Volume 16; Issue 9

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PLoS Computational Biology
Volume 16; Issue 9

PLoS Computational Biology

Volume 16; Issue 9

1

Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images

Pilcher, William, Yang, Xingyu, Zhurikhina, Anastasia, Chernaya, Olga, Xu, Yinghan, Qiu, Peng, Tsygankov, Denis, Saucerman, Jeffrey J.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 14.39 MB

2020

2

Ten simple rules for an inclusive summer coding program for non-computer-scienceÂ undergraduates

Pennings, Pleuni, Banuelos, Mayra M., Catalan, Francisca L., Caudill, Victoria R., Chakalov, Bozhidar, Hernandez, Selena, Jones, Jeanice, Okorie, Chinomnso, Modrek, Sepideh, Rohlfs, Rori, Adelstein, N

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.15 MB

2020

3

Ten simple rules for open human health research

Bafeta, AÃ¯da, Bobe, Jason, Clucas, Jon, Gonsalves, Pattie Pramila, Gruson-Daniel, CÃ©lya, Hudson, Kathy L., Klein, Arno, Krishnakumar, Anirudh, McCollister-Slipp, Anna, Lindner, Ariel B., Misevic, Du

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 877 KB

2020

4

Ten simple rules on how to write a standard operating procedure

Hollmann, Susanne, Frohme, Marcus, Endrullat, Christoph, Kremer, Andreas, DâElia, Domenica, Regierer, Babette, Nechyporenko, Alina, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 510 KB

2020

5

Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state

Papadopoulos, Lia, Lynn, Christopher W., Battaglia, Demian, Bassett, Danielle S., Marinazzo, Daniele

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 11.26 MB

2020

6

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

Zhang, Yunjun, Leitner, Thomas, Albert, Jan, Britton, Tom, Kouyos, Roger Dimitri

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.96 MB

2020

7

Microtubule instability driven by longitudinal and lateral strain propagation

Igaev, Maxim, GrubmÃ¼ller, Helmut, Haliloglu, Turkan

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.30 MB

2020

8

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution

Wen, Wei Xiong, Mead, Adam J., Thongjuea, Supat, Pertea, Mihaela

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.05 MB

2020

9

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures

Chen, Bo, Xu, Wei, Althouse, Benjamin

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.84 MB

2020

10

Integration of social cues and individual experiences during instrumental avoidance learning

PÃ¤rnamets, Philip, Olsson, Andreas, OâReilly, Jill

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 5.69 MB

2020

11

Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion

Korfhage, Nikolaus, MÃ¼hling, Markus, Ringshandl, Stephan, Becker, Anke, Schmeck, Bernd, Freisleben, Bernd, Schneidman-Duhovny, Dina

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.34 MB

2020

12

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

Tran, Thinh N., Bader, Gary D., Nie, Qing

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 5.70 MB

2020

13

NuSeT: A deep learning tool for reliably separating and analyzing crowded cells

Yang, Linfeng, Ghosh, Rajarshi P., Franklin, J. Matthew, Chen, Simon, You, Chenyu, Narayan, Raja R., Melcher, Marc L., Liphardt, Jan T., Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 12.26 MB

2020

14

Kinetic modeling of H2O2 dynamics in the mitochondria of HeLa cells

Stein, Kassi T., Moon, Sun Jin, Nguyen, Athena N., Sikes, Hadley D., Held, Jason M.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.81 MB

2020

15

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Gerlach, Gabriella J., Carrock, Rachel, Stix, Robyn, Stollar, Elliott J., Ball, K. Aurelia, Wei, Guanghong

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 8.71 MB

2020

16

Effects of spatial heterogeneity on bacterial genetic circuits

Barajas, Carlos, Del Vecchio, Domitilla, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.44 MB

2020

17

Genetic buffering and potentiation in metabolism

Poyatos, Juan F., Ma, Shuangge

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.86 MB

2020

18

Direction-selective motion discrimination by traveling waves in visual cortex

Heitmann, Stewart, Ermentrout, G. Bard, Berry, Hugues

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.89 MB

2020

19

MONET: Multi-omic module discovery by omic selection

Rappoport, Nimrod, Safra, Roy, Shamir, Ron, Przytycka, Teresa M.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.05 MB

2020

20

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology

Wei, Ziqiang, Lin, Bei-Jung, Chen, Tsai-Wen, Daie, Kayvon, Svoboda, Karel, Druckmann, Shaul, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 14.90 MB

2020

21

DeepHE: Accurately predicting human essential genes based on deep learning

Zhang, Xue, Xiao, Wangxin, Xiao, Weijia, Tyagi, Sonika

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.79 MB

2020

22

Discovering functional sequences with RELICS, an analysis method for CRISPR screens

Fiaux, Patrick C., Chen, Hsiuyi V., Chen, Poshen B., Chen, Aaron R., McVicker, Graham, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.61 MB

2020

23

Ten simple rules for writing scientific op-ed articles

Goh, Hoe-Han, Bourne, Philip, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 203 KB

2020

24

Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

Zhao, Zhengqiao, Sokhansanj, Bahrad A., Malhotra, Charvi, Zheng, Kitty, Rosen, Gail L., Segata, Nicola

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 7.29 MB

2020

25

All-atom simulation of the HET-s prion replication

Terruzzi, Luca, Spagnolli, Giovanni, Boldrini, Alberto, Requena, JesÃºs R., Biasini, Emiliano, Faccioli, Pietro, Shakhnovich, Eugene I.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 6.41 MB

2020

26

A new Graph Gaussian embedding method for analyzing the effects of cognitive training

Xu, Mengjia, Wang, Zhijiang, Zhang, Haifeng, Pantazis, Dimitrios, Wang, Huali, Li, Quanzheng, Inman, Cory

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 7.33 MB

2020

27

Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data

P. E. de Souza, Camila, Andronescu, Mirela, Masud, Tehmina, Kabeer, Farhia, Biele, Justina, Laks, Emma, Lai, Daniel, Ye, Patricia, Brimhall, Jazmine, Wang, Beixi, Su, Edmund, Hui, Tony, Cao, Qi, Wong,

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 19.63 MB

2020

28

Alcoholic liver disease: A registry view on comorbidities and disease prediction

Grissa, Dhouha, Nytoft Rasmussen, Ditlev, Krag, Aleksander, Brunak, SÃ¸ren, Juhl Jensen, Lars, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.98 MB

2020

29

Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium

Roy, Aditi, Varela, Marta, Chubb, Henry, MacLeod, Robert, Hancox, Jules C., Schaeffter, Tobias, Aslanidi, Oleg, Panfilov, Alexander V.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 16.64 MB

2020

30

Ten simple rules to make your research more sustainable

Ligozat, Anne-Laure, NÃ©vÃ©ol, AurÃ©lie, Daly, BÃ©nÃ©dicte, Frenoux, Emmanuelle, Schwartz, Russell

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 914 KB

2020

31

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

Pavlovicz, Ryan E., Park, Hahnbeom, DiMaio, Frank, Wallner, BjÃ¶rn

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.71 MB

2020

32

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

Kim, Hyeon-Jin, YardÄ±mcÄ±, Galip Gurkan, Bonora, Giancarlo, Ramani, Vijay, Liu, Jie, Qiu, Ruolan, Lee, Choli, Hesson, Jennifer, Ware, Carol B., Shendure, Jay, Duan, Zhijun, Noble, William Stafford, I

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.24 MB

2020

33

A greedy classifier optimization strategy to assess ion channel blocking activity and pro-arrhythmia in hiPSC-cardiomyocytes

Raphel, Fabien, De Korte, Tessa, Lombardi, Damiano, Braam, Stefan, Gerbeau, Jean-Frederic, Knudsen, Thomas B

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 9.99 MB

2020

34

A compiler for biological networks on silicon chips

Medley, J. Kyle, Teo, Jonathan, Woo, Sung Sik, Hellerstein, Joseph, Sarpeshkar, Rahul, Sauro, Herbert M., Mac Gabhann, Feilim

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 5.04 MB

2020

35

Inferring a complete genotype-phenotype map from a small number of measured phenotypes

Sailer, Zachary R., Shafik, Sarah H., Summers, Robert L., Joule, Alex, Patterson-Robert, Alice, Martin, Rowena E., Harms, Michael J., Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 7.47 MB

2020

36

The relative contributions of infectious and mitotic spread to HTLV-1 persistence

Laydon, Daniel J., Sunkara, Vikram, Boelen, Lies, Bangham, Charles R. M., Asquith, Becca, Regoes, Roland R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.98 MB

2020

37

Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops

Joanito, Ignasius, Yan, Ching-Cher Sanders, Chu, Jhih-Wei, Wu, Shu-Hsing, Hsu, Chao-Ping, CsikÃ¡sz-Nagy, Attila

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.25 MB

2020

38

Ten quick tips for teaching with participatory live coding

Nederbragt, Alexander, Harris, Rayna Michelle, Hill, Alison Presmanes, Wilson, Greg, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 261 KB

2020

39

Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder

Henco, Lara, Diaconescu, Andreea O., Lahnakoski, Juha M., Brandi, Marie-Luise, HÃ¶rmann, Sophia, Hennings, Johannes, Hasan, Alkomiet, Papazova, Irina, Strube, Wolfgang, Bolis, Dimitris, Schilbach, Leo

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.33 MB

2020

40

Response nonlinearities in networks of spiking neurons

Sanzeni, Alessandro, Histed, Mark H., Brunel, Nicolas, Cuntz, Hermann

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.27 MB

2020

41

Tuning network dynamics from criticality to an asynchronous state

Li, Jingwen, Shew, Woodrow L., Soltani, Alireza

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.47 MB

2020

42

Increased comparability between RNA-Seq and microarray data by utilization of gene sets

van der Kloet, Frans M., Buurmans, Jeroen, Jonker, Martijs J., Smilde, Age K., Westerhuis, Johan A., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 8.77 MB

2020

43

Characterizing chromatin folding coordinate and landscape with deep learning

Xie, Wen Jun, Qi, Yifeng, Zhang, Bin, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.07 MB

2020

44

Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes

ten Bosch, Quirine A., Wagman, Joseph M., Castro-Llanos, Fanny, Achee, Nicole L., Grieco, John P., Perkins, T. Alex, Flegg, Jennifer A.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.08 MB

2020

45

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

Herencias, Cristina, Salgado-Briegas, Sergio, Prieto, M. Auxiliadora, Nogales, Juan, Hatzimanikatis, Vassily

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.18 MB

2020

46

Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance

Baker, Cody, Zhu, Vicky, Rosenbaum, Robert, Ermentrout, Bard

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.13 MB

2020

47

Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells

Marchena, Miquel, Echebarria, Blas, Shiferaw, Yohannes, Alvarez-Lacalle, Enrique, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.68 MB

2020

48

A bacterial size law revealed by a coarse-grained model of cell physiology

Bertaux, FranÃ§ois, von KÃ¼gelgen, Julius, Marguerat, Samuel, Shahrezaei, Vahid, Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.85 MB

2020

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