physrevlett.120.225901">https://doi.org/10.1103/physrevlett.120.225901</a>'
  chicago: 'Cheng, Bingqing, Anthony T. Paxton, and Michele Ceriotti. “Hydrogen Diffusion
    and Trapping in α-Iron: The Role of Quantum and Anharmonic Fluctuations.” <i>Physical
    Review Letters</i>. American Physical Society, 2018. <a href="https://doi.org/10.1103/physrevlett.120.225901">https://doi.org/10.1103/physrevlett.120.225901</a>.'
  ieee: 'B. Cheng, A. T. Paxton, and M. Ceriotti, “Hydrogen diffusion and trapping
    in α-iron: The role of quantum and anharmonic fluctuations,” <i>Physical Review
    Letters</i>, vol. 120, no. 22. American Physical Society, 2018.'
  ista: 'Cheng B, Paxton AT, Ceriotti M. 2018. Hydrogen diffusion and trapping in
    α-iron: The role of quantum and anharmonic fluctuations. Physical Review Letters.
    120(22), 225901.'
  mla: 'Cheng, Bingqing, et al. “Hydrogen Diffusion and Trapping in α-Iron: The Role
    of Quantum and Anharmonic Fluctuations.” <i>Physical Review Letters</i>, vol.
    120, no. 22, 225901, American Physical Society, 2018, doi:<a href="https://doi.org/10.1103/physrevlett.120.225901">10.1103/physrevlett.120.225901</a>.'
  short: B. Cheng, A.T. Paxton, M. Ceriotti, Physical Review Letters 120 (2018).
date_created: 2021-07-15T12:22:41Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-08-09T12:36:22Z
day: '01'
doi: 10.1103/physrevlett.120.225901
extern: '1'
external_id:
  arxiv:
  - '1803.00600'
  pmid:
  - '29906144'
intvolume: '       120'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1803.00600
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
  eissn:
  - 1079-7114
  issn:
  - 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic
  fluctuations'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 120
year: '2018'
...
---
_id: '9668'
abstract:
- lang: eng
  text: Estimating the homogeneous ice nucleation rate from undercooled liquid water
    is crucial for understanding many important physical phenomena and technological
    applications, and challenging for both experiments and theory. From a theoretical
    point of view, difficulties arise due to the long time scales required, as well
    as the numerous nucleation pathways involved to form ice nuclei with different
    stacking disorders. We computed the homogeneous ice nucleation rate at a physically
    relevant undercooling for a single-site water model, taking into account the diffuse
    nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition
    rate of particles to the critical nucleus. We disentangled and investigated the
    relative importance of all the terms, including interfacial free energy, entropic
    contributions and the kinetic prefactor, that contribute to the overall nucleation
    rate. Breaking down the problem into pieces not only provides physical insights
    into ice nucleation, but also sheds light on the long-standing discrepancy between
    different theoretical predictions, as well as between theoretical and experimental
    determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings
    and suggest strategies to systematically improve the existing simulation methods.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Christoph
  full_name: Dellago, Christoph
  last_name: Dellago
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: 'Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous
    ice nucleation rate: Disentangling thermodynamics and kinetics. <i>Physical Chemistry
    Chemical Physics</i>. 2018;20(45):28732-28740. doi:<a href="https://doi.org/10.1039/c8cp04561e">10.1039/c8cp04561e</a>'
  apa: 'Cheng, B., Dellago, C., &#38; Ceriotti, M. (2018). Theoretical prediction
    of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics.
    <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href="https://doi.org/10.1039/c8cp04561e">https://doi.org/10.1039/c8cp04561e</a>'
  chicago: 'Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical
    Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics
    and Kinetics.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry,
    2018. <a href="https://doi.org/10.1039/c8cp04561e">https://doi.org/10.1039/c8cp04561e</a>.'
  ieee: 'B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous
    ice nucleation rate: Disentangling thermodynamics and kinetics,” <i>Physical Chemistry
    Chemical Physics</i>, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740,
    2018.'
  ista: 'Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous
    ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
    Chemical Physics. 20(45), 28732–28740.'
  mla: 'Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation
    Rate: Disentangling Thermodynamics and Kinetics.” <i>Physical Chemistry Chemical
    Physics</i>, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40,
    doi:<a href="https://doi.org/10.1039/c8cp04561e">10.1039/c8cp04561e</a>.'
  short: B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20
    (2018) 28732–28740.
date_created: 2021-07-15T12:51:44Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2021-08-09T12:36:47Z
day: '07'
doi: 10.1039/c8cp04561e
extern: '1'
external_id:
  arxiv:
  - '1807.05551'
  pmid:
  - '30412211'
intvolume: '        20'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1807.05551
month: '12'
oa: 1
oa_version: Preprint
page: 28732-28740
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
  eissn:
  - 1463-9084
  issn:
  - 1463-9076
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theoretical prediction of the homogeneous ice nucleation rate: Disentangling
  thermodynamics and kinetics'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 20
year: '2018'
...
---
_id: '9687'
abstract:
- lang: eng
  text: The Gibbs free energy is the fundamental thermodynamic potential underlying
    the relative stability of different states of matter under constant-pressure conditions.
    However, computing this quantity from atomic-scale simulations is far from trivial,
    so the potential energy of a system is often used as a proxy. In this paper, we
    use a combination of thermodynamic integration methods to accurately evaluate
    the Gibbs free energies associated with defects in crystals, including the vacancy
    formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron,
    and cobalt. We quantify the importance of entropic and anharmonic effects in determining
    the free energies of defects at high temperatures, and show that the potential
    energy approximation as well as the harmonic approximation may produce inaccurate
    or even qualitatively wrong results. Our calculations manifest the necessity to
    employ accurate free energy methods such as thermodynamic integration to estimate
    the stability of crystallographic defects at high temperatures.
article_number: '054102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: 'Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic
    simulations: Applications to defects in solids. <i>Physical Review B</i>. 2018;97(5).
    doi:<a href="https://doi.org/10.1103/physrevb.97.054102">10.1103/physrevb.97.054102</a>'
  apa: 'Cheng, B., &#38; Ceriotti, M. (2018). Computing the absolute Gibbs free energy
    in atomistic simulations: Applications to defects in solids. <i>Physical Review
    B</i>. American Physical Society. <a href="https://doi.org/10.1103/physrevb.97.054102">https://doi.org/10.1103/physrevb.97.054102</a>'
  chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
    Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical
    Review B</i>. American Physical Society, 2018. <a href="https://doi.org/10.1103/physrevb.97.054102">https://doi.org/10.1103/physrevb.97.054102</a>.'
  ieee: 'B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic
    simulations: Applications to defects in solids,” <i>Physical Review B</i>, vol.
    97, no. 5. American Physical Society, 2018.'
  ista: 'Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic
    simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.'
  mla: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
    Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical
    Review B</i>, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:<a
    href="https://doi.org/10.1103/physrevb.97.054102">10.1103/physrevb.97.054102</a>.'
  short: B. Cheng, M. Ceriotti, Physical Review B 97 (2018).
date_created: 2021-07-19T09:39:48Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2021-08-09T12:38:26Z
day: '01'
doi: 10.1103/physrevb.97.054102
extern: '1'
external_id:
  arxiv:
  - '1710.02815'
intvolume: '        97'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1710.02815
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
  eissn:
  - 2469-9969
  issn:
  - 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Computing the absolute Gibbs free energy in atomistic simulations: Applications
  to defects in solids'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 97
year: '2018'
...
---
_id: '9807'
abstract:
- lang: eng
  text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
    up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).
article_processing_charge: No
author:
- first_name: Juan
  full_name: Higareda Almaraz, Juan
  last_name: Higareda Almaraz
- first_name: Michael
  full_name: Karbiener, Michael
  last_name: Karbiener
- first_name: Maude
  full_name: Giroud, Maude
  last_name: Giroud
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
  orcid: 0000-0002-7462-0048
- first_name: Teresa
  full_name: Gerhalter, Teresa
  last_name: Gerhalter
- first_name: Stephan
  full_name: Herzig, Stephan
  last_name: Herzig
- first_name: Marcel
  full_name: Scheideler, Marcel
  last_name: Scheideler
citation:
  ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes. 2018. doi:<a href="https://doi.org/10.6084/m9.figshare.7295339.v1">10.6084/m9.figshare.7295339.v1</a>'
  apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
    Herzig, S., &#38; Scheideler, M. (2018). Additional file 1: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.7295339.v1">https://doi.org/10.6084/m9.figshare.7295339.v1</a>'
  chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
    Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
    Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
    Human White Adipocytes.” Springer Nature, 2018. <a href="https://doi.org/10.6084/m9.figshare.7295339.v1">https://doi.org/10.6084/m9.figshare.7295339.v1</a>.'
  ieee: 'J. Higareda Almaraz <i>et al.</i>, “Additional file 1: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes.” Springer Nature, 2018.'
  ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
    S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early
    regulatory network response in primary human white adipocytes, Springer Nature,
    <a href="https://doi.org/10.6084/m9.figshare.7295339.v1">10.6084/m9.figshare.7295339.v1</a>.'
  mla: 'Higareda Almaraz, Juan, et al. <i>Additional File 1: Of Norepinephrine Triggers
    an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>.
    Springer Nature, 2018, doi:<a href="https://doi.org/10.6084/m9.figshare.7295339.v1">10.6084/m9.figshare.7295339.v1</a>.'
  short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
    Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:26:53Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295339.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.7295339.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '20'
    relation: used_in_publication
    status: public
status: public
title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory
  network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9808'
abstract:
- lang: eng
  text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
article_processing_charge: No
author:
- first_name: Juan
  full_name: Higareda Almaraz, Juan
  last_name: Higareda Almaraz
- first_name: Michael
  full_name: Karbiener, Michael
  last_name: Karbiener
- first_name: Maude
  full_name: Giroud, Maude
  last_name: Giroud
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
  orcid: 0000-0002-7462-0048
- first_name: Teresa
  full_name: Gerhalter, Teresa
  last_name: Gerhalter
- first_name: Stephan
  full_name: Herzig, Stephan
  last_name: Herzig
- first_name: Marcel
  full_name: Scheideler, Marcel
  last_name: Scheideler
citation:
  ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes. 2018. doi:<a href="https://doi.org/10.6084/m9.figshare.7295369.v1">10.6084/m9.figshare.7295369.v1</a>'
  apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
    Herzig, S., &#38; Scheideler, M. (2018). Additional file 3: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.7295369.v1">https://doi.org/10.6084/m9.figshare.7295369.v1</a>'
  chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
    Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
    Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
    Human White Adipocytes.” Springer Nature, 2018. <a href="https://doi.org/10.6084/m9.figshare.7295369.v1">https://doi.org/10.6084/m9.figshare.7295369.v1</a>.'
  ieee: 'J. Higareda Almaraz <i>et al.</i>, “Additional file 3: Of Norepinephrine
    triggers an immediate-early regulatory network response in primary human white
    adipocytes.” Springer Nature, 2018.'
  ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
    S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early
    regulatory network response in primary human white adipocytes, Springer Nature,
    <a href="https://doi.org/10.6084/m9.figshare.7295369.v1">10.6084/m9.figshare.7295369.v1</a>.'
  mla: 'Higareda Almaraz, Juan, et al. <i>Additional File 3: Of Norepinephrine Triggers
    an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>.
    Springer Nature, 2018, doi:<a href="https://doi.org/10.6084/m9.figshare.7295369.v1">10.6084/m9.figshare.7295369.v1</a>.'
  short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
    Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:31:57Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295369.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.7295369.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '20'
    relation: used_in_publication
    status: public
status: public
title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory
  network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9810'
article_processing_charge: No
author:
- first_name: Waqas
  full_name: Chaudhry, Waqas
  last_name: Chaudhry
- first_name: Maros
  full_name: Pleska, Maros
  id: 4569785E-F248-11E8-B48F-1D18A9856A87
  last_name: Pleska
  orcid: 0000-0001-7460-7479
- first_name: Nilang
  full_name: Shah, Nilang
  last_name: Shah
- first_name: Howard
  full_name: Weiss, Howard
  last_name: Weiss
- first_name: Ingrid
  full_name: Mccall, Ingrid
  last_name: Mccall
- first_name: Justin
  full_name: Meyer, Justin
  last_name: Meyer
- first_name: Animesh
  full_name: Gupta, Animesh
  last_name: Gupta
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Bruce
  full_name: Levin, Bruce
  last_name: Levin
citation:
  ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018.
    doi:<a href="https://doi.org/10.1371/journal.pbio.2005971.s008">10.1371/journal.pbio.2005971.s008</a>
  apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
    B. (2018). Numerical data used in figures. Public Library of Science. <a href="https://doi.org/10.1371/journal.pbio.2005971.s008">https://doi.org/10.1371/journal.pbio.2005971.s008</a>
  chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
    Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used
    in Figures.” Public Library of Science, 2018. <a href="https://doi.org/10.1371/journal.pbio.2005971.s008">https://doi.org/10.1371/journal.pbio.2005971.s008</a>.
  ieee: W. Chaudhry <i>et al.</i>, “Numerical data used in figures.” Public Library
    of Science, 2018.
  ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
    Levin B. 2018. Numerical data used in figures, Public Library of Science, <a href="https://doi.org/10.1371/journal.pbio.2005971.s008">10.1371/journal.pbio.2005971.s008</a>.
  mla: Chaudhry, Waqas, et al. <i>Numerical Data Used in Figures</i>. Public Library
    of Science, 2018, doi:<a href="https://doi.org/10.1371/journal.pbio.2005971.s008">10.1371/journal.pbio.2005971.s008</a>.
  short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
    C.C. Guet, B. Levin, (2018).
date_created: 2021-08-06T12:43:44Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971.s008
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '82'
    relation: used_in_publication
    status: public
status: public
title: Numerical data used in figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9811'
abstract:
- lang: eng
  text: This document contains additional supporting evidence presented as supplemental
    tables. (XLSX 50Â kb)
article_processing_charge: No
author:
- first_name: Luis
  full_name: Zapata, Luis
  last_name: Zapata
- first_name: Oriol
  full_name: Pich, Oriol
  last_name: Pich
- first_name: Luis
  full_name: Serrano, Luis
  last_name: Serrano
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Stephan
  full_name: Ossowski, Stephan
  last_name: Ossowski
- first_name: Martin
  full_name: Schaefer, Martin
  last_name: Schaefer
citation:
  ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
    file 1: Of negative selection in tumor genome evolution acts on essential cellular
    functions and the immunopeptidome. 2018. doi:<a href="https://doi.org/10.6084/m9.figshare.6401390.v1">10.6084/m9.figshare.6401390.v1</a>'
  apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer,
    M. (2018). Additional file 1: Of negative selection in tumor genome evolution
    acts on essential cellular functions and the immunopeptidome. Springer Nature.
    <a href="https://doi.org/10.6084/m9.figshare.6401390.v1">https://doi.org/10.6084/m9.figshare.6401390.v1</a>'
  chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
    and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
    Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
    Nature, 2018. <a href="https://doi.org/10.6084/m9.figshare.6401390.v1">https://doi.org/10.6084/m9.figshare.6401390.v1</a>.'
  ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
    “Additional file 1: Of negative selection in tumor genome evolution acts on essential
    cellular functions and the immunopeptidome.” Springer Nature, 2018.'
  ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
    Additional file 1: Of negative selection in tumor genome evolution acts on essential
    cellular functions and the immunopeptidome, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.6401390.v1">10.6084/m9.figshare.6401390.v1</a>.'
  mla: 'Zapata, Luis, et al. <i>Additional File 1: Of Negative Selection in Tumor
    Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>.
    Springer Nature, 2018, doi:<a href="https://doi.org/10.6084/m9.figshare.6401390.v1">10.6084/m9.figshare.6401390.v1</a>.'
  short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
    (2018).
date_created: 2021-08-06T12:53:49Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2025-04-15T08:30:30Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401390.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.6401390.v1
month: '05'
oa: 1
oa_version: Preprint
publisher: Springer Nature
related_material:
  record:
  - id: '279'
    relation: used_in_publication
    status: public
status: public
title: 'Additional file 1: Of negative selection in tumor genome evolution acts on
  essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9812'
abstract:
- lang: eng
  text: This document contains the full list of genes with their respective significance
    and dN/dS values. (TXT 4499Â kb)
article_processing_charge: No
author:
- first_name: Luis
  full_name: Zapata, Luis
  last_name: Zapata
- first_name: Oriol
  full_name: Pich, Oriol
  last_name: Pich
- first_name: Luis
  full_name: Serrano, Luis
  last_name: Serrano
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Stephan
  full_name: Ossowski, Stephan
  last_name: Ossowski
- first_name: Martin
  full_name: Schaefer, Martin
  last_name: Schaefer
citation:
  ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
    file 2: Of negative selection in tumor genome evolution acts on essential cellular
    functions and the immunopeptidome. 2018. doi:<a href="https://doi.org/10.6084/m9.figshare.6401414.v1">10.6084/m9.figshare.6401414.v1</a>'
  apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer,
    M. (2018). Additional file 2: Of negative selection in tumor genome evolution
    acts on essential cellular functions and the immunopeptidome. Springer Nature.
    <a href="https://doi.org/10.6084/m9.figshare.6401414.v1">https://doi.org/10.6084/m9.figshare.6401414.v1</a>'
  chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
    and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
    Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
    Nature, 2018. <a href="https://doi.org/10.6084/m9.figshare.6401414.v1">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.'
  ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
    “Additional file 2: Of negative selection in tumor genome evolution acts on essential
    cellular functions and the immunopeptidome.” Springer Nature, 2018.'
  ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
    Additional file 2: Of negative selection in tumor genome evolution acts on essential
    cellular functions and the immunopeptidome, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.6401414.v1">10.6084/m9.figshare.6401414.v1</a>.'
  mla: 'Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor
    Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>.
    Springer Nature, 2018, doi:<a href="https://doi.org/10.6084/m9.figshare.6401414.v1">10.6084/m9.figshare.6401414.v1</a>.'
  short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
    (2018).
date_created: 2021-08-06T12:58:25Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2025-04-15T08:30:30Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401414.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.6401414.v1
month: '05'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '279'
    relation: used_in_publication
    status: public
status: public
title: 'Additional file 2: Of negative selection in tumor genome evolution acts on
  essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
  text: 'File S1 contains figures that clarify the following features: (i) effect
    of population size on the average number/frequency of SI classes, (ii) changes
    in the minimal completeness deficit in time for a single class, and (iii) diversification
    diagrams for all studied pathways, including the summary figure for k = 8. File
    S2 contains the code required for a stochastic simulation of the SLF system with
    an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
  full_name: Bod'ová, Katarína
  id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
  last_name: Bod'ová
  orcid: 0000-0002-7214-0171
- first_name: Tadeas
  full_name: Priklopil, Tadeas
  id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
  last_name: Priklopil
- first_name: David
  full_name: Field, David
  id: 419049E2-F248-11E8-B48F-1D18A9856A87
  last_name: Field
  orcid: 0000-0002-4014-8478
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Melinda
  full_name: Pickup, Melinda
  id: 2C78037E-F248-11E8-B48F-1D18A9856A87
  last_name: Pickup
  orcid: 0000-0001-6118-0541
citation:
  ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
    for Bodova et al., 2018. 2018. doi:<a href="https://doi.org/10.25386/genetics.6148304.v1">10.25386/genetics.6148304.v1</a>
  apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018).
    Supplemental material for Bodova et al., 2018. Genetics Society of America. <a
    href="https://doi.org/10.25386/genetics.6148304.v1">https://doi.org/10.25386/genetics.6148304.v1</a>
  chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
    Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
    of America, 2018. <a href="https://doi.org/10.25386/genetics.6148304.v1">https://doi.org/10.25386/genetics.6148304.v1</a>.
  ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
    material for Bodova et al., 2018.” Genetics Society of America, 2018.
  ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
    for Bodova et al., 2018, Genetics Society of America, <a href="https://doi.org/10.25386/genetics.6148304.v1">10.25386/genetics.6148304.v1</a>.
  mla: Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>.
    Genetics Society of America, 2018, doi:<a href="https://doi.org/10.25386/genetics.6148304.v1">10.25386/genetics.6148304.v1</a>.
  short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2025-04-15T07:17:08Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
  record:
  - id: '316'
    relation: used_in_publication
    status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
  text: 'Implementation of the inference method in Matlab, including three applications
    of the method: The first one for the model of ant motion, the second one for bacterial
    chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
  full_name: Bod’Ová, Katarína
  last_name: Bod’Ová
- first_name: Gabriel
  full_name: Mitchell, Gabriel
  id: 315BCD80-F248-11E8-B48F-1D18A9856A87
  last_name: Mitchell
- first_name: Roy
  full_name: Harpaz, Roy
  last_name: Harpaz
- first_name: Elad
  full_name: Schneidman, Elad
  last_name: Schneidman
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
    the inference method in Matlab. 2018. doi:<a href="https://doi.org/10.1371/journal.pone.0193049.s001">10.1371/journal.pone.0193049.s001</a>
  apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018).
    Implementation of the inference method in Matlab. Public Library of Science. <a
    href="https://doi.org/10.1371/journal.pone.0193049.s001">https://doi.org/10.1371/journal.pone.0193049.s001</a>
  chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
    Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
    Science, 2018. <a href="https://doi.org/10.1371/journal.pone.0193049.s001">https://doi.org/10.1371/journal.pone.0193049.s001</a>.
  ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
    of the inference method in Matlab.” Public Library of Science, 2018.
  ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
    of the inference method in Matlab, Public Library of Science, <a href="https://doi.org/10.1371/journal.pone.0193049.s001">10.1371/journal.pone.0193049.s001</a>.
  mla: Bod’Ová, Katarína, et al. <i>Implementation of the Inference Method in Matlab</i>.
    Public Library of Science, 2018, doi:<a href="https://doi.org/10.1371/journal.pone.0193049.s001">10.1371/journal.pone.0193049.s001</a>.
  short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '406'
    relation: used_in_publication
    status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
  text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
    are important in adaptation and speciation. However, biases in discovery and reporting
    of inversions make it difficult to assess their prevalence and biological importance.
    Here, we use an approach based on linkage disequilibrium among markers genotyped
    for samples collected across a transect between contrasting habitats to detect
    chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
    a single locality for the coastal marine snail, Littorina saxatilis. Patterns
    of diversity in the field and of recombination in controlled crosses provide strong
    evidence that at least the majority of these rearrangements are inversions. Most
    show clinal changes in frequency between habitats, suggestive of divergent selection,
    but only one appears to be fixed for different arrangements in the two habitats.
    Consistent with widespread evidence for balancing selection on inversion polymorphisms,
    we argue that a combination of heterosis and divergent selection can explain the
    observed patterns and should be considered in other systems spanning environmental
    gradients.
article_processing_charge: No
author:
- first_name: Rui
  full_name: Faria, Rui
  last_name: Faria
- first_name: Pragya
  full_name: Chaube, Pragya
  last_name: Chaube
- first_name: Hernán E.
  full_name: Morales, Hernán E.
  last_name: Morales
- first_name: Tomas
  full_name: Larsson, Tomas
  last_name: Larsson
- first_name: Alan R.
  full_name: Lemmon, Alan R.
  last_name: Lemmon
- first_name: Emily M.
  full_name: Lemmon, Emily M.
  last_name: Lemmon
- first_name: Marina
  full_name: Rafajlović, Marina
  last_name: Rafajlović
- first_name: Marina
  full_name: Panova, Marina
  last_name: Panova
- first_name: Mark
  full_name: Ravinet, Mark
  last_name: Ravinet
- first_name: Kerstin
  full_name: Johannesson, Kerstin
  last_name: Johannesson
- first_name: Anja M
  full_name: Westram, Anja M
  id: 3C147470-F248-11E8-B48F-1D18A9856A87
  last_name: Westram
  orcid: 0000-0003-1050-4969
- first_name: Roger K.
  full_name: Butlin, Roger K.
  last_name: Butlin
citation:
  ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
    in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href="https://doi.org/10.5061/dryad.72cg113">10.5061/dryad.72cg113</a>'
  apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
    E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
    in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href="https://doi.org/10.5061/dryad.72cg113">https://doi.org/10.5061/dryad.72cg113</a>'
  chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
    Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
    in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href="https://doi.org/10.5061/dryad.72cg113">https://doi.org/10.5061/dryad.72cg113</a>.'
  ieee: 'R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in
    a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
  ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
    M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
    Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
    ecotypes, Dryad, <a href="https://doi.org/10.5061/dryad.72cg113">10.5061/dryad.72cg113</a>.'
  mla: 'Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a
    Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href="https://doi.org/10.5061/dryad.72cg113">10.5061/dryad.72cg113</a>.'
  short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
    M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
    (2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
  record:
  - id: '6095'
    relation: used_in_publication
    status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
  saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
  text: 'Facial shape is the basis for facial recognition and categorization. Facial
    features reflect the underlying geometry of the skeletal structures. Here we reveal
    that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
    by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
    Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
    capsule, whereas the formation of a capsule roof is controlled by signals from
    the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
    out to be important for shaping membranous facial bones during development. This
    suggests that conserved neurosensory structures could benefit from protection
    and have evolved signals inducing cranial cartilages encasing them. Experiments
    with mutant mice revealed that the genomic regulatory regions controlling production
    of SHH in the nervous system contribute to facial cartilage morphogenesis, which
    might be a mechanism responsible for the adaptive evolution of animal faces and
    snouts.'
article_processing_charge: No
author:
- first_name: Marketa
  full_name: Kaucka, Marketa
  last_name: Kaucka
- first_name: Julian
  full_name: Petersen, Julian
  last_name: Petersen
- first_name: Marketa
  full_name: Tesarova, Marketa
  last_name: Tesarova
- first_name: Bara
  full_name: Szarowska, Bara
  last_name: Szarowska
- first_name: Maria Eleni
  full_name: Kastriti, Maria Eleni
  last_name: Kastriti
- first_name: Meng
  full_name: Xie, Meng
  last_name: Xie
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
- first_name: Karl
  full_name: Annusver, Karl
  last_name: Annusver
- first_name: Maria
  full_name: Kasper, Maria
  last_name: Kasper
- first_name: Orsolya
  full_name: Symmons, Orsolya
  last_name: Symmons
- first_name: Leslie
  full_name: Pan, Leslie
  last_name: Pan
- first_name: Francois
  full_name: Spitz, Francois
  last_name: Spitz
- first_name: Jozef
  full_name: Kaiser, Jozef
  last_name: Kaiser
- first_name: Maria
  full_name: Hovorakova, Maria
  last_name: Hovorakova
- first_name: Tomas
  full_name: Zikmund, Tomas
  last_name: Zikmund
- first_name: Kazunori
  full_name: Sunadome, Kazunori
  last_name: Sunadome
- first_name: Michael P
  full_name: Matise, Michael P
  last_name: Matise
- first_name: Hui
  full_name: Wang, Hui
  last_name: Wang
- first_name: Ulrika
  full_name: Marklund, Ulrika
  last_name: Marklund
- first_name: Hind
  full_name: Abdo, Hind
  last_name: Abdo
- first_name: Patrik
  full_name: Ernfors, Patrik
  last_name: Ernfors
- first_name: Pascal
  full_name: Maire, Pascal
  last_name: Maire
- first_name: Maud
  full_name: Wurmser, Maud
  last_name: Wurmser
- first_name: Andrei S
  full_name: Chagin, Andrei S
  last_name: Chagin
- first_name: Kaj
  full_name: Fried, Kaj
  last_name: Fried
- first_name: Igor
  full_name: Adameyko, Igor
  last_name: Adameyko
citation:
  ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
    and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
    2018. doi:<a href="https://doi.org/10.5061/dryad.f1s76f2">10.5061/dryad.f1s76f2</a>'
  apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
    M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
    control shaping of the mammalian nasal capsule cartilage. Dryad. <a href="https://doi.org/10.5061/dryad.f1s76f2">https://doi.org/10.5061/dryad.f1s76f2</a>'
  chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
    Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
    and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
    Dryad, 2018. <a href="https://doi.org/10.5061/dryad.f1s76f2">https://doi.org/10.5061/dryad.f1s76f2</a>.'
  ieee: 'M. Kaucka <i>et al.</i>, “Data from: Signals from the brain and olfactory
    epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
  ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
    A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
    T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
    M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
    olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
    Dryad, <a href="https://doi.org/10.5061/dryad.f1s76f2">10.5061/dryad.f1s76f2</a>.'
  mla: 'Kaucka, Marketa, et al. <i>Data from: Signals from the Brain and Olfactory
    Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage</i>. Dryad,
    2018, doi:<a href="https://doi.org/10.5061/dryad.f1s76f2">10.5061/dryad.f1s76f2</a>.'
  short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
    A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
    Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
    P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-04-14T13:02:22Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
  record:
  - id: '162'
    relation: used_in_publication
    status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
  of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
  text: Herd immunity, a process in which resistant individuals limit the spread of
    a pathogen among susceptible hosts has been extensively studied in eukaryotes.
    Even though bacteria have evolved multiple immune systems against their phage
    pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
    demonstrate that herd immunity arises during phage epidemics in structured and
    unstructured Escherichia coli populations consisting of differing frequencies
    of susceptible and resistant cells harboring CRISPR immunity. In addition, we
    develop a mathematical model that quantifies how herd immunity is affected by
    spatial population structure, bacterial growth rate, and phage replication rate.
    Using our model we infer a general epidemiological rule describing the relative
    speed of an epidemic in partially resistant spatially structured populations.
    Our experimental and theoretical findings indicate that herd immunity may be important
    in bacterial communities, allowing for stable coexistence of bacteria and their
    phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
  full_name: Payne, Pavel
  id: 35F78294-F248-11E8-B48F-1D18A9856A87
  last_name: Payne
  orcid: 0000-0002-2711-9453
- first_name: Lukas
  full_name: Geyrhofer, Lukas
  last_name: Geyrhofer
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Jonathan P
  full_name: Bollback, Jonathan P
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
citation:
  ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
    immunity limits phage epidemics in bacterial populations. 2018. doi:<a href="https://doi.org/10.5061/dryad.42n44">10.5061/dryad.42n44</a>'
  apa: 'Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data
    from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
    Dryad. <a href="https://doi.org/10.5061/dryad.42n44">https://doi.org/10.5061/dryad.42n44</a>'
  chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
    “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
    Dryad, 2018. <a href="https://doi.org/10.5061/dryad.42n44">https://doi.org/10.5061/dryad.42n44</a>.'
  ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
    herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
  ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
    herd immunity limits phage epidemics in bacterial populations, Dryad, <a href="https://doi.org/10.5061/dryad.42n44">10.5061/dryad.42n44</a>.'
  mla: 'Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage
    Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href="https://doi.org/10.5061/dryad.42n44">10.5061/dryad.42n44</a>.'
  short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2025-04-15T08:17:50Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
  record:
  - id: '423'
    relation: used_in_publication
    status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
  populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9841'
abstract:
- lang: eng
  text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
    50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
    Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
    and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
    signatures of termite eusociality by comparing the genomes and transcriptomes
    of three termites and the cockroach against the background of 16 other eusocial
    and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
    and perception of pheromones confirm the importance of chemical communication
    in the termites. These are accompanied by major changes in gene regulation and
    the molecular evolution of caste determination. Many of these results parallel
    molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
    solutions are remarkably different, thus revealing a striking case of convergence
    in one of the major evolutionary transitions in biological complexity.
article_processing_charge: No
author:
- first_name: Mark C.
  full_name: Harrison, Mark C.
  last_name: Harrison
- first_name: Evelien
  full_name: Jongepier, Evelien
  last_name: Jongepier
- first_name: Hugh M.
  full_name: Robertson, Hugh M.
  last_name: Robertson
- first_name: Nicolas
  full_name: Arning, Nicolas
  last_name: Arning
- first_name: Tristan
  full_name: Bitard-Feildel, Tristan
  last_name: Bitard-Feildel
- first_name: Hsu
  full_name: Chao, Hsu
  last_name: Chao
- first_name: Christopher P.
  full_name: Childers, Christopher P.
  last_name: Childers
- first_name: Huyen
  full_name: Dinh, Huyen
  last_name: Dinh
- first_name: Harshavardhan
  full_name: Doddapaneni, Harshavardhan
  last_name: Doddapaneni
- first_name: Shannon
  full_name: Dugan, Shannon
  last_name: Dugan
- first_name: Johannes
  full_name: Gowin, Johannes
  last_name: Gowin
- first_name: Carolin
  full_name: Greiner, Carolin
  last_name: Greiner
- first_name: Yi
  full_name: Han, Yi
  last_name: Han
- first_name: Haofu
  full_name: Hu, Haofu
  last_name: Hu
- first_name: Daniel S. T.
  full_name: Hughes, Daniel S. T.
  last_name: Hughes
- first_name: Ann K
  full_name: Huylmans, Ann K
  id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
  last_name: Huylmans
  orcid: 0000-0001-8871-4961
- first_name: Carsten
  full_name: Kemena, Carsten
  last_name: Kemena
- first_name: Lukas P. M.
  full_name: Kremer, Lukas P. M.
  last_name: Kremer
- first_name: Sandra L.
  full_name: Lee, Sandra L.
  last_name: Lee
- first_name: Alberto
  full_name: Lopez-Ezquerra, Alberto
  last_name: Lopez-Ezquerra
- first_name: Ludovic
  full_name: Mallet, Ludovic
  last_name: Mallet
- first_name: Jose M.
  full_name: Monroy-Kuhn, Jose M.
  last_name: Monroy-Kuhn
- first_name: Annabell
  full_name: Moser, Annabell
  last_name: Moser
- first_name: Shwetha C.
  full_name: Murali, Shwetha C.
  last_name: Murali
- first_name: Donna M.
  full_name: Muzny, Donna M.
  last_name: Muzny
- first_name: Saria
  full_name: Otani, Saria
  last_name: Otani
- first_name: Maria-Dolors
  full_name: Piulachs, Maria-Dolors
  last_name: Piulachs
- first_name: Monica
  full_name: Poelchau, Monica
  last_name: Poelchau
- first_name: Jiaxin
  full_name: Qu, Jiaxin
  last_name: Qu
- first_name: Florentine
  full_name: Schaub, Florentine
  last_name: Schaub
- first_name: Ayako
  full_name: Wada-Katsumata, Ayako
  last_name: Wada-Katsumata
- first_name: Kim C.
  full_name: Worley, Kim C.
  last_name: Worley
- first_name: Qiaolin
  full_name: Xie, Qiaolin
  last_name: Xie
- first_name: Guillem
  full_name: Ylla, Guillem
  last_name: Ylla
- first_name: Michael
  full_name: Poulsen, Michael
  last_name: Poulsen
- first_name: Richard A.
  full_name: Gibbs, Richard A.
  last_name: Gibbs
- first_name: Coby
  full_name: Schal, Coby
  last_name: Schal
- first_name: Stephen
  full_name: Richards, Stephen
  last_name: Richards
- first_name: Xavier
  full_name: Belles, Xavier
  last_name: Belles
- first_name: Judith
  full_name: Korb, Judith
  last_name: Korb
- first_name: Erich
  full_name: Bornberg-Bauer, Erich
  last_name: Bornberg-Bauer
citation:
  ama: 'Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes
    reveal molecular basis of termite eusociality. 2018. doi:<a href="https://doi.org/10.5061/dryad.51d4r">10.5061/dryad.51d4r</a>'
  apa: 'Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel,
    T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal
    molecular basis of termite eusociality. Dryad. <a href="https://doi.org/10.5061/dryad.51d4r">https://doi.org/10.5061/dryad.51d4r</a>'
  chicago: 'Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning,
    Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from:
    Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad,
    2018. <a href="https://doi.org/10.5061/dryad.51d4r">https://doi.org/10.5061/dryad.51d4r</a>.'
  ieee: 'M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular
    basis of termite eusociality.” Dryad, 2018.'
  ista: 'Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao
    H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu
    H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet
    L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau
    M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs
    RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from:
    Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a
    href="https://doi.org/10.5061/dryad.51d4r">10.5061/dryad.51d4r</a>.'
  mla: 'Harrison, Mark C., et al. <i>Data from: Hemimetabolous Genomes Reveal Molecular
    Basis of Termite Eusociality</i>. Dryad, 2018, doi:<a href="https://doi.org/10.5061/dryad.51d4r">10.5061/dryad.51d4r</a>.'
  short: M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel,
    H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner,
    Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee,
    A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny,
    S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C.
    Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles,
    J. Korb, E. Bornberg-Bauer, (2018).
date_created: 2021-08-09T13:13:48Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-11T14:10:56Z
day: '12'
department:
- _id: BeVi
doi: 10.5061/dryad.51d4r
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5061/dryad.51d4r
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
  record:
  - id: '448'
    relation: used_in_publication
    status: public
status: public
title: 'Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '6459'
article_processing_charge: No
author:
- first_name: Barbara
  full_name: Petritsch, Barbara
  id: 406048EC-F248-11E8-B48F-1D18A9856A87
  last_name: Petritsch
  orcid: 0000-0003-2724-4614
citation:
  ama: Petritsch B. <i>Open Access at IST Austria 2009-2017</i>. IST Austria; 2018.
    doi:<a href="https://doi.org/10.5281/zenodo.1410279">10.5281/zenodo.1410279</a>
  apa: 'Petritsch, B. (2018). <i>Open Access at IST Austria 2009-2017</i>. Presented
    at the OAT: Open Access Tage, Graz, Austria: IST Austria. <a href="https://doi.org/10.5281/zenodo.1410279">https://doi.org/10.5281/zenodo.1410279</a>'
  chicago: Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria,
    2018. <a href="https://doi.org/10.5281/zenodo.1410279">https://doi.org/10.5281/zenodo.1410279</a>.
  ieee: B. Petritsch, <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018.
  ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.
  mla: Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria,
    2018, doi:<a href="https://doi.org/10.5281/zenodo.1410279">10.5281/zenodo.1410279</a>.
  short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.
conference:
  end_date: 2018-09-26
  location: Graz, Austria
  name: 'OAT: Open Access Tage'
  start_date: 2018-09-24
date_created: 2019-05-16T07:27:14Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2026-03-31T12:35:03Z
day: '24'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.1410279
file:
- access_level: open_access
  checksum: 9063ab4d10ea93353c3a03bbf53fbcf1
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-16T07:26:25Z
  date_updated: 2020-07-14T12:47:30Z
  file_id: '6460'
  file_name: Poster_Beitrag_125_Petritsch.pdf
  file_size: 1967778
  relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
keyword:
- Open Access
- Publication Analysis
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
status: public
title: Open Access at IST Austria 2009-2017
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
