pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.7554/eLife.69975

Notch-induced endoplasmic reticulum-associated degradation governs mouse thymocyte β−selection
Cited by: 8
Author(s): Xia Liu, Jingjing Yu, Longyong Xu, Katharine Umphred-Wilson, Fanglue Peng, Yao Ding, Brendan M Barton, Xiangdong Lv, Michael Y Zhao, Shengyi Sun, Yuning Hong, Ling Qi, Stanley Adoro, Xi Chen
Software Mentions: 7
Published: almost 3 years ago

10.1038/s41598-017-13397-x

The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.ppat.1006767

Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection
Cited by: 50
Author(s): Ashton T. Belew, Caroline Junqueira, Gabriela F. Rodrigues-Luiz, Bruna M. Valente, Antônio Edson Rocha Oliveira, Rafael B. Polidoro, Luciana W. Zuccherato, Daniella Castanheira Bartholomeu, Sérgio Schenkman, Ricardo T. Gazzinelli, Barbara A. Burleigh, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 7
Published: over 6 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13148-020-0821-z

DNA methylation-driven EMT is a common mechanism of resistance to various therapeutic agents in cancer
Cited by: 49
Author(s): Eva Galle, Bernard Thienpont, Sarah Cappuyns, Tom Venken, Pieter Busschaert, Matthias Van Haele, Éric Van Cutsem, Tania Roskams, Jos van Pelt, Chris Verslype, Jeroen Dekervel, Diether Lambrechts
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-41940-5

The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5
Cited by: 15
Author(s): Zakia Abdelhamed, Dina Abdelmottaleb, Mohammed E. El‐Asrag, Subaashini Natarajan, Gabrielle Wheway, Chris F. Inglehearn, Carmel Toomes, Colin A. Johnson
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pbio.3000988

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures
Cited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
Software Mentions: 7
Published: about 3 years ago

10.1172/jci.insight.139930

Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis
Cited by: 88
Author(s): Johann E. Gudjonsson, Lam C. Tsoi, Feiyang Ma, Allison C. Billi, Kelsey R. van Straalen, Allard R. J. V. Vossen, Hessel H. van der Zee, Paul W. Harms, Rachael Wasikowski, Christopher Yee, Syed Monem Rizvi, Xianying Xing, Enze Xing, Olesya Plazyo, Chang Zeng, Matthew Patrick, Margaret M. Lowe, Richard E. Burney, Jeffrey H. Kozlow, Jill R. Cherry-Bukowiec, Yanyun Jiang, Joseph Kirma, Stephan Weidinger, Kelly C. Cushing, Michael D. Rosenblum, Céline C. Berthier, Amanda S. MacLeod, John J. Voorhees, Fei Wen, J. Michelle Kahlenberg, Emanual Maverakis, Robert L. Modlin, Errol P. Prens
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: about 6 years ago

10.1098/rstb.2019.0086

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Cited by: 22
Author(s): David M. Needham, Camille Poirier, Elisabeth Hehenberger, Valeria Jiménez, Jarred Swalwell, Alyson E. Santoro, Alexandra Z. Worden
Software Mentions: 7
Published: over 4 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pgen.1006402

Gene co-expression network connectivity is an important determinant of selective constraint
Cited by: 96
Author(s): Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K. Ingvarsson, Nathaniel R. Street, Torgeir R. Hvidsten
Software Mentions: 7
Published: about 7 years ago

10.1038/s42003-021-02440-3

Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation
Cited by: 7
Author(s): Payal Dhar, Fahmin Basher, Zhe Ji, Lei Huang, Si Qin, Derek A. Wainwright, Jerid W. Robinson, Shaye Hagler, Jing Zhou, Sean Mackay, Jennifer D. Wu
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: almost 3 years ago

10.7554/eLife.11215

Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells
Cited by: 35
Author(s): João D. Dias, Tiago Rito, Elena Torlai Triglia, Alexander Kukalev, Carmelo Ferrai, Mita Chotalia, Emily Brookes, Hiroshi Kimurâ, Ana Pombo
Software Mentions: 7
Published: over 8 years ago

10.1038/s41598-017-14366-0

Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells
Cited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-020-07338-8

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
Cited by: 10
Author(s): Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulín, Petri Auvinen
Software Mentions: 7
Published: over 3 years ago

10.1038/s41422-020-00412-6

Single-cell transcriptomic atlas of primate cardiopulmonary aging
Cited by: 76
Author(s): Shuai Ma, Shuhui Sun, Jiaming Li, Yanling Fan, Jing Qu, Liang Sun, Si Wang, Yiyuan Zhang, Shanshan Yang, Zunpeng Liu, Zeming Wu, Sheng Zhang, Qiaoran Wang, Ai Zheng, Shuguang Duo, Yang Yu, Juan Carlos Izpisúa Belmonte, Piu Chan, Qi Zhou, Moshi Song, Weiqi Zhang, Guang Hui Liu
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-020-71805-1

Northstar enables automatic classification of known and novel cell types from tumor samples
Cited by: 8
Author(s): Fabio Zanini, Bojk A. Berghuis, Robert C. Jones, Benedetta Nicolis di Robilant, Rachel Yuan Nong, Jeffrey A. Norton, Michael F. Clarke, Stephen R. Quake
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms8101528

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria
Cited by: 14
Author(s): Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer, Muriel Derrien
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.17145.2

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
Cited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: about 5 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in <i>Drosophila</i> heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: over 7 years ago

10.1038/srep41531

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence
Cited by: 23
Author(s): Matthew J. Neave, Agus Sunarto, Kenneth A. McColl
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-021-04198-1

Comparative evaluation of full-length isoform quantification from RNA-Seq
Cited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: almost 3 years ago

10.1038/s41418-021-00751-w

Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas
Cited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: about 3 years ago

10.1186/s13073-020-00788-5

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Cited by: 10
Author(s): Shi Yang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup, Enrico Petretto
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: over 4 years ago

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2021.631889

DWV Infection in vitro Using Honey Bee Pupal Tissue
Cited by: 3
Author(s): Yunfei Wu, Xuye Yuan, Jing Li, Tatsuhiko Kadowaki
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: about 4 years ago

10.1186/s12864-017-3662-1

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals
Cited by: 18
Author(s): Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
Software Mentions: 7
Published: about 7 years ago

10.1186/1471-2105-16-S13-S7

Enhancing cancer clonality analysis with integrative genomics
Cited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-020-1930-x

CUBIC: an atlas of genetic architecture promises directed maize improvement
Cited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: over 4 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: over 10 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: almost 4 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pgen.1006864

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Cited by: 101
Author(s): Tom S. Koemans, Tjitske Kleefstra, Melissa C. Chubak, Max H. Stone, Margot R.F. Reijnders, Sonja de Munnik, Marjolein H. Willemsen, Michaela Fencková, Connie Stumpel, Levinus A. Bok, Margarita Saenz, Kyna A. Byerly, Linda B. Baughn, Alexander P.A. Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M. Kramer
Software Mentions: 7
Published: over 6 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: almost 11 years ago

10.3389/fpls.2021.693039

Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition
Cited by: 5
Author(s): Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
Software Mentions: 7
Published: almost 3 years ago

10.3390/biomedicines9050454

mRNA Profiles of Porcine Parathyroid Glands Following Variable Phosphorus Supplies throughout Fetal and Postnatal Life
Cited by: 8
Author(s): Michael Oster, Henry Reyer, Christian Gerlinger, Nares Trakooljul, Puntita Siengdee, Jonas Keiler, Siriluck Ponsuksili, Petra Wolf, Klaus Wimmers
Software Mentions: 7
Published: about 3 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: over 7 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: about 3 years ago

10.1186/s40478-020-01020-6

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis
Cited by: 7
Author(s): Sharon Melamed, Roy Avraham, Deborah E. Rothbard, Noam Erez, Tomer Israely, Ziv Klausner, Anthony H. Futerman, Nir Paran, Einat B. Vitner
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2020.578505

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life
Cited by: 18
Author(s): Tue Bjerg Bennike, Benoit Fatou, Asimenia Angelidou, Joann Diray‐Arce, Reza Falsafi, Rebecca Ford, Erin E. Gill, Simon D. van Haren, Olubukola T. Idoko, Ahwon Lee, Rym Ben‐Othman, William Pomat, Casey P. Shannon, Kinga K. Smolen, Scott J. Tebbutt, Al Ozonoff, Peter Richmond, Anita H. J. van den Biggelaar, Robert E. W. Hancock, Beate Kampmann, Tobias R. Kollmann, Ofer Levy, Hanno Steen
Software Mentions: 7
Published: over 3 years ago

10.1093/bfgp/ely003

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system
Cited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: about 6 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: about 8 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: almost 10 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pgen.1009294

Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: about 8 years ago

10.1186/s13059-015-0683-4

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation
Cited by: 87
Author(s): Hannah Dueck, Mugdha Khaladkar, Tae Kyung Kim, Jennifer M. Spaethling, Chantal Francis, Sangita Suresh, Stephen Fisher, Patrick Seale, Sheryl G. Beck, Tamás Bartfai, Bernhard Kühn, James Eberwine, Junhyong Kim
Software Mentions: 7
Published: almost 9 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: almost 3 years ago

10.15252/msb.20167507

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation
Cited by: 43
Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: over 4 years ago

10.1097/j.pain.0000000000001416

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury
Cited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: over 2 years ago

10.1371/journal.pone.0233899

Recapitulation of prostate tissue cell type-specific transcriptomes by an in vivo primary prostate tissue xenograft model
Cited by: 2
Author(s): Nelson T. Gross, Jianmin Wang, Michael V. Fiandalo, Eduardo Cortes Gomez, Anica Watts, Alejandro Godoy, Gary J. Smith, Yue Wu
Software Mentions: 7
Published: almost 4 years ago

10.12688/f1000research.14880.4

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
Cited by: 0
Author(s): Syed Hussain Ather, Olaitan I. Awe, Thomas J. Butler, Tamiru Denka, Stephen A. Semick, Wanhu Tang, Ben Busby
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.15830.2

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
Cited by: 2
Author(s): Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael Reich, Jill P. Mesirov
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-018-4934-0

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola
Cited by: 30
Author(s): Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason, Guangyu Sun
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12967-021-02936-w

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: almost 3 years ago

10.3389/fcimb.2021.733619

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures
Cited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: over 2 years ago

10.1186/s13059-018-1438-9

UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Cited by: 80
Author(s): Wenan Chen, Yán Li, John Easton, David Finkelstein, Gang Wu, Xiang Chen
Software Mentions: 7
Published: almost 6 years ago

10.3390/brainsci10020109

Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
Cited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 4 years ago

10.1111/mec.15047

Caste‐ and pesticide‐specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees
Cited by: 53
Author(s): Thomas J. Colgan, Isabel Fletcher, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Eckart Stolle, Lars Chittka, Yannick Wurm
Software Mentions: 6
Published: about 5 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: over 4 years ago

10.15252/emmm.202013412

The immune suppressive microenvironment affects efficacy of radio‐immunotherapy in brain metastasis
Cited by: 23
Author(s): Katja Niesel, Marcel H. Schulz, Julian Anthes, Tijna Alekseeva, Jadranka Macas, Anna Salamero-Boix, Aylin Möckl, T. Oberwahrenbrock, Marco Lolies, Stefan Stein, Karl H. Plate, Yvonne Reiss, Franz Rödel, Lisa Sevenich
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-021-90093-x

Prematurity alters the progenitor cell program of the upper respiratory tract of neonates
Cited by: 6
Author(s): Jessica E. Shui, Wei Wang, Helu Liu, Анна Степанова, Grace Liao, Jun Qian, Xingbin Ai, Vadim S. Ten, Jining Lü, Wellington V. Cardoso
Software Mentions: 6
Published: almost 3 years ago

10.7150/thno.56141

Distinct placental molecular processes associated with early-onset and late-onset preeclampsia
Cited by: 31
Author(s): Zhonglu Ren, Yunfei Gao, Yue Gao, Guanmei Liang, Qian Chen, Sijia Jiang, Xiaoxue Yang, Cui-Xia Fan, Haizhen Wang, Jing Wang, Yi‐Wu Shi, Chaoqun Xiao, Ming Zhong, Xinping Yang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-81933-x

Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 3 years ago

10.15252/embr.201846401

Inherent <scp>DNA</scp> ‐binding specificities of the <scp>HIF</scp> ‐1α and <scp>HIF</scp> ‐2α transcription factors in chromatin
Cited by: 128
Author(s): James Smythies, Min Sun, Norma Masson, Rafik Salama, Peter Simpson, Elizabeth R. Murray, Viviana K. Neumann, Matthew E. Cockman, Hani Choudhry, Peter J. Ratcliffe, David R. Mole
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-83110-6

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 13
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Ludwig Knabl, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorotheé von Laer, Lothar Hennighausen
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-020-72671-7

Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica
Cited by: 10
Author(s): Nasrin Masoudzadeh, Malin Östensson, Josefine Persson, Vahid Mashayekhi Goyonlo, Christopher Agbajogu, Yasaman Taslimi, Reza Erfanian Salim, Farnaz Zahedifard, Amir Mizbani, Housein Malekafzali Ardekani, Bronwyn M. Gunn, Sima Rafati, Ali M. Harandi
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07819-4

Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly
Cited by: 7
Author(s): David A. Ernst, Erica L. Westerman
Software Mentions: 6
Published: almost 3 years ago

10.1038/s41598-020-74567-y

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Cited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-015-0729-3

htsint: a Python library for sequencing pipelines that combines data through gene set generation
Cited by: 1
Author(s): Adam Richards, Anthony Herrel, Camille Bonneaud
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: over 3 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: almost 3 years ago

10.1016/j.celrep.2019.03.104

Notch Signaling Mediates Secondary Senescence
Cited by: 72
Author(s): Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Núria Tarrats, Christos Kiourtis, Miryam Müller, Anthony Green, Peter D. Adams, Juan Carlos Acosta, Tom Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra
Software Mentions: 6
Published: about 5 years ago

10.21203/rs.3.rs-69657/v1

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 0
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorothee von Laer, Lothar Hennighausen
Software Mentions: 6
Published: over 3 years ago

10.21203/rs.3.rs-509143/v1

Impact of BNT162b First Vaccination on the Immune Transcriptome of Elderly Patients Infected with the B.1.351 SARS-CoV-2 Variant
Cited by: 3
Author(s): Ludwig Knabl, Hye Kyung Lee, Manuel Wieser, Anna Mur, August Zabernigg, Simon Rauch, Matthias Böck, Jana Schumacher, Norbert Kaiser, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: almost 3 years ago

10.26508/lsa.202000974

GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program
Cited by: 30
Author(s): Yôji Kojima, Chika Yamashiro, Yusuke Murase, Yukihiro Yabuta, Ikuhiro Okamoto, Chizuru Iwatani, Hideaki Tsuchiya, Masataka Nakaya, Tomoyuki Tsukiyama, Tomonori Nakamura, Takuya Yamamoto, Mitinori Saitou
Software Mentions: 6
Published: about 3 years ago

10.1099/mgen.0.000320

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Cited by: 0
Author(s): Amol C. Shetty, John Mattick, Matthew Chung, Carrie McCracken, Anup Mahurkar, Scott G. Filler, Claire M. Fraser, David A. Rasko, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 6
Published: over 4 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: almost 8 years ago

10.3390/cancers12113311

Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers
Cited by: 2
Author(s): Denílson Bezerra Marques, Layse Raynara Ferreira-Costa, Lorenna Larissa Ferreira-Costa, Ana Beatriz Bezerra-Oliveira, Romualdo da Silva Corrêa, Carlos César de Oliveira Ramos, Tatiana Vinasco-Sandoval, Kátia de Paiva Lopes, Ricardo Assunção Vialle, Amanda Ferreira Vidal, Vivian Nogueira Silbiger, Ândrea Ribeiro-dos-Santos
Software Mentions: 6
Published: over 3 years ago

10.1186/s13578-019-0334-7

The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency
Cited by: 6
Author(s): Meisam Yousefi, Sayed-Amir Marashi, Ali Sharifi‐Zarchi, Sara Taleahmad
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.ppat.1009875

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis
Cited by: 14
Author(s): Ian J. Groves, Emma L A Drane, Marco Michalski, Jack Monahan, Cinzia G. Scarpini, Stephen Smith, Giovanni Bussotti, Csilla Várnai, Stefan Schoenfelder, Peter Fraser, Anton J. Enright, Nicholas Coleman
Software Mentions: 6
Published: over 2 years ago

10.1186/1471-2105-14-320

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
Cited by: 40
Author(s): David Sturgill, John H. Malone, Xia Sun, Harold E. Smith, Léonard Rabinow, Marie-Laure Samson, Brian Oliver
Software Mentions: 6
Published: over 10 years ago

10.1186/s13073-021-00931-w

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma
Cited by: 25
Author(s): Clément Meiller, François Montagne, Théo Z. Hirsch, Stefano Caruso, Julien De Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie‐Christine Copin, Éric Letouzé, Arnaud Scherpereel, Jessica Zucman–Rossi, Françoise Le Pimpec‐Barthes, Marie-Claude Jaurand, Didier Jean
Software Mentions: 6
Published: almost 3 years ago

10.1016/j.ccell.2017.07.004

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.ppat.1009454

Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins
Cited by: 17
Author(s): Barbara Pees, Wentao Yang, Anke Kloock, Carola Petersen, Lena Peters, Liancheng Fan, Meike Friedrichsen, Sabrina Butze, Alejandra Zárate-Potes, Hinrich Schulenburg, Katja Dierking
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.ppat.1009539

Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis
Cited by: 8
Author(s): Jae Hak Son, Brian L. Weiss, Daniela Schneider, Kiswend-Sida Mikhailou Dera, Fabian Gstöttenmayer, Robert Opiro, Richard Echodu, Norah P. Saarman, Geoffrey M. Attardo, Maria G Onyango, Adly M. M. Abd-Alla, Serap Aksoy
Software Mentions: 6
Published: over 2 years ago

10.1128/mSystems.00329-20

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Cited by: 8
Author(s): Adrián López García de Lomana, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan Péricles Rodrigues Lorenzetti, Robert L. Moritz, Nitin S. Baliga
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0150705

Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications
Cited by: 26
Author(s): Simon Schafferer, Rimpi Khurana, Violetta Refolo, Serena Venezia, Edith Sturm, Paolo Piatti, Clara Hechenberger, Hubert Hackl, Roman Kessler, Michaela Willi, Ronald Gstir, Anne Krogsdam, Alexandra Lusser, Werner Poewe, Gregor K. Wenning, Alexander Hüttenhofer, Nadia Stefanova
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0186324

Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant
Cited by: 12
Author(s): Tobias Ahsendorf, Franz‐Josef Müller, V.V. Topkar, Jeremy Gunawardena, Roland Eils
Software Mentions: 6
Published: over 6 years ago

10.1186/s13059-018-1415-3

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
Cited by: 49
Author(s): Andreas J. Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martín, Erik van Nimwegen, Mihaela Zavolan
Software Mentions: 6
Published: about 6 years ago

10.1111/acel.13381

Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
Cited by: 7
Author(s): Rebecca L. McIntyre, Simone Denis, Rashmi Kamble, Marte Molenaars, Michael Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli, Aldo Jongejan, Morten Scheibye‐Knudsen, Riekelt H. Houtkooper, Georges E. Janssens
Software Mentions: 6
Published: almost 3 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071