Volume 14; Issue 4

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PLoS Computational Biology
Volume 14; Issue 4

PLoS Computational Biology

Volume 14; Issue 4

1

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

Mitra, Sneha, Biswas, Anushua, Narlikar, Leelavati, Marz, Manja

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 16.32 MB

english, 2018

2

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

Zhang, Huanan, Lee, Catherine A. A., Li, Zhuliu, Garbe, John R., Eide, Cindy R., Petegrosso, Raphael, Kuang, Rui, Tolar, Jakub, Khan, Aly

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 16.01 MB

english, 2018

3

Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer

Irurzun-Arana, Itziar, Janda, Alvaro, Ardanza-Trevijano, Sergio, Trocóniz, Iñaki F., Gallo, James

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.22 MB

english, 2018

4

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Hannigan, Geoffrey D., Duhaime, Melissa B., Koutra, Danai, Schloss, Patrick D., Segata, Nicola

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.78 MB

english, 2018

5

Correcting for batch effects in case-control microbiome studies

Gibbons, Sean M., Duvallet, Claire, Alm, Eric J., Langille, Morgan

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 25.56 MB

english, 2018

6

A computational model of shared fine-scale structure in the human connectome

Guntupalli, J. Swaroop, Feilong, Ma, Haxby, James V., Yarkoni, Tal

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.58 MB

english, 2018

7

Automated plant species identification—Trends and future directions

Wäldchen, Jana, Rzanny, Michael, Seeland, Marco, Mäder, Patrick, Bucksch, Alexander

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.01 MB

english, 2018

8

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

Adolf-Bryfogle, Jared, Kalyuzhniy, Oleks, Kubitz, Michael, Weitzner, Brian D., Hu, Xiaozhen, Adachi, Yumiko, Schief, William R., Dunbrack, Roland L., Ben-Tal, Nir

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.59 MB

english, 2018

9

A modelling approach for exploring muscle dynamics during cyclic contractions

Ross, Stephanie A., Nigam, Nilima, Wakeling, James M., Marsden, Alison L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.79 MB

english, 2018

10

Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey

Mills, Robin, Hildenbrandt, Hanno, Taylor, Graham K., Hemelrijk, Charlotte K., Ayers, Joseph

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.59 MB

english, 2018

11

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin

Westerlund, Annie M., Delemotte, Lucie, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.53 MB

english, 2018

12

Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition

Byrne, Catherine M., Gantt, Soren, Coombs, Daniel, Regoes, Roland R

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.59 MB

english, 2018

13

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Zarai, Yoram, Tuller, Tamir, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.76 MB

english, 2018

14

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Kaiser, Florian, Bittrich, Sebastian, Salentin, Sebastian, Leberecht, Christoph, Haupt, V. Joachim, Krautwurst, Sarah, Schroeder, Michael, Labudde, Dirk, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.13 MB

english, 2018

15

Ten quick tips for teaching programming

Brown, Neil C. C., Wilson, Greg, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.21 MB

english, 2018

16

A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability

Flanagan, Bronac, McDaid, Liam, Wade, John, Wong-Lin, KongFatt, Harkin, Jim, Gillespie, Dirk

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 17.63 MB

english, 2018

17

Propagating annotations of molecular networks using in silico fragmentation

da Silva, Ricardo R., Wang, Mingxun, Nothias, Louis-Félix, van der Hooft, Justin J. J., Caraballo-Rodríguez, Andrés Mauricio, Fox, Evan, Balunas, Marcy J., Klassen, Jonathan L., Lopes, Norberto Pepori

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 16.50 MB

english, 2018

18

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

Mykuliak, Vasyl V., Haining, Alexander William M., von Essen, Magdaléna, del Río Hernández, Armando, Hytönen, Vesa P., van der Spoel, David

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 9.87 MB

english, 2018

19

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning

Kim, Ji-Sung, Gao, Xin, Rzhetsky, Andrey, Vert, Jean-Philippe

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.59 MB

english, 2018

20

Computational mechanisms underlying cortical responses to the affordance properties of visual scenes

Bonner, Michael F., Epstein, Russell A., Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.60 MB

english, 2018

21

Toward a theory of coactivation patterns in excitable neural networks

Messé, Arnaud, Hütt, Marc-Thorsten, Hilgetag, Claus C., Marinazzo, Daniele

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.61 MB

english, 2018

22

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Rimbaud, Loup, Papaïx, Julien, Rey, Jean-François, Barrett, Luke G., Thrall, Peter H., Alizon, Samuel

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.36 MB

english, 2018

23

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

Weigert, Martin, Subramanian, Kaushikaram, Bundschuh, Sebastian T., Myers, Eugene W., Kreysing, Moritz, Jbabdi, Saad

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.90 MB

english, 2018

24

Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms

Martínez-García, Ricardo, Nadell, Carey D., Hartmann, Raimo, Drescher, Knut, Bonachela, Juan A., Igoshin, Oleg A

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.10 MB

english, 2018

25

Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease

Sarkar, Joydeep, Potdar, Alka A., Saidel, Gerald M., Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.95 MB

english, 2018

26

Eleven quick tips for finding research data

Gregory, Kathleen, Khalsa, Siri Jodha, Michener, William K., Psomopoulos, Fotis E., de Waard, Anita, Wu, Mingfang, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 932 KB

english, 2018

27

Black-boxing and cause-effect power

Marshall, William, Albantakis, Larissa, Tononi, Giulio, Schrater, Paul

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.25 MB

english, 2018

28

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data

Ching, Travers, Zhu, Xun, Garmire, Lana X., Markowetz, Florian

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.07 MB

english, 2018

29

Rational metareasoning and the plasticity of cognitive control

Lieder, Falk, Shenhav, Amitai, Musslick, Sebastian, Griffiths, Thomas L., Gershman, Samuel J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.73 MB

english, 2018

30

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level

Kardyńska, Małgorzata, Paszek, Anna, Śmieja, Jarosław, Spiller, David, Widłak, Wiesława, White, Michael R. H., Paszek, Pawel, Kimmel, Marek, Saucerman, Jeffrey J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.54 MB

english, 2018

31

Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse

Buckley, Reuben M., Kortschak, R. Daniel, Adelson, David L., Ma, Jian

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.18 MB

english, 2018

32

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations

Davidson, Russell B., Hendrix, Josie, Geiss, Brian J., McCullagh, Martin, Haliloglu, Turkan

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 17.22 MB

english, 2018

33

Need for speed: An optimized gridding approach for spatially explicit disease simulations

Sellman, Stefan, Tsao, Kimberly, Tildesley, Michael J., Brommesson, Peter, Webb, Colleen T., Wennergren, Uno, Keeling, Matt J., Lindström, Tom, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.37 MB

english, 2018

34

New computational approaches to understanding molecular protein function

Fetrow, Jacquelyn S., Babbitt, Patricia C.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.49 MB

english, 2018

35

Exploiting glycan topography for computational design of Env glycoprotein antigenicity

Yu, Wen-Han, Zhao, Peng, Draghi, Monia, Arevalo, Claudia, Karsten, Christina B., Suscovich, Todd J., Gunn, Bronwyn, Streeck, Hendrik, Brass, Abraham L., Tiemeyer, Michael, Seaman, Michael, Mascola, Jo

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.64 MB

english, 2018

36

Bayesian reconstruction of transmission within outbreaks using genomic variants

De Maio, Nicola, Worby, Colin J., Wilson, Daniel J., Stoesser, Nicole, Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.07 MB

english, 2018

37

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape

Pleydell, David R. J., Soubeyrand, Samuel, Dallot, Sylvie, Labonne, Gérard, Chadœuf, Joël, Jacquot, Emmanuel, Thébaud, Gaël, Alizon, Samuel

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.41 MB

english, 2018

38

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

Schott, Benjamin, Traub, Manuel, Schlagenhauf, Cornelia, Takamiya, Masanari, Antritter, Thomas, Bartschat, Andreas, Löffler, Katharina, Blessing, Denis, Otte, Jens C., Kobitski, Andrei Y., Nienhaus, G

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.60 MB

english, 2018

39

Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1

Fujita, Hironori, Kawaguchi, Masayoshi, Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.52 MB

english, 2018

40

Personalizing physical exercise in a computational model of fuel homeostasis

Palumbo, Maria Concetta, Morettini, Micaela, Tieri, Paolo, Diele, Fasma, Sacchetti, Massimo, Castiglione, Filippo, Komarova, Natalia L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.67 MB

english, 2018

41

Automated evaluation of quaternary structures from protein crystals

Bliven, Spencer, Lafita, Aleix, Parker, Althea, Capitani, Guido, Duarte, Jose M., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.54 MB

english, 2018

42

Compositional clustering in task structure learning

Franklin, Nicholas T., Frank, Michael J., Daunizeau, Jean

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.77 MB

english, 2018

43

Decision making improves sperm chemotaxis in the presence of noise

Kromer, Justus A., Märcker, Steffen, Lange, Steffen, Baier, Christel, Friedrich, Benjamin M., Olson, Sarah D

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.24 MB

english, 2018

44

Organization of the core respiratory network: Insights from optogenetic and modeling studies

Ausborn, Jessica, Koizumi, Hidehiko, Barnett, William H., John, Tibin T., Zhang, Ruli, Molkov, Yaroslav I., Smith, Jeffrey C., Rybak, Ilya A., Ayers, Joseph

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 22.75 MB

english, 2018

45

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

Ouma, Wilberforce Zachary, Pogacar, Katja, Grotewold, Erich, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.59 MB

english, 2018

46

Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly

Viso, Juan Francisco, Belelli, Patricia, Machado, Matías, González, Humberto, Pantano, Sergio, Amundarain, María Julia, Zamarreño, Fernando, Branda, Maria Marta, Guérin, Diego M. A., Costabel, Marcelo

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 23.15 MB

english, 2018

47

A probabilistic, distributed, recursive mechanism for decision-making in the brain

Caballero, Javier A., Humphries, Mark D., Gurney, Kevin N., Daunizeau, Jean

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.49 MB

english, 2018

48

Material and shape perception based on two types of intensity gradient information

Sawayama, Masataka, Nishida, Shin'ya, Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 18.95 MB

english, 2018

49

On the role of extrinsic noise in microRNA-mediated bimodal gene expression

Del Giudice, Marco, Bo, Stefano, Grigolon, Silvia, Bosia, Carla, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.59 MB

english, 2018

50

Interactions of spatial strategies producing generalization gradient and blocking: A computational approach

Dollé, Laurent, Chavarriaga, Ricardo, Guillot, Agnès, Khamassi, Mehdi, Bush, Daniel

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.27 MB

english, 2018

51

Principles that govern competition or co-existence in Rho-GTPase driven polarization

Chiou, Jian-Geng, Ramirez, Samuel A., Elston, Timothy C., Witelski, Thomas P., Schaeffer, David G., Lew, Daniel J., Nie, Qing

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.42 MB

english, 2018

52

Using pseudoalignment and base quality to accurately quantify microbial community composition

Reppell, Mark, Novembre, John, McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.70 MB

english, 2018

53

Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics

Flynn, Kevin J., Skibinski, David O. F., Lindemann, Christian, Komarova, Natalia L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.31 MB

english, 2018

54

Identifying robust hysteresis in networks

Gedeon, Tomáš, Cummins, Bree, Harker, Shaun, Mischaikow, Konstantin, You, Lingchong

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.17 MB

english, 2018

55

Switchable slow cellular conductances determine robustness and tunability of network states

Drion, Guillaume, Dethier, Julie, Franci, Alessio, Sepulchre, Rodolphe, Lytton, William W.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.53 MB

english, 2018

56

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction

Giese, Wolfgang, Milicic, Gregor, Schröder, Andreas, Klipp, Edda, Nielsen, Jens

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.17 MB

english, 2018

57

Origins of scale invariance in vocalization sequences and speech

Khatami, Fatemeh, Wöhr, Markus, Read, Heather L., Escabí, Monty A., Theunissen, Frédéric E.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.94 MB

english, 2018

58

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

Sherman, Thomas D., Kagohara, Luciane T., Cao, Raymon, Cheng, Raymond, Satriano, Matthew, Considine, Michael, Krigsfeld, Gabriel, Ranaweera, Ruchira, Tang, Yong, Jablonski, Sandra A., Stein-O'Brien, G

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 5.28 MB

english, 2019

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