Alexander Hoffmann
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Computer Science Biology
Alexander Hoffmann's Degrees
- PhD Bioinformatics University of California, San Diego
- Masters Computer Science Stanford University
- Bachelors Computer Science Stanford University
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(Suggest an Edit or Addition)Alexander Hoffmann's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation (2002) (1648)
- The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. (2002) (893)
- Molecular Determinants of Crosstalk between Nuclear Receptors and Toll-like Receptors (2005) (663)
- A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling (2009) (574)
- Signaling via the NFκB system (2016) (558)
- Transcriptional regulation via the NF-κB signaling module (2006) (553)
- Differential activation and antagonistic function of HIF-{alpha} isoforms in macrophages are essential for NO homeostasis. (2010) (531)
- Circuitry of nuclear factor κB signaling (2006) (512)
- Circuitry of nuclear factor kappaB signaling. (2006) (457)
- A single NFκB system for both canonical and non-canonical signaling (2011) (389)
- Genetic analysis of NF‐κB/Rel transcription factors defines functional specificities (2003) (376)
- Crystal structure of TFIID TATA-box binding protein (1992) (370)
- One Nucleotide in a κB Site Can Determine Cofactor Specificity for NF-κB Dimers (2004) (370)
- A Fourth IκB Protein within the NF-κB Signaling Module (2007) (360)
- Selective requirement for c-Rel during IL-12 P40 gene induction in macrophages. (2000) (338)
- Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-kappaB as key regulators. (2005) (322)
- Transcriptional regulation via the NF-kappaB signaling module. (2006) (313)
- Accurate information transmission through dynamic biochemical signaling networks (2014) (310)
- CK2 Is a C-Terminal IκB Kinase Responsible for NF-κB Activation during the UV Response (2003) (287)
- Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity (2005) (284)
- Induction of NR4A Orphan Nuclear Receptor Expression in Macrophages in Response to Inflammatory Stimuli* (2005) (276)
- ER Stress Activates NF-κB by Integrating Functions of Basal IKK Activity, IRE1 and PERK (2012) (268)
- Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. (1991) (266)
- Structural similarity between TAFs and the heterotetrameric core of the histone octamer (1996) (261)
- Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID) (1990) (254)
- A fourth IkappaB protein within the NF-kappaB signaling module. (2007) (210)
- IκBɛ provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression (2006) (201)
- Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (2017) (200)
- Mitotic regulation of TFIID: inhibition of activator-dependent transcription and changes in subcellular localization. (1996) (194)
- Regulation of IL-6 and IL-8 Expression in Rheumatoid Arthritis Synovial Fibroblasts: the Dominant Role for NF-κB But Not C/EBPβ or c-Jun1 (2000) (191)
- A histone octamer-like structure within TFIID (1996) (190)
- One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. (2004) (188)
- Nucleosome remodeling at the IL-12 p40 promoter is a TLR-dependent, Rel-independent event (2001) (185)
- Unique TATA‐binding protein‐containing complexes and cofactors involved in transcription by RNA polymerases II and III. (1993) (185)
- CK2 Is a C-Terminal IkappaB Kinase Responsible for NF-kappaB Activation during the UV Response. (2003) (184)
- Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20. (2008) (183)
- Cutting Edge: Innate Immunity Conferred by B Cells Is Regulated by Caspase-81 (2005) (176)
- Understanding NF-κB signaling via mathematical modeling (2008) (175)
- NF‐κB dictates the degradation pathway of IκBα (2008) (166)
- Cross-talk between Aryl Hydrocarbon Receptor and the Inflammatory Response (2013) (165)
- Fbxw7α- and GSK3-mediated degradation of p100 is a pro-survival mechanism in multiple myeloma (2012) (164)
- Control of RelB during dendritic cell activation integrates canonical and non-canonical NF-κB pathways (2012) (164)
- Understanding the temporal codes of intra-cellular signals. (2010) (160)
- Nuclear Localization of IκBα Is Mediated by the Second Ankyrin Repeat: the IκBα Ankyrin Repeats Define a Novel Class of cis-Acting Nuclear Import Sequences (1998) (153)
- Crosstalk via the NF-kappaB signaling system. (2008) (148)
- Generation and Activation of Multiple Dimeric Transcription Factors within the NF-κB Signaling System (2008) (146)
- A homeostatic model of IκB metabolism to control constitutive NF-κB activity (2007) (142)
- Unique CD40-mediated biological program in B cell activation requires both type 1 and type 2 NF-kappaB activation pathways. (2004) (140)
- Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytes (2002) (137)
- Antigen-mediated T cell expansion regulated by parallel pathways of death (2008) (137)
- The Nfkb1 and Nfkb2 proteins p105 and p100 function as the core of high-molecular-weight heterogeneous complexes. (2009) (133)
- Transient IκB Kinase Activity Mediates Temporal NF-κB Dynamics in Response to a Wide Range of Tumor Necrosis Factor-α Doses* (2006) (129)
- Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (2011) (128)
- IκBβ acts to both inhibit and activate gene expression at different stages of the inflammatory response (2010) (128)
- Arabidopsis thaliana contains two genes for TFIID (1990) (127)
- The Dynamics of Signaling as a Pharmacological Target (2013) (124)
- Lessons from mathematically modeling the NF‐κB pathway (2012) (119)
- NF‐κB signaling (2009) (116)
- A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. (2005) (116)
- Analysis of the RelA:CBP/p300 Interaction Reveals Its Involvement in NF-κB-Driven Transcription (2013) (114)
- Coordination between NF-kappaB family members p50 and p52 is essential for mediating LTbetaR signals in the development and organization of secondary lymphoid tissues. (2006) (114)
- High-Content Quantification of Single-Cell Immune Dynamics (2016) (110)
- Regulation of IL-6 and IL-8 expression in rheumatoid arthritis synovial fibroblasts: the dominant role for NF-kappa B but not C/EBP beta or c-Jun. (2000) (103)
- The regulatory logic of the NF-kappaB signaling system. (2010) (103)
- Kinetic control of negative feedback regulators of NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificity (2009) (103)
- Suppression of Steady-state, but not Stimulus-induced NF-κB Activity Inhibits Alphavirus-induced Apoptosis (1998) (101)
- The Transcriptional Specificity of NF-κB Dimers Is Coded within the κB DNA Response Elements (2012) (97)
- Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation (2015) (95)
- Transient IKK activity mediates NF-κB temporal dynamics in response to a wide range of TNFα doses (2005) (93)
- A Structural Basis for IκB Kinase 2 Activation Via Oligomerization-Dependent Trans Auto-Phosphorylation (2013) (93)
- Immune response and myoblasts that express Fas ligand. (1997) (88)
- Positive Feedback Within a Kinase Signaling Complex Functions as a Switch Mechanism for NF-κB Activation (2014) (87)
- Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions? (1997) (85)
- Comment on "Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression" (2005) (85)
- Structural motifs and potential a homologies in the large subunit of human general transcription factor TFIIE (1991) (85)
- UV as an amplifier rather than inducer of NF-kappaB activity. (2008) (81)
- Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIID. (1990) (80)
- Initiation and termination of NF-κB signaling by the intracellular protozoan parasite Toxoplasma gondii (2005) (75)
- NEMO ensures signaling specificity of the pleiotropic IKKβ by directing its kinase activity toward IκBα. (2012) (75)
- The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF-κB p50 (2011) (73)
- Network dynamics determine the autocrine and paracrine signaling functions of TNF (2014) (72)
- Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. (2006) (72)
- Kinetic enhancement of NF-κB·DNA dissociation by IκBα (2009) (71)
- Stabilization of RelB Requires Multidomain Interactions with p100/p52* (2008) (69)
- Striking homology of the 'variable' N-terminal as well as the 'conserved core' domains of the mouse and human TATA-factors (TFIID). (1991) (64)
- Identification of human TFIID components and direct interaction between a 250-kDa polypeptide and the TATA box-binding protein (TFIID tau). (1992) (61)
- Regulation and function of the caspase-1 in an inflammatory microenvironment (2015) (61)
- A miR-155–Peli1–c-Rel pathway controls the generation and function of T follicular helper cells (2016) (57)
- LBP-p40 binds DNA tightly through associations with histones H2A, H2B, and H4. (1998) (54)
- NF-κB–inducing kinase plays an essential T cell–intrinsic role in graft-versus-host disease and lethal autoimmunity in mice. (2011) (53)
- Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation (2018) (51)
- The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitis (2016) (50)
- Immortalized fibroblasts from NF-κB RelA knockout mice show phenotypic heterogeneity and maintain increased sensitivity to tumor necrosis factor α after transformation by v-Ras (2005) (48)
- Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module (2013) (47)
- Nuclear localization of IkappaB alpha is mediated by the second ankyrin repeat: the IkappaB alpha ankyrin repeats define a novel class of cis-acting nuclear import sequences. (1998) (45)
- IκBε Is a Key Regulator of B Cell Expansion by Providing Negative Feedback on cRel and RelA in a Stimulus-Specific Manner (2014) (45)
- Cloning and Characterization of Human TAF20/15 (1996) (45)
- NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages (2020) (43)
- Negative regulation of constitutive NF‐κB and JNK signaling by PKN1‐mediated phosphorylation of TRAF1 (2008) (40)
- A Pathway Switch Directs BAFF Signaling to Distinct NFκB Transcription Factors in Maturing and Proliferating B Cells (2014) (39)
- Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses (2021) (38)
- A Regulatory Circuit Controlling the Dynamics of NF&kgr;B cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation (2019) (38)
- Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer. (2013) (37)
- Human autoantibody to topoisomerase II. (1989) (37)
- Nuclear export of the NF-κB inhibitor IκBα is required for proper B cell and secondary lymphoid tissue formation. (2011) (37)
- IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer (2015) (36)
- Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. (2020) (36)
- A Fourth IkB Protein within the NF-kB Signaling Module (2007) (35)
- B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel. (2016) (35)
- Integrating Computational and Biochemical Studies to Explore Mechanisms in NF-κB Signaling* (2009) (34)
- Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB (2019) (33)
- Encoding NF- (cid:1) B temporal control in response to TNF: distinct roles for the negative regulators I (cid:1) B (cid:2) and A20 (2008) (32)
- Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. (2017) (32)
- Paternal RLIM/Rnf12 Is a Survival Factor for Milk-Producing Alveolar Cells (2012) (29)
- Defective Regulation of CXCR2 Facilitates Neutrophil Release from Bone Marrow Causing Spontaneous Inflammation in Severely NF-κB–Deficient Mice (2010) (28)
- Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant (2017) (28)
- An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms (2019) (26)
- Tunable signal processing through a kinase control cycle: the IKK signaling node. (2013) (25)
- How do pleiotropic kinase hubs mediate specific signaling by TNFR superfamily members? (2011) (25)
- Anatomy of a negative feedback loop: the case of IκBα (2015) (25)
- Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics (2020) (24)
- Limited specificity of IRF3 and ISGF3 in the transcriptional innate‐immune response to double‐stranded RNA (2015) (23)
- A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide (2015) (22)
- MAP kinase p38α regulates type III interferon (IFN‐λ1) gene expression in human monocyte‐derived dendritic cells in response to RNA stimulation (2015) (21)
- Understanding the logic of IκB:NF-κB regulation in structural terms. (2011) (21)
- Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions (2019) (21)
- Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse (2018) (21)
- NF-κB responds to absolute differences in cytokine concentrations (2021) (21)
- NF-κB Potentiates Caspase Independent Hydrogen Peroxide Induced Cell Death (2011) (21)
- Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. (2017) (21)
- Oscillation dynamics underlie functional switching of NF-κB for B-cell activation (2016) (17)
- Quantifying information accumulation encoded in the dynamics of biochemical signaling (2021) (15)
- Inflammatory tales of liver cancer. (2007) (15)
- Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models (2013) (15)
- The Regulatory Logic of the NFk B Signaling System (2009) (15)
- Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing (2014) (14)
- Training the 21st Century Immunologist. (2015) (14)
- Identifying Noise Sources governing cell-to-cell variability. (2018) (14)
- Epigenetic control: slow and global, nimble and local. (2008) (14)
- FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses (2013) (14)
- A Regulated, Ubiquitin-Independent Degron in IκBα. (2015) (12)
- A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways (2013) (10)
- Coherent activation of a synthetic mammalian gene network (2009) (9)
- Identification of human TFIID components and direct interaction between a 250-kDa polypeptide and the TATA box-binding protein ( TFIIDT ) ( RNA polymerase li / transcriptional action / tr ti inittion / subunit structure ) (9)
- Systems biology of cellular rhythms: from cacophony to symphony. (2010) (9)
- Immune Response Signaling: Combinatorial and Dynamic Control. (2016) (8)
- Melanoma dedifferentiation induced by interferon-gamma epigenetic remodeling in response to anti-PD-1 therapy. (2021) (8)
- Ex Vivo Innate Immune Cytokine Signature of Enhanced Risk of Relapsing Brucellosis (2013) (8)
- An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions (2020) (8)
- Stimulus-specificity in the Responses of Immune Sentinel Cells. (2019) (8)
- Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing (2018) (7)
- A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. (2015) (7)
- EBP κ the Dominant Role for NF-Rheumatoid Arthritis Synovial Fibroblasts : Regulation of IL-6 and IL-8 Expression in (2000) (6)
- Studying NF-κB signaling with mathematical models. (2015) (6)
- LBP-p 40 Binds DNA Tightly through Associations with Histones (1998) (5)
- NF-kappaB as a determinant of distinct cell death pathways. (2008) (5)
- A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness. (2012) (5)
- Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB (2019) (5)
- A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. (2016) (5)
- What Can Immunologists Learn from Systems Approaches? (2018) (4)
- B Signaling System κ The Regulatory Logic of the NF (2010) (4)
- I kappa B epsilon provides negative feedback to control NF-kappa B oscillations, signaling dynamics, and inflammatory gene expression (2006) (4)
- IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells (2021) (3)
- IκBα Nuclear Export Enables 4-1BB–Induced cRel Activation and IL-2 Production to Promote CD8 T Cell Immunity (2020) (3)
- Studying the information capacity of biological signaling pathways: progress with machine-learning approaches. (2022) (3)
- High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells (2021) (3)
- IkBb enhances the generation of the low-affinity NFkB/RelA homodimer (2015) (3)
- I k B b enhances the generation of the low-affinity NF k B / RelA homodimer (2015) (2)
- Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing (2019) (2)
- NF‐κB dictates the degradation pathway of IκBα (2013) (2)
- Training the 21 st Century Immunologist (2015) (2)
- Identification and physiological significance of temporal NFκB signaling codewords deployed by macrophages to classify immune threats (2020) (2)
- Of elections and cell-death decisions. (2009) (2)
- ErratumNuclear Export of the NF-κB Inhibitor IκBα Is Required for Proper B Cell and Secondary Lymphoid Tissue Formation (2011) (1)
- Polypyrimidine Tract Binding Protein blocks microRNA-124 biogenesis to enforce its neuronal specific expression (2018) (1)
- Interferon Response Elements by NF-{ kappa } B p 50 The Specificity of Innate Immune Responses Is Enforced by Repression of (2011) (1)
- Regulation and Function of the Caspase-1 in an In fl ammatory Microenvironment (2015) (1)
- A Molecular Characterization of Human General Transcription Factor IID (1994) (1)
- HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA (1996) (1)
- High dose IFN-β activates GAF to enhance expression of ISGF3 target genes in epithelial cells (2020) (1)
- Input dose differentiation by NF-κB (2019) (1)
- Anatomy of a negative feedback loop : the case of I k B a (2015) (1)
- NF-k B as a Determinant of Distinct Cell Death Pathways (2008) (1)
- Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells (2022) (1)
- Suppression of Steady-state, but not Stimulus-induced NF- (cid:107) B Activity Inhibits Alphavirus-induced Apoptosis (1998) (0)
- DROSOPHILA TBP ASSOCIATED FACTORS DTAFII42/DTAFII62 HETEROTETRAMER (1996) (0)
- and Quantifying the phenotypic information in mRNA and receptor complex abundances (2022) (0)
- Cancer Cell Previews Inflammatory Tales of Liver Cancer (2007) (0)
- Cooperation of multiple sign in CD40-regulated gene expr in B lymphocytes (2016) (0)
- A regulatory circuit motif dictates whether protein turnover fluxes are more predictive as biomarkers than protein abundances (2021) (0)
- of a synthetic mammalian gene network. (2010) (0)
- Bioinformatics and Systems Biology (2012) (0)
- Science Signaling Podcast: 22 February 2011 (2011) (0)
- functions of TNF Network dynamics determine the autocrine and paracrine signaling Material (2014) (0)
- Nfkappab Systems Regulates Flt3-Mediated Hematopoiesis (2018) (0)
- Caspase‐8 regulates a form of death that is distinct from apoptosis in T cells (2008) (0)
- Signal Processing by the Control Cycle of the IKK Kinase in the NFκB Signaling Axis (2012) (0)
- A Regulatory Circuit Contr olling the Dynamics of NF k B cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation Graphical (2019) (0)
- Generation and Activation of Multiple Dimeric Transcription Factors within the NF- (cid:2) B Signaling System (cid:1) (2008) (0)
- Resource High-Content Quantificatio n of Single-Cell Immune Dynamics Graphical (2016) (0)
- A biochemical necroptosis model explains cell type-specific responses to cell-death cues. (2023) (0)
- FACTOR-Receptor and the Inflammatory Response : Cross-talk between Aryl Hydrocarbon Gene Regulation : (2014) (0)
- X-ray crystal structure of human IKK2 in an active conformation (2013) (0)
- Abstract 2326: Time-resolved studies of necroptosis reveal distinct regulatory functions for NFκB (2018) (0)
- Rela Dynamics Regulate Developmental Pacing in Early B Lymphopoiesis (2018) (0)
- The NFkB System Regulates Flt3-Mediated Hematopoiesis (2015) (0)
- NF-j B dictates the degradation pathway of I j B a (2008) (0)
- Spotlight Immune Response Signaling : Combinatorial and Dynamic Control (2016) (0)
- Abstract 3155: Interferon-gamma-induced melanoma plasticity and response to PD-1 blockade therapy (2020) (0)
- Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments. (2018) (0)
- The alternative NF-kappa B pathway is essential for OX40-induced CD4 T cell differentiation and effector function (47.19) (2009) (0)
- Series : Training the next generation Training the 21 st Century Immunologist (2015) (0)
- Addressing the digital divide in contemporary biology: Lessons from teaching UNIX (2017) (0)
- Controlling Cancer Cell Death Types to Optimize Anti-Tumor Immunity (2022) (0)
- Takehito Koganezawa: Luftlinien (2012) (0)
- Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students (2022) (0)
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