Genetic compensation: A phenomenon in search of mechanisms

Network biology: understanding the cell's functional organization

Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903

Untitled work

(2008) · doi:10.1038/nrg2290 · Cited by 5,199

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316

Gene Action in the X-chromosome of the Mouse (Mus musculus L.)

LYON, M. F. (1961) · Nature · doi:10.1038/190372a0 · Cited by 3,978

The Transcriptional Landscape of the Mammalian Genome

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Raj, A., & van Oudenaarden, A. (2008) · Cell · doi:10.1016/j.cell.2008.09.050 · Cited by 2,593

Antisense Transcription in the Mammalian Transcriptome

Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.-S., Suzuki, M., Kawai, J., et al. (2005) · Science · doi:10.1126/science.1112009 · Cited by 1,699

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship

Pasquinelli, A. E. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3162 · Cited by 1,642

Aquaporin-4 deletion in mice reduces brain edema after acute water intoxication and ischemic stroke

Manley, G. T., Fujimura, M., Ma, T., Noshita, N., Filiz, F., Bollen, A. W., Chan, P. H., & Verkman, A. S. (2000) · Nature Medicine · doi:10.1038/72256 · Cited by 1,501

RNA‐binding proteins and post‐transcriptional gene regulation

Glisovic, T., Bachorik, J. L., Yong, J., & Dreyfuss, G. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.03.004 · Cited by 1,398

MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation

Ørom, U. A., Nielsen, F. C., & Lund, A. H. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.001 · Cited by 1,384

RNA regulons: coordination of post-transcriptional events

Keene, J. D. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2111 · Cited by 1,321

MicroRNA-373 induces expression of genes with complementary promoter sequences

Place, R. F., Li, L., Pookot, D., Noonan, E. J., & Dahiya, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707594105 · Cited by 1,266

Dynamic m6A mRNA methylation directs translational control of heat shock response

Zhou, J. L., Wan, J., Gao, X., Zhang, X., Jaffrey, S. R., & Qian, S. (2015) · Nature · doi:10.1038/nature15377 · Cited by 1,228

Genetic compensation induced by deleterious mutations but not gene knockdowns

Rossi, A., Kontarakis, Z., Gerri, C., Nolte, H., Hölper, S., Krüger, M., & Stainier, D. Y. R. (2015) · Nature · doi:10.1038/nature14580 · Cited by 1,226

High-throughput discovery of novel developmental phenotypes

The International Mouse Phenotyping Consortium, Dickinson, M. E., Flenniken, A. M., Ji, X., Teboul, L., Wong, M. D., White, J. K., Meehan, T. F., Weninger, W. J., Westerberg, H., et al. (2016) · Nature · doi:10.1038/nature19356 · Cited by 1,196

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

Jackson, A. L., & Linsley, P. S. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd3010 · Cited by 1,126

Canalization of Development and Genetic Assimilation of Acquired Characters

Waddington, C. H. (1959) · Nature · doi:10.1038/1831654a0 · Cited by 1,109

Cdk1 is sufficient to drive the mammalian cell cycle

Santamarı́a, D., Barrière, C., Cerqueira, A., Hunt, S. L., Tardy, C., Newton, K., Cáceres, J. F., Dubus, P. R., Malumbres, M., & Barbacid, M. (2007) · Nature · doi:10.1038/nature06046 · Cited by 1,096

p53 Activation by Knockdown Technologies

Robu, M. E., Larson, J. D., Nasevicius, A., Beiraghi, S., Brenner, C., Farber, S. A., & Ekker, S. C. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0030078 · Cited by 1,049

A Morphological Distinction between Neurones of the Male and Female, and the Behaviour of the Nucleolar Satellite during Accelerated Nucleoprotein Synthesis

Barr, M. L., & Bertram, E. G. (1949) · Nature · doi:10.1038/163676a0 · Cited by 1,030

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

Schwartz, S., Bernstein, D. A., Mumbach, M. R., Jovanović, M., Herbst, R. H., León-Ricardo, B. X., Engreitz, J., Guttman, M., Satija, R., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.028 · Cited by 1,013

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

Calvo, S. E., Pagliarini, D. J., & Mootha, V. K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810916106 · Cited by 914

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes

Lykke‐Andersen, S., & Jensen, T. H. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4063 · Cited by 843

Altered microtubule organization in small-calibre axons of mice lacking tau protein

Harada, A., Oguchi, K., Okabe, S., Kuno, J., Terada, S., Ohshima, T., Sato-Yoshitake, R., Takei, Y., Noda, T., & Hirokawa, N. (1994) · Nature · doi:10.1038/369488a0 · Cited by 802

Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish

Kok, F. O., Shin, M., Ni, C., Gupta, A., Grosse, A. S., van Impel, A., Kirchmaier, B. C., Peterson-Maduro, J., Kourkoulis, G., Male, I., et al. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.11.018 · Cited by 789

Small dsRNAs induce transcriptional activation in human cells

Li, L., Okino, S. T., Zhao, H., Pookot, D., Place, R. F., Urakami, S., Enokida, H., & Dahiya, R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607015103 · Cited by 779

Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation

Barreto, G., Schäfer, A., Marhold, J., Stach, D., Swaminathan, S. K., Handa, V., Doederlein, G., Maltry, N., Wu, W., Lyko, F., et al. (2007) · Nature · doi:10.1038/nature05515 · Cited by 771

Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression

Lagger, G., O'Carroll, D., Rembold, M., Khier, H., Tischler, J., Weitzer, G., Schuettengruber, B., Hauser, C., Brunmeir, R., Jenuwein, T., et al. (2002) · The EMBO Journal · doi:10.1093/emboj/21.11.2672 · Cited by 760

Utrophin–dystrophin-deficient mice as a model for Duchenne muscular dystrophy

Deconinck, A. E., Rafael, J. A., Skinner, J. A., Brown, S. C., Potter, A. C., Metzinger, L., Watt, D. J., Dickson, J. G., Tinsley, J. M., & Davies, K. E. (1997) · Cell · doi:10.1016/s0092-8674(00)80532-2 · Cited by 752

Aquaporin‐4 facilitates reabsorption of excess fluid in vasogenic brain edema

Papadopoulos, M. C., Manley, G. T., Krishna, S., & Verkman, A. S. (2004) · The FASEB Journal · doi:10.1096/fj.04-1723fje · Cited by 749

Upstream Open Reading Frames as Regulators of mRNA Translation

Morris, D. R., & Geballe, A. P. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.23.8635-8642.2000 · Cited by 736

Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway

Ziv, Y., Bielopolski, D., Galanty, Y., Lukas, C., Taya, Y., Schultz, D. C., Lukas, J., Bekker-Jensen, S., Bartek, J., & Shiloh, Y. (2006) · Nature Cell Biology · doi:10.1038/ncb1446 · Cited by 735

Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

Gerber, A. P., Herschlag, D., & Brown, P. O. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020079 · Cited by 670

Inhibition of neurite polarity by tau antisense oligonucleotides in primary cerebellar neurons

Cáceres, A., & Kosik, K. S. (1990) · Nature · doi:10.1038/343461a0 · Cited by 656

Widespread occurrence of antisense transcription in the human genome

Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., et al. (2003) · Nature Biotechnology · doi:10.1038/nbt808 · Cited by 646

Variability in gene expression underlies incomplete penetrance

Raj, A., Rifkin, S. A., Andersen, E. C., & van Oudenaarden, A. (2010) · Nature · doi:10.1038/nature08781 · Cited by 642

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcriptionPreprint

Chambeyron, S., & Bickmore, W. A. (2004) · Genes & Development · doi:10.1101/gad.292104 · Cited by 618

Multiple upstream AUG codons mediate translational control of GCN4

Mueller, P. P., & Hinnebusch, A. G. (1986) · Cell · doi:10.1016/0092-8674(86)90384-3 · Cited by 600

Modifier genes in mice and humans

Nadeau, J. H. (2001) · Nature Reviews Genetics · doi:10.1038/35056009 · Cited by 576

A Role for Small RNAs in DNA Double-Strand Break Repair

Wei, W., Ba, Z., Gao, M., Wu, Y., Ma, Y., Amiard, S., White, C. I., Danielsen, J. M. R., Yang, Y., & Qi, Y. (2012) · Cell · doi:10.1016/j.cell.2012.03.002 · Cited by 575

Site-specific DICER and DROSHA RNA products control the DNA-damage response

Francia, S., Michelini, F., Saxena, A., Tang, D. T. P., de Hoon, M., Anelli, V., Mione, M., Carninci, P., & di Fagagna, F. D. (2012) · Nature · doi:10.1038/nature11179 · Cited by 553

Acute mutation of retinoblastoma gene function is sufficient for cell cycle re-entry

Sage, J., Miller, A. L., Pérez-Mancera, P. A., Wysocki, J. M., & Jacks, T. (2003) · Nature · doi:10.1038/nature01764 · Cited by 538

Activating gene expression in mammalian cells with promoter-targeted duplex RNAs

Janowski, B. A., Younger, S. T., Hardy, D. B., Ram, R. R., Huffman, K. E., & Corey, D. R. (2007) · Nature Chemical Biology · doi:10.1038/nchembio860 · Cited by 521

Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

White, J. K., Gerdin, A.-K., Karp, N. A., Ryder, E., Buljan, M., Bussell, J. N., Salisbury, J., Clare, S., Ingham, N. J., Podrini, C., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.022 · Cited by 509

Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

Dawlaty, M. M., Ganz, K., Powell, B. E., Hu, Y.-C., Markoulaki, S., Cheng, A. W., Gao, Q., Kim, J., Choi, S.-W., Page, D. C., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.07.010 · Cited by 508

Dosage compensation in mammals: fine-tuning the expression of the X chromosomePreprint

Heard, É., & Distèche, C. M. (2006) · Genes & Development · doi:10.1101/gad.1422906 · Cited by 504

Eukaryotic mRNPs May Represent Posttranscriptional Operons

Keene, J. D., & Tenenbaum, S. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00559-2 · Cited by 462

Genetical control of stability in development

Mather, K. (1953) · Heredity · doi:10.1038/hdy.1953.41 · Cited by 457

Generation and phenotype of a transgenic knockout mouse lacking the mercurial-insensitive water channel aquaporin-4.

Ma, T., Yang, B., Gillespie, A. M., Carlson, E. J., Epstein, C. J., & Verkman, A. S. (1997) · Journal of Clinical Investigation · doi:10.1172/jci231 · Cited by 446

Transcriptional regulatory functions of nuclear long noncoding RNAs

Vance, K. W., & Ponting, C. P. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.06.001 · Cited by 434

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

Evers, B., Jastrzebski, K., Heijmans, J. P. M., Grernrum, W., Beijersbergen, R. L., & Bernards, R. (2016) · Nature Biotechnology · doi:10.1038/nbt.3536 · Cited by 431

Variability in gene expression underlies incomplete penetrance

van Oudenaarden, A., Rifkin, S. A., Raj, A., & Andersen, E. C. (2010) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 424

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

Morgens, D. W., Deans, R. M., Li, A., & Bassik, M. C. (2016) · Nature Biotechnology · doi:10.1038/nbt.3567 · Cited by 398

CD44 Regulates Hematopoietic Progenitor Distribution, Granuloma Formation, and Tumorigenicity

Schmits, R., Filmus, J., Gerwin, N., Senaldi, G., Kiefer, F., Kündig, T. M., Wakeham, A. C., Shahinian, A., Catzavelos, C., Rak, J. W., et al. (1997) · Blood · doi:10.1182/blood.v90.6.2217 · Cited by 390

A Drosophila Genetic Resource of Mutants to Study Mechanisms Underlying Human Genetic Diseases

Yamamoto, S., Jaiswal, M., Charng, W., Gambin, T., Karaca, E., Mirzaa, G., Wiszniewski, W. K., Sandoval, H., Haelterman, N. A. T., Xiong, B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.002 · Cited by 383

skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo

Bowerman, B. A., Eaton, B. A., & Priess, J. R. (1992) · Cell · doi:10.1016/0092-8674(92)90078-q · Cited by 374

Epstein-Barr virus-encoded EBNA1 inhibits the canonical NF-κB pathway in carcinoma cells by inhibiting IKK phosphorylation

Valentine, R., Dawson, W. O., Hu, C., Shah, K. M., Owen, T. J., Date, K. L., Pinheiro-Maia, S., Shao, J., Arrand, J. R., Young, L. S., et al. (2010) · Molecular Cancer · doi:10.1186/1476-4598-9-1 · Cited by 353

β-Actin specifically controls cell growth, migration, and the G-actin pool

Bunnell, T. M., Burbach, B. J., Shimizu, Y., & Ervasti, J. M. (2011) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-06-0582 · Cited by 345

Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development

Gao, Y., Zhang, Y., Zhang, D., Dai, X., Estelle, M. A., & Zhao, Y. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1500365112 · Cited by 339

Requirement for cyclin D3 in lymphocyte development and T cell leukemias

Sicińska, E., Aifantis, I., Cam, L. L., Swat, W., Borowski, C., Yu, Q., Ferrando, A. A., Levin, S. D., Geng, Y., von Boehmer, H., et al. (2003) · Cancer Cell · doi:10.1016/s1535-6108(03)00301-5 · Cited by 338

Generation of APLP2 KO Mice and Early Postnatal Lethality in APLP2/APP Double KO Mice

von Koch, C. S., Zheng, H., Chen, H., Trumbauer, M. E., Thinakaran, G., der Ploeg, L. H. T. V., Price, D. L., & Sisodia, S. S. (1997) · Neurobiology of Aging · doi:10.1016/s0197-4580(97)00151-6 · Cited by 336

Gene regulatory networks

Davidson, E., & Levin, M. G. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502024102 · Cited by 326

Over 20% of human transcripts might form sense-antisense pairs

Chen, J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh818 · Cited by 325

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

Li, L., Lyu, X., Hou, C., Takenaka, N., Nguyen, H. Q., Ong, C., Cubeñas-Potts, C., Hu, M., Lei, E. P., Bosco, G., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.023 · Cited by 315

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Chen, R., Shi, L., Hakenberg, J., Naughton, B., Sklar, P., Zhang, J., Zhou, H., Tian, L., Prakash, O., Lemire, M., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3514 · Cited by 310

Arabidopsis gene knockout: phenotypes wanted

Bouché, N. (2001) · Current Opinion in Plant Biology · doi:10.1016/s1369-5266(00)00145-x · Cited by 302

Chromatin dynamics and the preservation of genetic information

Downs, J. A., Nussenzweig, M. C., & Nussenzweig, A. (2007) · Nature · doi:10.1038/nature05980 · Cited by 296

roX1 RNA Paints the X Chromosome of Male Drosophila and Is Regulated by the Dosage Compensation System

Meller, V. H., Wu, K. H., Roman, G., Kuroda, M. I., & Davis, R. L. (1997) · Cell · doi:10.1016/s0092-8674(00)81885-1 · Cited by 288

Health and population effects of rare gene knockouts in adult humans with related parents

Narasimhan, V. M., Hunt, K. A., Mason, D., Baker, C. L., Karczewski, K. J., Barnes, M. R., Barnett, A. H., Bates, C., Bellary, S., Bockett, N. A., et al. (2016) · Science · doi:10.1126/science.aac8624 · Cited by 286

Kindlin-2 cooperates with talin to activate integrins and induces cell spreading by directly binding paxillin

Theodosiou, M., Widmaier, M., Böttcher, R. T., Rognoni, E., Veelders, M., Bharadwaj, M., Lambacher, A., Austen, K., Müller, D. J., Zent, R., et al. (2016) · eLife · doi:10.7554/elife.10130 · Cited by 279

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

Chew, G.-L., Pauli, A., Rinn, J. L., Regev, A., Schier, A. F., & Valen, E. (2013) · Development · doi:10.1242/dev.098343 · Cited by 275

Antisense transcripts are targets for activating small RNAs

Schwartz, J. C., Younger, S. T., Nguyen, N.-B., Hardy, D. B., Monia, B. P., Corey, D. R., & Janowski, B. A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1444 · Cited by 273

Development of mice expressing a single D-type cyclin

Ciemerych, M. A., Kenney, A. M., Sicinska, E., Kalaszczynska, I., Bronson, R. T., Rowitch, D. H., Gardner, H., & Sicinski, P. (2002) · Genes & Development · doi:10.1101/gad.1023602 · Cited by 267

RNA Induction and Inheritance of Epigenetic Cardiac Hypertrophy in the Mouse

Wagner, K., Wagner, N., Ghanbarian, H., Grandjean, V., Gounon, P., Cuzin, F., & Rassoulzadegan, M. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.03.009 · Cited by 264

Pyruvate Kinase Isoform Expression Alters Nucleotide Synthesis to Impact Cell Proliferation

Lunt, S. Y., Muralidhar, V., Hosios, A. M., Israelsen, W. J., Gui, D. Y., Newhouse, L., Ogrodzinski, M. P., Hecht, V. C., Xu, K., Acevedo, P. N. M., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.10.027 · Cited by 263

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene RegulationPreprint

Kiyosawa, H., Yamanaka, I., Osato, N., Kondo, S., RIKEN GER Group, GSLMembers, & Hayashizaki, Y. (2003) · Genome Research · doi:10.1101/gr.982903 · Cited by 254

uAUG and uORFs in human and rodent 5′untranslated mRNAs

Iacono, M., Mignone, F., & Pesole, G. (2005) · Gene · doi:10.1016/j.gene.2004.11.041 · Cited by 244

Loss-of-function genetic tools for animal models: cross-species and cross-platform differences

Housden, B. E., Muhar, M., Gemberling, M. P., Gersbach, C. A., Stainier, D. Y. R., Seydoux, G., Mohr, S. E., Zuber, J. A., & Perrimon, N. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.118 · Cited by 225

An NMD Pathway in Yeast Involving Accelerated Deadenylation and Exosome-Mediated 3′→5′ Degradation

Mitchell, P., & Tollervey, D. W. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00190-4 · Cited by 222

Identification of a large set of rare complete human knockouts

Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S. A., Zink, F., Hjartarson, E., Sigurdsson, G. T., Jonasdottir, A., Jonasdottir, A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3243 · Cited by 220

Genes Expressed in Neurons of Adult Male Drosophila

Amrein, H., & Axel, R. (1997) · Cell · doi:10.1016/s0092-8674(00)81886-3 · Cited by 218

Allele‐specific histone lysine methylation marks regulatory regions at imprinted mouse genes

Fournier, C., Goto, Y., Ballestar, E., Delaval, K., Hever, A. M., Esteller, M., & Feil, R. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf655 · Cited by 217

Triggering neural differentiation of ES cells by subtype switching of importin-α

Yasuhara, N., Shibazaki, N., Tanaka, S., Nagai, M., Kamikawa, Y. F., Oe, S., Asally, M., Kamachi, Y., Kondoh, H., & Yoneda, Y. (2006) · Nature Cell Biology · doi:10.1038/ncb1521 · Cited by 207

The rox1 and rox2 RNAs Are Essential Components of the Compensasome, which Mediates Dosage Compensation in Drosophila

Franke, A., & Baker, B. S. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80193-8 · Cited by 206

Sequence-non-specific effects of RNA interference triggers and microRNA regulators

Olejniczak, M., Galka-Marciniak, P., & Krzyżosiak, W. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp829 · Cited by 204

Problems and paradigms: Redundancies, development and the flow of information

Tautz, D. (1992) · BioEssays · doi:10.1002/bies.950140410 · Cited by 202

Genome-wide Consequences of Deleting Any Single Gene

Teng, X., Dayhoff-Brannigan, M., Cheng, W., Gilbert, C. E., Sing, C. N., Diny, N. L., Wheelan, S. J., Dunham, M. J., Boeke, J. D., Pineda, F. J., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.09.026 · Cited by 199

Analysis of microRNA-target interactions across diverse cancer types

Skanderup, A. J., Silber, J., Harinath, G., Huse, J. T., Schultz, N. D., & Sander, C. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2678 · Cited by 197

Synthesis of Ribonucleic Acid by the X-Chromosomes of Drosophila melanogaster and the Problem of Dosage Compensation

Mukherjee, A. S., & Beermann, W. (1965) · Nature · doi:10.1038/207785a0 · Cited by 196

CD44-Deficient Mice Develop Normally with Changes in Subpopulations and Recirculation of Lymphocyte Subsets

Protin, U., Schweighoffer, T., Jochum, W., & Hilberg, F. (1999) · The Journal of Immunology · doi:10.4049/jimmunol.163.9.4917 · Cited by 194

The effect of tau antisense oligonucleotides on neurite formation of cultured cerebellar macroneurons

Cáceres, A., Potrebic, S., & Kosik, K. S. (1991) · Journal of Neuroscience · doi:10.1523/jneurosci.11-06-01515.1991 · Cited by 193

Cerebellar histogenesis is disturbed in mice lacking cyclin D2

Huard, J. M. T., Forster, C. L., Carter, M. L., Siciński, P., & Ross, M. E. (1999) · Development · doi:10.1242/dev.126.9.1927 · Cited by 193

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

Nedvetzki, S., Gonen, E., Assayag, N., Reich, R., Williams, R. O., Thurmond, R. L., Huang, J.-F., Neudecker, B. A., Wang, F.-S., Turley, E. A., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407378102 · Cited by 193

Conditional Repression of AUXIN BINDING PROTEIN1 Reveals That It Coordinates Cell Division and Cell Expansion during Postembryonic Shoot Development in Arabidopsis and Tobacco

Braun, N., Wyrzykowska, J., Müller, P., David, K. M., Couch, D., Perrot‐Rechenmann, C., & Fleming, A. J. (2008) · The Plant Cell · doi:10.1105/tpc.108.059048 · Cited by 180

Involvement of maternal embryonic leucine zipper kinase (MELK) in mammary carcinogenesis through interaction with Bcl-G, a pro-apoptotic member of the Bcl-2 family

Lin, M.-L., Park, J.-H., Nishidate, T., Nakamura, Y., & Katagiri, T. (2007) · Breast Cancer Research · doi:10.1186/bcr1650 · Cited by 169

New possible roles for aquaporin‐4 in astrocytes: cell cytoskeleton and functional relationship with connexin43

Nicchia, G. P., Srinivas, M., Li, W., Brosnan, C. F., Frigeri, A., & Spray, D. C. (2005) · The FASEB Journal · doi:10.1096/fj.04-3281fje · Cited by 162

Functional redundancy of the muscle-specific transcription factors Myf5 and myogenin

Wang, Y., Schnegelsberg, P. N. J., Dausman, J. A., & Jaenisch, R. (1996) · Nature · doi:10.1038/379823a0 · Cited by 159

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

Licht, K., & Jantsch, M. F. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201511041 · Cited by 154

Germline loss of PKM2 promotes metabolic distress and hepatocellular carcinomaPreprint

Dayton, T. L., Gocheva, V., Miller, K. M., Israelsen, W. J., Bhutkar, A. J., Clish, C. B., Davidson, S. M., Luengo, A., Bronson, R. T., Jacks, T., et al. (2016) · Genes & Development · doi:10.1101/gad.278549.116 · Cited by 154

CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials

Lin, A., Giuliano, C. J., Sayles, N. M., & Sheltzer, J. M. (2017) · eLife · doi:10.7554/elife.24179 · Cited by 147

No‐go decay: a quality control mechanism for RNA in translation

Harigaya, Y., & Parker, R. (2010) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.17 · Cited by 143

Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules

Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., Bertrand-Rakusova, H., Benková, E., Perrot‐Rechenmann, C., & Friml, J. (2014) · Nature · doi:10.1038/nature13889 · Cited by 143

The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1

O’Leary, M. N., Schreiber, K. H., Zhang, Y., Duc, A. E., Rao, S., Hale, J. S., Academia, E. C., Shah, S. R., Morton, J., Holstein, C. A., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003708 · Cited by 141

A direct role for small non-coding RNAs in DNA damage response

di Fagagna, F. D. (2013) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.09.008 · Cited by 132

Acute Versus Chronic Loss of Mammalian Azi1/Cep131 Results in Distinct Ciliary Phenotypes

Hall, E. A., Keighren, M., Ford, M. J., Davey, T., Jarman, A. P., Smith, L. B., Jackson, I. J., & Mill, P. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003928 · Cited by 130

Post-transcriptional operons and regulons co-ordinating gene expression

Keene, J. D., & Lager, P. J. (2005) · Chromosome Research · doi:10.1007/s10577-005-0848-1 · Cited by 124

Liver Steatosis and Increased ChREBP Expression in Mice Carrying a Liver Specific SIRT1 Null Mutation under a Normal Feeding Condition

Wang, R., Li, C., & Deng, C. (2010) · International Journal of Biological Sciences · doi:10.7150/ijbs.6.682 · Cited by 123

Maternal Embryonic Leucine Zipper Kinase (MELK) as a Novel Mediator and Biomarker of Radioresistance in Human Breast Cancer

Speers, C. W., Zhao, S. G., Kothari, V., Santola, A., Liu, M., Wilder-Romans, K., Evans, J. R., Batra, N., Bartelink, H. G. M. M., Hayes, D. F., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2711 · Cited by 122

MELK is an oncogenic kinase essential for mitotic progression in basal-like breast cancer cells

Wang, Y., Lee, Y., Baitsch, L., Huang, A., Xiang, Y., Tong, H., Lako, A., Von, T., Choi, C. H., Lim, E., et al. (2014) · eLife · doi:10.7554/elife.01763 · Cited by 118

Cyclin D3 Compensates for Loss of Cyclin D2 in Mouse B-lymphocytes Activated via the Antigen Receptor and CD40

Lam, E. W. ‐., Glassford, J., Banerji, L., Thomas, N. S. B., Siciński, P., & Klaus, G. G. B. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.5.3479 · Cited by 114

Distinct and redundant functions of histone deacetylases HDAC1 and HDAC2 in proliferation and tumorigenesis

Jurkin, J., Zupkovitz, G., Lagger, S., Grausenburger, R., Hagelkrüys, A., Kenner, L., & Seiser, C. (2011) · Cell Cycle · doi:10.4161/cc.10.3.14712 · Cited by 112

Transcriptional and phenotypic comparisons of Ppara knockout and siRNA knockdown mice

Souza, A. T. D., Dai, X., Spencer, A. G., Reppen, T. W., Menzie, A. M., Roesch, P. L., He, Y. D., Caguyong, M. J., Bloomer, S., Herweijer, H., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl609 · Cited by 110

Primary and Compensatory Roles for RB Family Members at Cell Cycle Gene Promoters That Are Deacetylated and Downregulated in Doxorubicin-Induced Senescence of Breast Cancer Cells

Jackson, J. G., & Pereira-Smith, O. M. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.26.7.2501-2510.2006 · Cited by 108

Chronic Deletion and Acute Knockdown of Parkin Have Differential Responses to Acetaminophen-induced Mitophagy and Liver Injury in Mice

Williams, J. A. R., Ni, H., Haynes, A., Manley, S., Li, Y., Jaeschke, H., & Ding, W. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.602284 · Cited by 101

Off-Target Effect of doublecortin Family shRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation

Baek, S. T., Kerjan, G., Bielas, S. L., Lee, J. E., Fenstermaker, A. G., Novarino, G., & Gleeson, J. G. (2014) · Neuron · doi:10.1016/j.neuron.2014.04.036 · Cited by 98

Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity

Freudenberg, J., Ghosh, S., Lackford, B. L., Yellaboina, S., Zheng, X., Li, R., Cuddapah, S., Wade, P. A., Hu, G., & Jothi, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1253 · Cited by 98

Transcription of the Constitutively Expressed Yeast Enolase Gene ENO1 Is Mediated by Positive and Negative cis -Acting Regulatory Sequences

Cohen, R., Yokoi, T., Holland, J. P., Pepper, A. E., & Holland, M. J. (1987) · Molecular and Cellular Biology · doi:10.1128/mcb.7.8.2753-2761.1987 · Cited by 92

Talin, vinculin and DRP (utrophin) concentrations are increased at mdx myotendinous junctions following onset of necrosis

Law, D. J., Allen, D. L., & Tidball, J. G. (1994) · Journal of Cell Science · doi:10.1242/jcs.107.6.1477 · Cited by 90

Knockdown of cyclin D1 inhibits proliferation, induces apoptosis, and attenuates the invasive capacity of human glioblastoma cells

Wang, J., Wang, Q., Cui, Y., Liu, Z. Y., Zhao, W., Wang, C. L., Dong, Y., Hou, L., Hu, G., Luo, C., et al. (2011) · Journal of Neuro-Oncology · doi:10.1007/s11060-011-0692-4 · Cited by 89

Cells Lacking β-Actin are Genetically Reprogrammed and Maintain Conditional Migratory Capacity*

Tondeleir, D., Lambrechts, A., Müller, M., Jonckheere, V., Doll, T., Vandamme, D., Bakkali, K., Waterschoot, D., Lemaistre, M., Debeir, O., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.015099 · Cited by 88

Functional redundancy: the respective roles of the two sloppy paired genes in Drosophila segmentation.

Cadigan, K. M., Grossniklaus, U., & Gehring, W. J. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.14.6324 · Cited by 86

Downregulation of the microtubule associated protein Tau impairs process outgrowth and myelin basic protein m RNA transport in oligodendrocytes

Seiberlich, V., Bauer, N. G., Schwarz, L., Ffrench‐Constant, C., Goldbaum, O., & Richter‐Landsberg, C. (2015) · Glia · doi:10.1002/glia.22832 · Cited by 84

Maternal Embryonic Leucine Zipper Kinase Is Upregulated and Required in Mammary Tumor-Initiating Cells In vivo

Hebbard, L., Maurer, J., Miller, A., Lesperance, J., Hassell, J. A., Oshima, R. G., & Terskikh, A. V. (2010) · Cancer Research · doi:10.1158/0008-5472.can-10-1295 · Cited by 82

Knockout of the prion protein (PrP)-like Sprn gene does not produce embryonic lethality in combination with PrP C -deficiency

Daude, N., Wohlgemuth, S. L., Brown, R. J., Pitstick, R., Gapeshina, H., Yang, J., Carlson, G. A., & Westaway, D. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202130109 · Cited by 75

Allele-specific histone modifications regulate expression of the Dlk1–Gtl2 imprinted domain

Carr, M. S., Yevtodiyenko, A., Schmidt, C. L., & Schmidt, J. V. (2006) · Genomics · doi:10.1016/j.ygeno.2006.10.005 · Cited by 72

p130 Is Dispensable in Peripheral T Lymphocytes: Evidence for Functional Compensation by p107 and pRB

Mulligan, G., Wong, J., & Jacks, T. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.1.206 · Cited by 72

The Histone Code Regulating Expression of the Imprinted MouseIgf2rGene

Yang, Y., Li, T., Vu, T. H., Ulaner, G. A., Hu, J., & Hoffman, A. R. (2003) · Endocrinology · doi:10.1210/en.2003-0798 · Cited by 71

The prion or the related Shadoo protein is required for early mouse embryogenesis

Young, R. A., Passet, B., Vilotte, M., Cribiu, E.-P., Béringue, V., Provost, F. L., Laude, H., & Vilotte, J. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.09.027 · Cited by 67

A Specific Role for Cyclin D1 in Mammary Gland Development

Siciński, P., & Weinberg, R. A. (1997) · Journal of Mammary Gland Biology and Neoplasia · doi:10.1023/a:1026391128117 · Cited by 64

Drosophila abl and genetic redundancy in signal transduction

HOFFMANN, F. (1991) · Trends in Genetics · doi:10.1016/0168-9525(91)90254-f · Cited by 62

Redundant functions of the genes knirps and knirps-related for the establishment of anterior Drosophila head structures.

González‐Gaitán, M., Rothe, M., Wimmer, E. A., Taubert, H., & Jäckle, H. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.18.8567 · Cited by 58

Notch signaling functions in lymphatic valve formation

Murtomaki, A., Uh, M. K., Kitajewski, C., Zhao, J., Nagasaki, T., Shawber, C. J., & Kitajewski, J. (2014) · Development · doi:10.1242/dev.101188 · Cited by 55

FGFR3 Deficiency Causes Multiple Chondroma-like Lesions by Upregulating Hedgehog Signaling

Zhou, S., Xie, Y., Tang, J., Huang, J., Huang, Q., Xu, W., Wang, Z., Luo, F., Wang, Q., Chen, H., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005214 · Cited by 53

Epidermal-specific deletion of CD44 reveals a function in keratinocytes in response to mechanical stress

Shatirishvili, M., Burk, A., Franz, C. M., Pace, G., Kastilan, T., Breuhahn, K., Hinterseer, E., Dierich, A., Bakiri, L., Wagner, E. F., et al. (2016) · Cell Death and Disease · doi:10.1038/cddis.2016.342 · Cited by 51

Guilt by association: non-coding RNAs, chromosome-specific proteins and dosage compensation in Drosophila

Stuckenholz, C. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(99)01855-7 · Cited by 50

Reversible suppression of an essential gene in adult mice using transgenic RNA interference

McJunkin, K., Mazurek, A., Premsrirut, P. K., Zuber, J. A., Dow, L. E., Simon, J. M., Stillman, B., & Lowe, S. W. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104097108 · Cited by 49

The role of antisense long noncoding RNA in small RNA-triggered gene activation

Zhang, X., Li, H., Burnett, J., & Rossi, J. J. (2014) · RNA · doi:10.1261/rna.043968.113 · Cited by 46

The Serine-Threonine Protein Kinase PAK4 Is Dispensable in Zebrafish: Identification of a Morpholino-Generated Pseudophenotype

Law, S. H. W., & Sargent, T. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100268 · Cited by 45

Cyclin D2 and the CDK substrate p220NPAT are required for self‐renewal of human embryonic stem cells

Becker, K. A., Ghule, P. N., Lian, J. B., Stein, J. L., van Wijnen, A. J., & Stein, G. S. (2009) · Journal of Cellular Physiology · doi:10.1002/jcp.21967 · Cited by 44

RNAi-mediated knockdown of dystrophin expression in adult mice does not lead to overt muscular dystrophy pathology

Seno, M. M. G., Graham, I. R., Athanasopoulos, T., Trollet, C., Pohlschmidt, M., Crompton, M. R., & Dickson, G. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn162 · Cited by 44

Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma

Radulovich, N., Pham, N., Strumpf, D., Leung, L., Xie, W., Jurišica, I., & Tsao, M. (2010) · Molecular Cancer · doi:10.1186/1476-4598-9-24 · Cited by 43

The nonessentiality of essential genes in yeast provides therapeutic insights into a human diseasePreprint

Chen, P., Wang, D., Chen, H., Zhou, Z., & He, X. (2016) · Genome Research · doi:10.1101/gr.205955.116 · Cited by 42

Analysis of Nitric Oxide-Stabilized mRNAs in Human Fibroblasts Reveals HuR-Dependent Heme Oxygenase 1 Upregulation

Kuwano, Y., Rabinovic, A., Srikantan, S., Gorospe, M., & Demple, B. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01495-08 · Cited by 39

Normal brain development in importin-α5 deficient-mice

Shmidt, T., Hampich, F., Ridders, M., Schultrich, S., Hans, V., Tenner, K., Vilianovich, L., Qadri, F., Alenina, N. V., Hartmann, E., et al. (2007) · Nature Cell Biology · doi:10.1038/ncb1207-1337 · Cited by 38

Messenger RNA Surveillance Systems Monitoring Proper Translation Termination

Akimitsu, N. (2007) · The Journal of Biochemistry · doi:10.1093/jb/mvm204 · Cited by 38

Relative importance of βcyto- and γcyto-actin in primary mouse embryonic fibroblasts

Patrinostro, X., O’Rourke, A. R., Chamberlain, C. M., Moriarity, B. S., Perrin, B. J., & Ervasti, J. M. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-07-0503 · Cited by 37

Metallothionein 2 regulates endothelial cell migration through transcriptional regulation of vegfc expression

Schuermann, A., Helker, C. S., & Herzog, W. (2015) · Angiogenesis · doi:10.1007/s10456-015-9473-6 · Cited by 35

Probing Yeast Polarity with Acute, Reversible, Optogenetic Inhibition of Protein Function

Jost, A. P.-T., & Weiner, O. D. (2015) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00053 · Cited by 34

Changes in Nuclease Sensitivity of Mammalian Cells after Irradiation with 60 Co γ-rays

Takahashi, K., & Kaneko, I. (1985) · International Journal of Radiation Biology and Related Studies in Physics Chemistry and Medicine · doi:10.1080/09553008514551391 · Cited by 29

p21 gene knock down does not identify genetic effectors seen with gene knock out

Karakas, B., Weeraratna, A. T., Abukhdeir, A. M., Konishi, H., Gustin, J. P., Vitolo, M. I., Bachman, K. E., & Park, B. H. (2007) · Cancer Biology & Therapy · doi:10.4161/cbt.6.7.4202 · Cited by 24

Small RNA-directed epigenetic programming of embryonic stem cell cardiac differentiation

Ghanbarian, H., Wagner, N., Michiels, J., Cuzin, F., Wagner, K., & Rassoulzadegan, M. (2017) · Scientific Reports · doi:10.1038/srep41799 · Cited by 22

IL‐1β enhances cell adhesion to degraded fibronectin

Rajshankar, D., Downey, G. P., & McCulloch, C. A. (2012) · The FASEB Journal · doi:10.1096/fj.12-207381 · Cited by 21

Biological Implications and Regulatory Mechanisms of Long-range Chromosomal Interactions

Wei, Z., Huang, D., Gao, F., Chang, W.-H., An, W., Coetzee, G. A., Wang, K., & Lu, W. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.r113.485292 · Cited by 20

Sequence-non-specific effects generated by various types of RNA interference triggers

Olejniczak, M., Urbanek-Trzeciak, M. O., Jaworska, E., Witucki, Ł., Szcześniak, M. W., Makałowska, I., & Krzyżosiak, W. J. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.11.005 · Cited by 19

Genomic Imprinting – A Model for Roles of Histone Modifications in Epigenetic Control

McEwen, K. R., & Ferguson‐Smith, A. C. (2008) · Epigenomics · doi:10.1007/978-1-4020-9187-2_14 · Cited by 8

Genetic compensation triggered by mutant mRNA degradation

El-Brolosy, M. A., Kontarakis, Z., Rossi, A., Kuenne, C., Günther, S., Fukuda, N., Kikhi, K., Boezio, G. L. M., Takacs, C. M., Lai, S.-L., et al. (2019) · Nature · doi:10.1038/s41586-019-1064-z · Cited by 1,028

IGF-Binding Proteins: Why Do They Exist and Why Are There So Many?

Allard, J. B., & Duan, C. (2018) · Frontiers in Endocrinology · doi:10.3389/fendo.2018.00117 · Cited by 517

The molecular biology of FMRP: new insights into fragile X syndrome

Richter, J. D., & Zhao, X. (2021) · Nature Reviews Neuroscience · doi:10.1038/s41583-021-00432-0 · Cited by 390

Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts

Kingdom, R., & Wright, C. F. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.920390 · Cited by 326

MALAT1 Long Non-Coding RNA: Functional Implications

Arun, G., Aggarwal, D., & Spector, D. L. (2020) · Non-Coding RNA · doi:10.3390/ncrna6020022 · Cited by 278

The recent advances and future perspectives of genetic compensation studies in the zebrafish model

Rouf, M. A., Wen, L., Mahendra, Y., Wang, J., Zhang, K., Liang, S., Wang, Y., Li, Z., Wang, Y., & Wang, G. (2022) · Genes & Diseases · doi:10.1016/j.gendis.2021.12.003 · Cited by 72

Genetic compensation induced by deleterious mutations but not gene knockdowns

Rossi, A., Kontarakis, Z., Gerri, C., Nolte, H., Hölper, S., Krüger, M., & Stainier, D. Y. R. (2015) · Nature · doi:10.1038/nature14580 · Cited by 1,226

Detouring the roadblocks in gene expression

Junker, J. P. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0107-5 · Cited by 4

How widespread is the phenomenon of dosage compensation?

Lucchesi, J. C. (1993) · Seminars in Developmental Biology · doi:10.1006/sedb.1993.1016 · Cited by 5

Genetics in Light of Transcriptional Adaptation

Kontarakis, Z., & Stainier, D. Y. R. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.08.008 · Cited by 41