pypi: sh | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02295-1

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Cited by: 77
Author(s): Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
Software Mentions: 18
Published: over 3 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: almost 4 years ago

10.3390/cells9030779

Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)
Cited by: 12
Author(s): Yury V. Malovichko, O. Y. Shtark, Ekaterina N. Vasileva, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 10
Published: over 4 years ago

10.1099/mgen.0.000303

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'
Cited by: 5
Author(s): Tegan M. Harris, Erin P. Price, Derek S. Sarovich, Niels Nørskov‐Lauritsen, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-019-2615-x

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
Cited by: 10
Author(s): Nikolay Martyushenko, Eivind Almaas
Software Mentions: 5
Published: almost 6 years ago

10.1111/1462-2920.14862

Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry
Cited by: 31
Author(s): Sara F. Paver, Ryan J. Newton, Maureen L. Coleman
Software Mentions: 5
Published: almost 5 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: about 8 years ago

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1006373

Designing and running an advanced Bioinformatics and genome analyses course in Tunisia
Cited by: 6
Author(s): Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2164-14-494

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Cited by: 6
Author(s): Quang Trinh, Fei-Yang Arthur Jen, Ziru Zhou, Kar Ming Chu, Marc D. Perry, Ellen Kephart, Sergio Contrino, Peter Ruzanov, Lincoln Stein
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pcbi.1009285

ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
Cited by: 26
Author(s): Eric D. Musselman, Jake E. Cariello, Warren M. Grill, Nicole A. Pelot
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.6842

ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean
Cited by: 41
Author(s): Javier Arellano‐Verdejo, Hugo-Enrique Lazcano-Hernández, Nancy Cabañillas-Terán
Software Mentions: 4
Published: over 5 years ago

10.1002/hbm.24920

Human body odor increases familiarity for faces during encoding‐retrieval task
Cited by: 15
Author(s): Cinzia Cecchetto, Florian Ph. S. Fischmeister, Sarah Gorkiewicz, Wolfgang Schuehly, Deepika Bagga, Valentina Parma, Veronika Schöpf
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2016.01744

Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals
Cited by: 17
Author(s): Erich M. Schwarz, Adrienne Roeder
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12859-019-3031-y

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data
Cited by: 14
Author(s): Emiliano Pereira-Flores, Frank Oliver Glöckner, Antonio Fernández-Guerra
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms8091350

Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake
Cited by: 14
Author(s): Diana E. Ayala, William D. Burgos, Javier Sánchez España, Estelle Couradeau, Carmen Falagán, Jennifer L. Macalady
Software Mentions: 4
Published: about 4 years ago

10.1038/s42003-020-1096-9

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Cited by: 27
Author(s): Austin B. Mudd, Jessen V. Bredeson, Rachel Baum, Dirk Hockemeyer, Daniel S. Rokhsar
Software Mentions: 3
Published: about 4 years ago

10.1002/hbm.25474

Improved normalization of lesioned brains via cohort‐specific templates
Cited by: 5
Author(s): Ioannis Pappas, Henrik Hector, Kari A. Haws, Brian Curran, Andrew S. Kayser, Mark D’Esposito
Software Mentions: 3
Published: over 3 years ago

10.1186/s13071-020-04035-z

Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation
Cited by: 10
Author(s): Katherine Omueti Ayoade, Faith R. Carranza, Woong Hee Cho, Zhu Wang, Steven A. Kliewer, David J. Mangelsdorf, Jonathan D. C. Stoltzfus
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.6995

ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
Cited by: 72
Author(s): Andrew Low, Adam Koziol, Paul Manninger, Burton W. Blais, Catherine D. Carrillo
Software Mentions: 3
Published: over 5 years ago

10.1016/j.str.2019.09.007

Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes
Cited by: 14
Author(s): Sanchaita Das, Andrew W. Malaby, Agata Nawrotek, Wenhua Zhang, Mahel Zeghouf, Sarah Maslen, Mark Skehel, Srinivas Chakravarthy, Thomas C. Irving, Osman Bilsel, Jacqueline Cherfils, David G. Lambright
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.63551

Temporo-parietal cortex involved in modeling one’s own and others’ attention
Cited by: 10
Author(s): Arvid Guterstam, Branden J. Bio, Andrew I. Wilterson, Michael S. A. Graziano
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-71662-y

Choosing to view morbid information involves reward circuitry
Cited by: 20
Author(s): Suzanne Oosterwijk, Lukas Snoek, Jurriaan Tekoppele, Lara H. Engelbert, H. Steven Scholte
Software Mentions: 3
Published: about 4 years ago

10.3390/nu12010174

Theanine, the Main Amino Acid in Tea, Prevents Stress-Induced Brain Atrophy by Modifying Early Stress Responses
Cited by: 24
Author(s): Keiko Unno, Akira Sumiyoshi, Tomokazu Konishi, Michiko Hayashi, Kyoko Taguchi, Yoshio Muguruma, Kōichi Inoue, Kazuaki Iguchi, Hiroi Nonaka, Ryuta Kawashima, Sanae Hasegawa-Ishii, Atsuyoshi Shimada, Yoriyuki Nakamura
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12870-019-1905-9

The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce
Cited by: 11
Author(s): Patrik Inderbitzin, Marilena Christopoulou, Dean Lavelle, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Krishna V. Subbarao, Ivan Šimko
Software Mentions: 2
Published: over 5 years ago

10.1007/s00429-014-0763-3

Characterizing longitudinal white matter development during early childhood
Cited by: 142
Author(s): Douglas C. Dean, Jonathan O’Muircheartaigh, Holly Dirks, Nicole Waskiewicz, Lindsay Walker, Ellen Doernberg, Irene Piryatinsky, Sean Deoni
Software Mentions: 2
Published: over 10 years ago

10.3390/mps3010022

Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis
Cited by: 4
Author(s): David Molik, Michael E. Pfrender, Scott J. Emrich
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.00986-20

Complete Genome Sequence of the Novel Psychrobacter sp. Strain AJ006, Which Has the Potential for Biomineralization
Cited by: 0
Author(s): Jun Ho Lee, Pyung Cheon Lee
Software Mentions: 2
Published: about 4 years ago

10.1093/cercor/bhz132

Enhanced Bottom-Up and Reduced Top-Down fMRI Activity Is Related to Long-Lasting Nonreinforced Behavioral Change
Cited by: 16
Author(s): Rotem Botvinik‐Nezer, Tom Salomon, Tom Schönberg
Software Mentions: 2
Published: about 5 years ago

10.1093/database/bay099

Tripal Developer Toolkit
Cited by: 3
Author(s): Bradford Condon, Abdullah Almsaeed, Ming Chen, Joe West, Margaret Staton
Software Mentions: 2
Published: almost 7 years ago

10.3389/fdata.2021.659986

CutLang v2: Advances in a Runtime-Interpreted Analysis Description Language for HEP Data
Cited by: 1
Author(s): G. Ünel, S. Sekmen, Anna Monica Toon, Burak Göktürk, Bora Orgen, Arpon Paul, N. Ravel, Jinen Setpal
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.705986

N6 -Methyladenosine Modification in Chronic Stress Response Due to Social Hierarchy Positioning of Mice
Cited by: 3
Author(s): Malena dos Santos Guilherme, Theodora Tsoutsouli, Hristo Todorov, Sina Teifel, Vu Thu Thuy Nguyen, Susanne Gerber, Kristina Endres
Software Mentions: 2
Published: about 3 years ago

10.3389/fninf.2017.00035

ATPP: A Pipeline for Automatic Tractography-Based Brain Parcellation
Cited by: 17
Author(s): Hai Li, Lingzhong Fan, Junjie Zhuo, Jiaojian Wang, Yu Zhang, Zhengyi Yang, Tianzi Jiang
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.117.300438

Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice
Cited by: 26
Author(s): Paul L. Maurizio, Martin T. Ferris, Gregory R. Keele, Darla R. Miller, Ginger D Shaw, Alan C. Whitmore, Ande West, Clayton R. Morrison, Kelsey E. Noll, Kenneth S. Plante, Adam S. Cockrell, David W. Threadgill, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, William Valdar
Software Mentions: 2
Published: almost 7 years ago

10.1038/sdata.2017.130

Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida
Cited by: 5
Author(s): Samuel J. White, Brent Vadopalas, Katherine Silliman, Steven B. Roberts
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-76857-x

Natural bladder filling alters resting brain function at multiple spatial scales: a proof-of-concept MAPP Network Neuroimaging Study
Cited by: 8
Author(s): Ishtiaq Mawla, Andrew Schrepf, Eric Ichesco, Steven E. Harte, David J. Klumpp, James W. Griffith, Eric Strachan, Claire C. Yang, H. Henry Lai, Gerald L. Andriole, Vincent A. Magnotta, Karl J. Kreder, Daniel J. Clauw, Richard E. Harris, J. Quentin Clemens, J. Richard Landis, Chris Mullins, Larissa V. Rodríguez, Emeran A. Mayer, Jason J. Kutch
Software Mentions: 2
Published: almost 4 years ago

10.1093/scan/nsab035

Brain activation during the observation of real soccer game situations predicts creative goal scoring
Cited by: 5
Author(s): Christian Rominger, Karl Koschutnig, Daniel Memmert, Ilona Papousek, Corinna M. Perchtold‐Stefan, Mathias Benedek, Andreas Schwerdtfeger, Andréas Fink
Software Mentions: 2
Published: over 3 years ago

10.1111/1759-7714.13641

<scp>Hsa_circRNA</scp> _0000518 facilitates breast cancer development via regulation of the <scp>miR</scp> ‐326/ <scp>FGFR1</scp> axis
Cited by: 16
Author(s): Jing Jiang, Hui Ching Lin, Shenghong Shi, Ying Hong, Xianan Bai, Xuchen Cao
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-9-S6-S10

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs
Cited by: 6
Author(s): Hiroyuki Mishima, Andrew C. Lidral, Jun Ni
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-021-84906-2

Decreased amygdala volume in adults after premature birth
Cited by: 15
Author(s): Benita Schmitz‐Koep, Juliana Zimmermann, Aurore Menegaux, Rachel Nuttall, Josef Bäuml, Sebastian Schneider, Marcel Daamen, Henning Boecker, Claus Zimmer, Dieter Wolke, Peter Bartmann, Dennis M. Hedderich, Christian Sorg
Software Mentions: 1
Published: over 3 years ago

10.1186/s40168-019-0752-0

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
Cited by: 64
Author(s): Vinicius Silva Kavagutti, Adrian‐Ștefan Andrei, Maliheh Mehrshad, Michaela M. Salcher, Rohit Ghai
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.8065

Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis
Cited by: 20
Author(s): Ahmad Bazli Ramzi, Muhammad Lutfi Che Me, Ummul Syafiqah Ruslan, Syarul Nataqain Baharum, Nor Azlan Nor Muhammad
Software Mentions: 1
Published: almost 5 years ago

10.1523/ENEURO.0044-19.2019

Chronic Alcohol Drinking Slows Brain Development in Adolescent and Young Adult Nonhuman Primates
Cited by: 22
Author(s): Tatiana A. Shnitko, Zheng Liu, Xiaojie Wang, Kathleen A. Grant, Christopher D. Kroenke
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0038130

ANKRD26 and Its Interacting Partners TRIO, GPS2, HMMR and DIPA Regulate Adipogenesis in 3T3-L1 Cells
Cited by: 27
Author(s): Xiufen Liu, Tapan K. Bera, Charissa N. Kahue, Thelma M. Escobar, Zhaoliang Fei, Gregory Alexander Raciti, Ira Pastan
Software Mentions: 1
Published: over 12 years ago

10.1098/rsos.171901

Molecular evidence for the first records of facultative parthenogenesis in elapid snakes
Cited by: 11
Author(s): Luke Allen, Kate L. Sanders, Vicki A. Thomson
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41396-018-0220-z

Endosymbiont genomes yield clues of tubeworm success
Cited by: 32
Author(s): Yuanning Li, Mark R. Liles, Kenneth M. Halanych
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0150361

Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland
Cited by: 67
Author(s): Timofey Skvortsov, Colin de Leeuwe, John P. Quinn, John W. McGrath, Christopher C. R. Allen, Y. McElarney, C. J. Watson, Ksenia Arkhipova, Rob Lavigne, Leonid Kulakov
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.06426

Functional subregions of the human entorhinal cortex
Cited by: 179
Author(s): Anne Maaß, David Berron, Laura A. Libby, Charan Ranganath, Emrah Düzel
Software Mentions: 1
Published: over 9 years ago

Projects: pypi: sh

Papers Mentioning sh 48